Covid-19 Pandemic. Uganda in blackets

COVID-19 PANDEMIC. UGANDA IN BLACKETS
By Minani Leodegard. Tel. 256775048575. Email: minanileodegard@gmail.com
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COVID-19 PANDEMIC: UGANDA IN BLACKETS
FROM OUTBREAK TO VACCINATION
DETAILED PACKAGE FOR EDUCATIONAL PURPOSE
April 2021
Volume 1
BY MINANI LEODEGARD
minanileodegard@gmail.com
+256775048575

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FOREWORD
The word Corona was not so popular until late in 2019 when it gained the popularity in the
entire world community and quickly became the central point of the year 2020 history. The
pandemic first appeared in China in November 2019 where in March 2020, it was already
present in almost every country. In Uganda, the first case was discovered in March 2020. This
global darkness-like period imposed the closure of education system, sports events suspension,
restriction of movements and mass gathering that lead to temporal stagnation of both public
and private sectors. In March and April 2020, there were lockdowns in most of the country.
This was the time for high rate infections and deathes. Emerging medical trials for the pandemic
treatment were only the weapon to save life of positive cases until December 2020 when
vaccines against COVID-19 were approved. As of early April 2021, the summary of total
number of cases is 135 million, 3 million deathes, and 159 million vaccinated persons. In
Uganda alone, the total number of cases was rotating to around 41 thousand, 337 deathes and
150 thousand vaccinated persons. The extension of total details on COVID-19 require extra
energy, time and resources. It is however important that our generation and the coming
generation be educated about the COVID-19 pendemic as part of the world history. This book
comes as a compilation of details on COVID-19 pandemic educational material. Hope it will
contribute globally to the awareness of COVID-19 pandemic.

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THE BOOK SUMMARY
The COVID-19 pandemic book is a compilation of detailed information on the disease from its
outbreak to its vaccination. The book explains the disease in global context and the Uganda
context in particular. The writer of the book collected information from different sources and
he expects that it will be used for teaching this generation and the generations to come,
understand the COVID-19 pandemic in its scientific and historical descriptions. The writer, to
make the book easily readable, broke it down into ten chapters. Chapter one deals with
epidemiology of the COVID-19 pandemic. Under this chapter, the writer laid down
explanations on the study and analysis of the disease conditions, its determinants, its patterns
and its distribution. More clarifications were focused on the name of the disease, its history,
its transmission and its pathophysiology. Chapter two highlights is the diagnosis of the
COVID-19 pandemic. The focal points under this chapter are the testing of COVID-19, its
complications, the pathological findings, its immunity resistance and the management of
COVID-19. Chapter three of this COVID-19 pandemic book, concentrates on prevention and
treatment of the disease. Prevention described in this chapter involves the use of Standard
Operating Procedures (SOPs). These are hand washing with detergent soap, use of sanitizers,
putting on face mask, social distancing, surface cleaning, use of ventilation and eating healthy
diet. Chapter four describes key statistics of the COVID-19 pandemic from its outbreak to its
vaccination (Late 2019 to March 2021). The author reviewed statistics on global cases,
recovery, deaths, vaccinations and their mitigations. In chapter five, the writer explains the
COVID-19 pandemic related researches. He detailed the medical treatment research emerged
to counter the COVID-10 disease. Also the chapter explained the researches involved in the
fight against COVID-19 pandemic. The next chapter (6), was raised to not miss information
about responses to COVID-19 pandemic by governments and United Nations. From chapter
seven to chapter ten, the author discussed the common global impacts of COVID-19. These are
impacts on global economy, impacts on education, impacts on health sector, impacts on arts,
entertainment and sports and impacts on social movements in communities. Chapter eleven
came up with details on the COVID-19 misinformation. It explains the misinformation about
the origin of the disease, misinformation about cases and deaths reports, treatment
misinformation and effort to combat misinformation about COVID-19 pandemic. Chapter
twelve of the book collected information on protests over responses to COVID-19 pandemic in
Africa, Asia, Europe and America. The thirteenth chapter being the last chapter gives details
of information about COVID-19 pandemic in Uganda. It gives the timelines of the diseases in
Uganda, Public Private Partnership responses to the diseases and socio-economic impacts of
COVID-19 in Uganda. The book ends with indices of brief data of COVID-19 15 most affected
countries in the world, the graphical presentation of key COVID-19 statistics.

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TABLE OF CONTENTS
FOREWORD..............................................................................................................................ii
THE BOOK SUMMARY .......................................................................................................... iii
TABLE OF CONTENTS................................................................................................................... iv
INTRODUCTION ......................................................................................................................0
CHAPTER ONE: EPIDEMIOLOGY OF COVID-19.................................................................1
1.1. Overview................................................................................................................................1
1.2. Name ...........................................................................................................................................2
1.3. History COVID-19.....................................................................................................................2
1.4. First appearance.........................................................................................................................4
1.5. Signs and symptoms...................................................................................................................5
1.5. Cause...........................................................................................................................................6
1.6. Virology ........................................................................................................................6
1.7. SARS-CoV-2 variants................................................................................................................7
1.8. Transmission of COVID-19.......................................................................................................7
1.8.1. Routes ........................................................................................................................8
1.8.2. Respiratory droplets...................................................................................................8
1.8.3. Aerosols......................................................................................................................9
1.8.4. Respiratory ................................................................................................................9
1.8.5. Medical .................................................................................................................... 10
1.8.6. Toilet........................................................................................................................ 10
1.8.7. Controversy ............................................................................................................. 10
1.8.8. Direct contact........................................................................................................... 11
Physical intimacy............................................................................................................... 11
Mother to child.................................................................................................................. 11
1.8.9. Indirect contact ........................................................................................................ 11
Objects and surfaces.......................................................................................................... 11
Food and water.................................................................................................................. 12
Animal vectors .................................................................................................................. 12
1.9. Reproduction number .............................................................................................................13
1.10. Duration of transmissibility ..................................................................................................14
1.11. Reinfection..............................................................................................................................14
1.12. Pathophysiology .....................................................................................................................14
1.13. Immunopathology..................................................................................................................16
1.14. Viral and host factors................................................................................................ 17

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1.14.1. Virus proteins......................................................................................................... 17
1.14.2. Host factors ............................................................................................................ 17
1.14.3. Host cytokine response ........................................................................................... 17
CHAPTER TWO: DIAGNOSIS OF COVID-19 .........................................................................19
2.1. COVID-19 testing.....................................................................................................................19
2.2. Viral testing ..............................................................................................................................19
2.3. Imaging .....................................................................................................................................20
2.4. COVID-19 Accuracy................................................................................................................20
2.5. Sensitivity and specificity ........................................................................................................21
2.6. Causes of test error ..................................................................................................................21
2.7. PCR-based test .........................................................................................................................22
2.8. Confirmatory testing ...............................................................................................................23
2.9. Coding.......................................................................................................................................23
2.10. Pathology ................................................................................................................................23
2.11. Complications.........................................................................................................................23
2.12. Longer-term effects................................................................................................................24
2.13. Immunity ................................................................................................................................24
2.14. Management of COVID-19 ...................................................................................................25
2.14.1. Contact tracing....................................................................................................... 25
2.14.2. Health care............................................................................................................. 25
2.15. Disease spread ........................................................................................................................26
2.16. Resistance/susceptibility based on ethnicity ........................................................................26
2.17. Lifetime of the virus...............................................................................................................26
CHAPTER THREE: PREVENTION AND TREATMENT OF COVID-19.............................27
3.1. Prevention.................................................................................................................................27
3.1.1. Efficacy of hand sanitizer and "antibacterial" soaps ........................................................28
3.1.2. Public use of face masks .......................................................................................................28
3.1.3. Social distancing....................................................................................................................30
3.1.4. Self-isolation............................................................................................................. 31
3.1.5. Surface cleaning....................................................................................................... 31
3.1.6. Ventilation and air filtration .................................................................................... 31
3.1.7. Healthy diet and lifestyle.......................................................................................... 31
3.2. Treatment .................................................................................................................................32
CHAPTER FOUR: COVID-19 MORTALITY......................................................................... 33
4.1. COVID-19 stages to death.......................................................................................................33
4.2. Fatality diversification.............................................................................................................34

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4.3. Infection fatality rate ...............................................................................................................35
4.3.1. Current estimates..................................................................................................... 35
4.3.2. Earlier estimates of IFR ........................................................................................... 35
4.4. Sex differences..........................................................................................................................36
4.5. Ethnic differences.....................................................................................................................36
4.6. Comorbidities...........................................................................................................................37
CHAPTER FIVE: COVID-19 RELATED RESEARCH........................................................... 38
5.1. Introduction..............................................................................................................................38
5.1.1. Existing drugs trials ................................................................................................. 38
5.1.2. Cytokine storm......................................................................................................... 39
5.1.3. Passive antibodies..................................................................................................... 40
5.2. COVID-19 drug development.................................................................................................41
5.2.1. Repurposed drug candidates.................................................................................... 42
5.2.2. Novel monoclonal antibody drugs ............................................................................ 43
Casirivimab/imdevimab .................................................................................................... 43
Bamlanivimab and etesevimab .......................................................................................... 43
5.2.3. Planning and coordination ....................................................................................... 44
Early planning................................................................................................................... 44
International Solidarity and Discovery Trials.................................................................... 45
5.2.4. Adaptive COVID-19 Treatment Trial ...................................................................... 46
5.2.5. Recovery Trial.......................................................................................................... 46
5.3. COVID-19 vaccine ...................................................................................................................47
5.3.1. Overview.................................................................................................................. 47
5.3.2. Planning and development ....................................................................................... 49
5.3.3. Organizations........................................................................................................... 49
5.3.4. History ..................................................................................................................... 50
5.3.5. Vaccine types............................................................................................................ 52
5.3.6. RNA vaccines ........................................................................................................... 53
5.3.7. Adenovirus vector vaccines ...................................................................................... 53
5.3.8. Inactivated virus vaccines......................................................................................... 53
5.3.9. Subunit vaccines....................................................................................................... 54
5.4. Trial and authorization status ................................................................................................54
5.4.1. List of authorized and approved vaccines................................................................. 54
Vaccine candidates............................................................................................................. 60
5.5. Efficacy......................................................................................................................................68
5.6. Formulation..............................................................................................................................69

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5.7. Deployment...............................................................................................................................69
5.8. Cost............................................................................................................................................74
5.9. Liability.....................................................................................................................................75
5.10. Market.....................................................................................................................................75
5.11. Side effects ..............................................................................................................................76
5.12. Vaccine hesitancy...................................................................................................................76
CHAPTER SIX: RESPONSES TO COVID-19 ...........................................................................77
6.1. Overview...................................................................................................................................77
6.2. International responses............................................................................................................78
6.2.1. Travel restrictions.................................................................................................... 78
6.2.2. Evacuation of foreign citizens................................................................................... 78
6.2.3. United Nations response measures ........................................................................... 79
6.2.4. WHO response measures.......................................................................................... 79
CHAPTER SEVEN: IMPACT OF THE COVID-19 PANDEMIC ON EDUCATION.............. 81
7.1. Overview...................................................................................................................................81
7.2. Consequences of schools closure.............................................................................................83
7.3. Virtual learning among responses..........................................................................................84
7.4. Student learning outcomes......................................................................................................85
7.5. Impact on early childhood education.....................................................................................85
7.6. Impact on primary and secondary education........................................................................86
7.7. Impact on tertiary education ..................................................................................................87
CHAPTER EIGHT: ECONOMIC IMPACTS OF THE COVID-19......................................... 89
8.2. Global economic recession.......................................................................................................90
8.3. Food crisis contexts..................................................................................................................91
8.4. Financial markets instability...................................................................................................91
8.4.1. 2020 stock market crash........................................................................................... 92
8.5. Impact on manufacturing and trade industry.......................................................................93
8.5.1. Supply shortages ...................................................................................................... 94
8.6. Impact on tourism....................................................................................................................95
8.7. Impact on transportation ........................................................................................................95
8.7.1. Aviation.................................................................................................................... 96
8.7.2. Cruise lines............................................................................................................... 96
8.7.3. Railways................................................................................................................... 96
8.8. Unemployment during COVID-19 .........................................................................................97
8.9. Economic impact by region and country ...............................................................................98
8.9.1. Mainland China ..................................................................................................... 100

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8.9.2. Europe ................................................................................................................... 101
8.9.3. North America ....................................................................................................... 102
Canada............................................................................................................................ 102
Mexico............................................................................................................................. 102
United States ................................................................................................................... 103
8.9.4. Brazil ..................................................................................................................... 104
8.9.5. Australia ................................................................................................................ 105
CHAPTER NINE: IMPACT ON OTHER SECTORS............................................................ 106
9.1. Impacts on art and entertainment industry.........................................................................106
9.2. Impact on politics...................................................................................................................108
9.2.1. Critics to countries................................................................................................. 108
9.3. Impact of the COVID-19 pandemic on the environment ...................................................111
9.4. Xenophobia and racism.........................................................................................................111
9.5. Health care workers at risk...................................................................................................112
9.5.1. Risk of infection ..................................................................................................... 112
9.5.2. Shortage of PPEs.................................................................................................... 112
9.5.3. Deaths .................................................................................................................... 113
9.5.4. Psychological impact .............................................................................................. 113
9.5.5. Impact on female staff............................................................................................ 114
CHAPTER TEN: IMPACT OF THE COVID-19 PANDEMIC ON RELIGION .................... 115
10.1. Overview...............................................................................................................................115
10.2. Impact on Christianity and response .................................................................................115
10.3. Islam......................................................................................................................................117
10.4. Judaism.................................................................................................................................118
10.5. Hinduism ................................................................................................................ 118
10.6. Buddhism..............................................................................................................................119
CHAPTER ELEVEN: COVID-19 MISINFORMATION ....................................................... 120
11.1. Overview...............................................................................................................................120
11.2. Virus origin...........................................................................................................................121
11.2.1. Wuhan lab leak story ........................................................................................... 121
11.2.2. Chinese espionage involving Canadian lab ........................................................... 122
11.2.3. United States biological weapon ........................................................................... 123
11.2.4. Jewish origin ........................................................................................................ 124
In the Muslim world........................................................................................................ 124
In the United States ......................................................................................................... 125
11.2.5. Anti-Muslim......................................................................................................... 125

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11.2.6. Population-control scheme ................................................................................... 125
11.2.7. 5G mobile phone networks ................................................................................... 126
11.2.8. American scientist selling virus to China.............................................................. 128
11.3. Misreporting misinformation..............................................................................................128
11.3.1. Chinese under-reporting during early 2020.......................................................... 128
11.3.2. Allegations of inflated death counts...................................................................... 129
11.2.3. Nurse whistle blower ............................................................................................ 129
11.3. Efforts to combat misinformation ......................................................................................129
11.3.1. Social media ......................................................................................................... 130
11.3.2. Wikipedia............................................................................................................. 130
11.3.3. Scams ................................................................................................................... 131
HAPTER TWELVE: PROTESTS OVER RESPONSES TO THE COVID-19 PANDEMIC .. 132
12.1. Africa.....................................................................................................................................132
Ivory Coast ....................................................................................................................... 132
Kenya............................................................................................................................... 132
Malawi............................................................................................................................. 132
Nigeria ............................................................................................................................. 133
Rwanda............................................................................................................................ 133
South Africa...................................................................................................................... 133
Zimbabwe ........................................................................................................................ 133
12.2. Asia........................................................................................................................................133
China................................................................................................................................ 133
Hong Kong........................................................................................................................ 134
India................................................................................................................................. 134
Indonesia ......................................................................................................................... 134
Israel................................................................................................................................ 134
Iraq .................................................................................................................................. 135
Lebanon ........................................................................................................................... 135
Pakistan ........................................................................................................................... 135
Philippines ....................................................................................................................... 135
Thailand........................................................................................................................... 136
12.3. Europe...................................................................................................................................136
Belgium............................................................................................................................ 136
Bulgaria............................................................................................................................ 136
France.............................................................................................................................. 137
Germany .......................................................................................................................... 137

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Ireland ............................................................................................................................. 137
Italy.................................................................................................................................. 138
Netherlands ..................................................................................................................... 138
Poland.............................................................................................................................. 138
Russia............................................................................................................................... 138
Serbia............................................................................................................................... 138
Spain................................................................................................................................ 139
United Kingdom ............................................................................................................... 139
12.4. North America......................................................................................................................139
Canada............................................................................................................................. 139
Mexico............................................................................................................................. 140
United States.................................................................................................................... 140
12.5. Oceania..................................................................................................................................142
Australia........................................................................................................................... 142
New Zealand .................................................................................................................... 143
12.6. South America......................................................................................................................144
Argentina ......................................................................................................................... 144
Brazil................................................................................................................................ 145
Chile................................................................................................................................. 145
CHAPTER THIRTEEN: COVID-19 PANDEMIC IN UGANDA........................................... 146
13.2. Time lines of the pandemic..................................................................................................146
March 2020 ..................................................................................................................... 146
April 2020........................................................................................................................ 147
May 2020......................................................................................................................... 148
June 2020 ........................................................................................................................ 149
July 2020 ......................................................................................................................... 149
August 2020..................................................................................................................... 149
September 2020............................................................................................................... 150
October 2020 ................................................................................................................... 150
November 2020................................................................................................................ 150
December 2020................................................................................................................ 150
January 2021................................................................................................................... 150
February 2021................................................................................................................. 150
13.3. Responses to COVID-19 ................................................................................................. 151
13.3.1. The creation of COVID-19 Preparedness and Response Plan ................................... 151
13.3.2 Introduction of protection equipment by NYTIL...........................................................151

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13.3.3. COVID-19 Donations.............................................................................................. 152
13.4. Impacts of COVID-19 in Uganda .......................................................................................153
INDEX.................................................................................................................................... 156
Infographics about COVID-19 (Reports reference up to March 2021).................................... 156
15 MOST-AFFECTED COUNTRIES (DATA COMPILED UP TO March 2021)................161
United States.................................................................................................................... 161
Brazil................................................................................................................................ 161
India................................................................................................................................. 162
Russia............................................................................................................................... 162
France.............................................................................................................................. 163
United Kingdom ............................................................................................................... 163
Italy.................................................................................................................................. 164
Spain................................................................................................................................ 164
Turkey.............................................................................................................................. 165
Germany .......................................................................................................................... 165
Colombia.......................................................................................................................... 166
Argentina ......................................................................................................................... 166
Mexico............................................................................................................................. 167
Poland.............................................................................................................................. 168
Iran .................................................................................................................................. 168
China................................................................................................................................ 169
REFERENCES....................................................................................................................................170

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INTRODUCTION
New infectious diseases impose a serious threat to the health of the general public. Their
origins are often mysterious despite intensive research efforts. Although human
coronaviruses (CoVs) had been known as major pathogens to cause the common cold, a new
species of coronavirus, namely SARS-CoV caused an epidemic involving 29 countries during
2002–03 which infected 8098 persons and killed 774 of them. The evidence shows that the
virus might have originated from an animal coronavirus, but somehow entered the human
population. Its outbreak also implies that animal coronaviruses could be a potential danger
to humans.
Since the 2003 SARS outbreak, the general public and the scientific community in China have
been worried about the potential return of the deadly virus which motivated the Chinese
government to reform its public health system to handle the next public health crisis. As part
of the reform, China expanded the laboratory networks to handle the pathogens of the
infectious diseases which included a newly built BSL-4 laboratory in Wuhan and a national key
laboratory to investigate into pneumonia with unclear causes. Zeng Guang, the Chief Scientist
at China CDC believed that a quicker publication of the epidemic information was a lesson
that China learned from the SARS outbreak as the lack of information release worsened the
outbreak.
With the improved public health system, China managed to handle several public health
emergencies. In coping with the 2009 H1N1 flu outbreak starting from Mexico, China
developed and distributed vaccines to 100 million people within months as an active
prevention. During the 2013 H7N9 outbreak in East China, the country's health system
identified the pathogen 5 days after the outbreak. Test kits for diagnosis were designed and
distributed to all mainland provinces 3 days after the identification. Within months, effective
vaccines were developed. Besides, Chinese academic Li Lanjuan and her group was the first
to reveal the virus's transmission methods, molecular mechanisms and effective treatment.
However, Southern Metropolis Daily stated that although people paid more attention to
public health, the government's funding to the health system was far from enough as CDCs in
smaller municipalities had to reduce their staff. 10 years after the SARS outbreak, few people
wore a face mask when they had respiratory symptoms and the hospitals were cutting the
fever clinics off. Despite confidence in winning the next battle against SARS, Zhong Nanshan
who earned fame in fighting the SARS outbreak in 2003 still held a conservative attitude to
whether the Chinese officials would lie to the people about a disease outbreak.
Early cases surrounding the animal market suggested potential animal-to-human
transmission while later the virus was found to be able to transmit from ill people to others.
There have been cases where asymptomatic patients transmitted the virus to others.
According to China NHC, the virus transmits by droplets or close contact while some proposed
that faeces could also be where the virus hides and transmits from. The typical symptoms of
the viral infection included fever, dry cough, dyspnoea, headache and pneumonia which are
usually developed after an incubation time lasting as long as 2 weeks. The existence of mild
but infectious cases complicated the epidemic control efforts. It is also noticed that patients
might be able to transmit the virus even during the incubation period.

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CHAPTER ONE: EPIDEMIOLOGY OF COVID-19
1.1. Overview
The COVID-19 pandemic1, also known as the
coronavirus pandemic, is an ongoing pandemic
of coronavirus disease 2019 (COVID-19) caused
by severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2). It was first
identified in December 2019 in Wuhan, China.
The World Health Organization declared the
outbreak a Public Health Emergency of
International Concern in January 2020 and a
pandemic in March 2020. As of 20 February
2021, more than 110 million cases have been
confirmed, with more than 2.45 million deaths
attributed to COVID-19.
The virus spreads mainly through the air when people are near each other. It leaves an
infected person as they breathe, cough, sneeze, or speak and enters another person via their
mouth, nose, or eyes. It may also spread via contaminated surfaces. People remain infectious
for up to two weeks, and can spread the virus even if they do not show symptoms.
Recommended preventive measures include social distancing, wearing face masks in public,
ventilation and air-filtering, hand washing, covering one's mouth when sneezing or coughing,
disinfecting surfaces, and monitoring and self-isolation for people exposed or symptomatic.
Several vaccines are being developed and distributed. Current treatments focus on
addressing symptoms while work is underway to develop therapeutic drugs that inhibit the
virus. Authorities worldwide have responded by implementing travel restrictions, lockdowns,
workplace hazard controls, and facility closures. Many places have also worked to increase
testing capacity and trace contacts of the infected.
The responses to the pandemic have resulted in global social and economic disruption,
including the largest global recession since the Great Depression. It has led to the
postponement or cancellation of events, widespread supply shortages exacerbated by panic
buying, agricultural disruption and food shortages, and decreased emissions of pollutants and
greenhouse gases. Many educational institutions and public areas have been partially or fully
closed. Misinformation has circulated through social media and mass media. The pandemic
has raised issues of racial and geographic discrimination, health equity, and the balance
between public health imperatives and individual rights.
1
A pandemic is an epidemic of an infectious disease that has spread across a large region, for instance
multiple continents or worldwide, affecting a substantial number of people.
Figure 1: Respiratory system of human body as a host of
COVID-19. Source: Google photos

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1.2. Name
During the initial outbreak in Wuhan, China, the virus and disease were commonly referred
to as "coronavirus" and "Wuhan coronavirus", with the disease sometimes called "Wuhan
pneumonia". In the past, many diseases have been named after geographical locations, such
as the Spanish flu, Middle East Respiratory Syndrome, and Zika virus.
In January 2020, the WHO recommended 2019-nCov and 2019-nCoV acute respiratory
disease as interim names for the virus and disease per 2015 guidance and international
guidelines against using geographical locations (e.g. Wuhan, China), animal species, or groups
of people in disease and virus names in part to prevent social stigma.
The official names COVID-19 and SARS-CoV-2 were issued by the WHO on 11 February 2020.
Tedros Adhanom2 explained: CO for corona, VI for virus, D for disease and 19 for when the
outbreak was first identified (31 December 2019). The WHO additionally uses "the COVID-19
virus" and "the virus responsible for COVID-19" in public communications.
1.3. History COVID-19
The virus is thought to be natural and has an animal origin through spill over infection. There
are several theories about where the first case (the so-called patient zero) originated.
Phylogenetic estimates that SARS-CoV-2 arose in October or November 2019. Evidence
suggests that it descends from a coronavirus that infects wild bats and spread to humans
through an intermediary wildlife host.
The first known human infections were in Wuhan3, Hubei, China. A study of the first 41 cases
of confirmed COVID-19, published in January 2020 in The Lancet, reported the earliest date
of onset of symptoms as 1 December 2019. Official publications from the WHO reported the
earliest onset of symptoms as 8 December 2019. Human-to-human transmission4 was
confirmed by the WHO and Chinese authorities by 20 January 2020. According to official
Chinese sources, these were mostly linked to the Huanan Seafood Wholesale Market, which
also sold live animals. In May 2020, George Gao, the director of the CDC, said animal samples
collected from the seafood market had tested negative for the virus, indicating that the
market was the site of an early super spreading event, but it was not the site of the initial
outbreak. Traces of the virus have been found in wastewater that was collected from Milan
and Turin, Italy, on 18 December 2019.
2
Tedros Adhanom Ghebreyesus (born 3 March 1965) is an Ethiopian biologist, public health researcher,
and official who has served since 2017 as Director-General of the World Health Organization. Tedros is
the first African in the role; he was endorsed by the African Union.
3
Wuhan is the capital of Hubei Province in the People's Republic of China. It is the largest city in Hubei
and the most populous city in Central China, with a population of over 11 million, the ninth-most populous
Chinese city and one of the nine National Central Cities of China.
4
Human-to-human transmission (HHT) is a particularly problematic epidemiologic vector, especially in
case the disease is borne by individuals known as superspreaders. In these cases, the basic reproduction
number of the virus, which is the average number of additional people that a single case will infect without
any preventative measures, can be as high as 3.9. Interhuman transmission is a synonym for HHT.

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By December 2019, the spread of infection was almost entirely driven by human-to-human
transmission. The number of coronavirus cases in Hubei gradually increased, reaching 60 by
20 December and at least 266 by 31 December. On 24 December, Wuhan Central Hospital
sent a Broncho alveolar lavage fluid (BAL) sample from an unresolved clinical case to
sequencing company Vision Medicals. On 27 and 28 December, Vision Medicals informed the
Wuhan Central Hospital and the Chinese CDC of the results of the test, showing a new
coronavirus. A pneumonia cluster of unknown cause was observed on 26 December and
treated by the doctor Zhang Jixian in Hubei Provincial Hospital, who informed the Wuhan
Jianghan CDC on 27 December. On 30 December, a test report addressed to Wuhan Central
Hospital, from company CapitalBio Medlab, stated an erroneous positive result for SARS,
causing a group of doctors at Wuhan Central Hospital to alert their colleagues and relevant
hospital authorities of the result. That evening, the Wuhan Municipal Health Commission
issued a notice to various medical institutions on "the treatment of pneumonia of unknown
cause". Eight of these doctors, including Li Wenliang (punished on 3 January), were later
admonished by the police for spreading false rumours, and another, Ai Fen, was reprimanded
by her superiors for raising the alarm.
The Wuhan Municipal Health Commission made the first public announcement of a
pneumonia outbreak of unknown cause on 31 December, confirming 27 cases enough to
trigger an investigation.
During the early stages of the outbreak, the number of cases doubled approximately every
seven and a half days. In early and mid-January 2020, the virus spread to other Chinese
provinces, helped by the Chinese New Year migration and Wuhan being a transport hub and
major rail interchange. On 20 January, China reported nearly 140 new cases in one day,
including two people in Beijing and one in Shenzhen. Later official data shows 6,174 people
had already developed symptoms by then, and more may have been infected. A report in The
Lancet on 24 January indicated human transmission, strongly recommended personal
protective equipment for health workers, and said testing for the virus was essential due to
its "pandemic potential". On 30 January, the WHO declared the coronavirus a Public Health
Emergency of International Concern. By this time, the outbreak spread by a factor of 100 to
200 times.
On 31 January 2020, Italy had its first confirmed cases, two tourists from China. As of 13 March
2020, the WHO considered Europe the active centre of the pandemic. On 19 March 2020,
Italy overtook China as the country with the most deaths. By 26 March, the United States had
overtaken China and Italy with the highest number of confirmed cases in the world. Research
on coronavirus genomes indicates the majority of COVID-19 cases in New York came from
European travellers, rather than directly from China or any other Asian country. Retesting of
prior samples found a person in France who had the virus on 27 December 2019 and a person
in the United States who died from the disease on 6 February 2020.
On 11 June 2020, after 55 days without a locally transmitted case, Beijing reported the first
COVID-19 case, followed by two more cases on 12 June. By 15 June 79 cases were officially
confirmed. Most of these people went to Xinfadi Wholesale Market.

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RT-PCR testing of untreated wastewater samples from Brazil and Italy have suggested
detection of SARS-CoV-2 as early as November and December 2019, respectively, but the
methods of such sewage studies have not been optimised, many have not been peer
reviewed, details are often missing, and there is a risk of false positives due to contamination
or if only one gene target is detected. A September 2020 review journal article said, "The
possibility that the COVID-19 infection had already spread to Europe at the end of last year is
now indicated by abundant, even if partially circumstantial, evidence", including pneumonia
case numbers and radiology in France and Italy in November and December.
1.4. First appearance
Although it is still unknown exactly where
the outbreak first started, many early
cases of COVID-19 have been attributed to
people who have visited the Huanan
Seafood Wholesale Market, located in
Wuhan, Hubei, China. On 11 February
2020, the World Health Organization
(WHO) named the disease "COVID-19",
which is short for coronavirus disease
2019. The virus that caused the outbreak
is known as severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), a newly discovered virus closely related to bat
coronaviruses, pangolin coronaviruses, and SARS-CoV. Scientific consensus is that COVID-19
is a zoonotic virus that arose from bats in a natural setting.
The earliest known person with symptoms was later discovered to have fallen ill on
1 December 2019, and that person did not have visible connections with the later wet market
cluster. However, an earlier case of infection could have occurred on 17 November. Of the
early cluster of cases reported that month, two thirds were found to have a link with the
market. There are several theories about when and where the very first case (the so-called
patient zero) originated.
Symptoms of COVID-19 are variable, but often include fever, cough, fatigue, breathing
difficulties, and loss of smell and taste. Symptoms begin one to fourteen days after exposure
to the virus. Of those people who develop noticeable symptoms, most (81%) develop mild to
moderate symptoms (up to mild pneumonia), while 14% develop severe symptoms (dyspnoea,
hypoxia, or more than 50% lung involvement on imaging), and 5% suffer critical symptoms
(respiratory failure, shock, or multi organ dysfunction). At least a third of the people who are
infected with the virus remain asymptomatic and do not develop noticeable symptoms at any
point in time, but they still can spread the disease. Some people continue to experience a
range of effects—known as long COVID—for months after recovery, and damage to organs
has been observed. Multi-year studies are underway to further investigate the long-term
effects of the disease.
Figure 2: SARS-COV-2 Cell aspect. Source: Google photos

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The virus that causes COVID-19 spreads mainly when an infected person is in close contact
with another person. Small droplets and aerosols containing the virus can spread from an
infected person's nose and mouth as they breathe, cough, sneeze, sing, or speak. Other
people are infected if the virus gets into their mouth, nose or eyes. The virus may also spread
via contaminated surfaces, although this is not thought to be the main route of transmission.
The exact route of transmission is rarely proven conclusively, but infection mainly happens
when people are near each other for long enough. People who are infected can transmit the
virus to another person up to two days before they themselves show symptoms, as can people
who do not experience symptoms. People remain infectious for up to ten days after the onset
of symptoms in moderate cases and up to 20 days in severe cases. Several testing methods
have been developed to diagnose the disease. The standard diagnostic method is by detection
of the virus' nucleic acid by real-time reverse transcription polymerase chain reaction (rRT-
PCR), transcription-mediated amplification5 (TMA), or by loop-mediated isothermal
amplification from a nasopharyngeal swab.
Preventive measures include physical or social distancing, quarantining, and ventilation of
indoor spaces, covering coughs and sneezes, hand washing, and keeping unwashed hands
away from the face. The use of face masks or coverings has been recommended in public
settings to minimise the risk of transmissions. Several vaccines have been developed and
several countries have initiated mass vaccination campaigns.
Although work is underway to develop drugs that inhibit the virus, the primary treatment is
currently symptomatic. Management involves the treatment of symptoms, supportive care,
isolation, and experimental measures.
1.5. Signs and symptoms
Symptoms of COVID-19 are
variable, ranging from mild
symptoms to severe illness.
Common symptoms include
headache, loss of smell and
taste, nasal congestion and
rhinorrhoea, cough, muscle
pain, sore throat, fever,
diarrhoea, and breathing
difficulties. People with the
same infection may have
different symptoms, and their
symptoms may change over
5
Transcription-mediated amplification (TMA) is an isothermal (does not change the nucleic acid
temperature), single-tube nucleic acid amplification system utilizing two enzymes, RNA polymerase and
reverse transcriptase. TMA technology allows a clinical laboratory to perform nucleic acid test (NAT)
assays for blood screening with fewer steps, less processing time, and faster results.
Figure 3: Symptoms of COVID-19. Source: Wikipedia

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time. In people without prior ears, nose, and throat disorders, loss of taste combined with
loss of smell is associated with COVID-19.
Most people (81%) develop mild to moderate symptoms (up to mild pneumonia), while 14%
develop severe symptoms (dyspnoea, hypoxia, or more than 50% lung involvement on
imaging) and 5% of patients suffer critical symptoms (respiratory failure, shock, or multiorgan
dysfunction). At least a third of the people who are infected with the virus do not develop
noticeable symptoms at any point in time. These asymptomatic carriers tend not to get tested
and can spread the disease. Other infected people will develop symptoms later, called "pre-
symptomatic", or have very mild symptoms and can also spread the virus.
As is common with infections, there is a delay between the moment a person first becomes
infected and the appearance of the first symptoms. The median delay for COVID-19 is four to
five days. Most symptomatic people experience symptoms within two to seven days after
exposure, and almost all will experience at least one symptom within 12 days.
Most people recover from the acute phase of the disease. However, some people continue
to experience a range of effects for months after recovery—named long COVID—and damage
to organs has been observed. Multi-year studies are underway to further investigate the long-
term effects of the disease.
1.5. Cause
COVID-19 is caused by infection with the severe acute respiratory syndrome coronavirus 2
(SARS-CoV-2) virus strain.
1.6. Virology6
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel severe acute
respiratory syndrome coronavirus. It was first isolated from three people with pneumonia
connected to the cluster of acute respiratory illness cases in Wuhan. All structural features
of the novel SARS-CoV-2 virus particle occur in related coronaviruses in nature. Outside the
human body, the virus is destroyed by household soap, which bursts its protective bubble.
SARS-CoV-2 is closely related to the original SARS-CoV. It is thought to have an animal
(zoonotic) origin. Genetic analysis has revealed that the coronavirus genetically clusters with
the genus Betacoronavirus7, in subgenus Sarbecovirus (lineage B) together with two bat-
derived strains. It is 96% identical at the whole genome level to other bat coronavirus samples
(BatCov RaTG13). The structural proteins of SARS-CoV-2 include membrane glycoprotein (M),
envelope protein (E), nucleocapsid protein (N), and the spike protein (S). The M protein of
SARS-CoV-2 is about 98% similar to the M protein of bat SARS-CoV, maintains around 98%
6
Virology is the study of viruses – submicroscopic, parasitic particles of genetic material contained in a
protein coat– and virus-like agents.
7
Betacoronavirus (β-CoVs or Beta-CoVs) is one of four genera (Alpha-, Beta-, Gamma-, and Delta-) of
coronaviruses. Member viruses are enveloped, positive-strand RNA viruses that infect mammals (of which
humans are part). The natural reservoir for betacoronaviruses are bats and rodents. Rodents are the
reservoir for the subgenus Embecovirus, while bats are the reservoir for the other subgenera.

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homology with pangolin SARS-CoV, and has 90% homology with the M protein of SARS-CoV;
whereas, the similarity is only around 38% with the M protein of MERS-CoV8.
The many thousands of SARS-CoV-2 variants are grouped into clades. Several different clade
nomenclatures have been proposed. Nextstrain divides the variants into five clades (19A, 19B,
20A, 20B, and 20C), while GISAID divides them into seven (L, O, V, S, G, GH, and GR).
Several notable variants of SARS-CoV-2 emerged in late 2020. Cluster 5 emerged among minks
and mink farmers in Denmark. After strict quarantines and a mink euthanasia campaign, it is
believed to have been eradicated. The Variant of Concern 202012/019 (VOC 202012/01) is
believed to have emerged in the United Kingdom in September. The 501Y.V2 Variant, which
has the same N501Y mutation, arose independently in South Africa.
1.7. SARS-CoV-2 variants
Three known variants of COVID-19 are currently spreading among global populations as of
January 2021 including the UK Variant (referred to as B.1.1.7) first found in London and Kent,
a variant discovered in South Africa (referred to as 1.351), and a variant discovered in Brazil
(referred to as P.1).
Using Whole Genome Sequencing, epidemiology and modelling suggest the new UK variant
‘VUI – 202012/01’ (the first Variant Under Investigation in December 2020) transmits more
easily than other strains.
1.8. Transmission of COVID-19
Coronavirus disease 2019 (COVID-19) spreads from person to person mainly through the
respiratory route after an infected person coughs, sneezes, sings, talks or breathes. A new
infection occurs when virus-containing particles exhaled by an infected person, either
respiratory droplets or aerosols, get into the mouth, nose, or eyes of other people who are in
close contact with the infected person. During human-to-human transmission, an average
1000 infectious SARS-CoV-2 virions are thought to initiate a new infection.
The closer people interact, and the longer they interact, the more likely they are to transmit
COVID-19. Closer distances can involve larger droplets (which fall to the ground) and aerosols,
whereas longer distances only involve aerosols. Larger droplets can also turn into aerosols
(known as droplet nuclei) through evaporation. The relative importance of the larger droplets
and the aerosols is not clear as of November 2020; however, the virus is not known to spread
between rooms over long distances such as through air ducts. Airborne transmission10 is able
to particularly occur indoors, in high risk locations such as restaurants, choirs, gyms,
nightclubs, offices, and religious venues, often when they are crowded or less ventilated. It
8
Middle East respiratory syndrome (MERS) is a viral respiratory disease caused by a novel coronavirus
(Middle East respiratory syndrome coronavirus, or MERS‐CoV) that was first identified in Saudi Arabia
in 2012.
9
The first Variant Under Investigation in December 2020 (VUI – 202012/01), also known as B.1.1.7, is a
mutation of SARS-CoV-2, the virus that causes COVID-19.
10
An airborne transmission is disease transmission through small particulates that can be transmitted
through the air over time and distance.

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also occurs in healthcare settings, often when aerosol-generating medical procedures are
performed on COVID-19 patients.
Although it is considered possible there is no direct evidence of the virus being transmitted
by skin to skin contact. A person could get COVID-19 indirectly by touching a contaminated
surface or object before touching their own mouth, nose, or eyes, though this is not thought
to be the main way the virus spreads, and there is no direct evidence of this method either.
The virus is not known to spread through feces, urine, breast milk, food, wastewater, drinking
water, or via animal disease vectors (although some animals can contract the virus from
humans). It very rarely transmits from mother to baby during pregnancy.
Social distancing and the wearing of cloth face masks, surgical masks, respirators, or other
face coverings are controls for droplet transmission. Transmission may be decreased indoors
with well-maintained heating and ventilation systems to maintain good air circulation and
increase the use of outdoor air.
The number of people generally infected by one infected person varies; as of September 2020
it was estimated that one infected person will, on average, infect between two and three
other people. This is more infectious than influenza, but less so than measles. It often spreads
in clusters, where infections can be traced back to an index case or geographical location.
There is a major role of "super-spreading events", where many people are infected by one
person.
A person who is infected can transmit the virus to others up to two days before they
themselves show symptoms, and even if symptoms never appear. People remain infectious
in moderate cases for 7–12 days, and up to two weeks in severe cases. In October 2020,
medical scientists reported evidence of reinfection in one patient.
1.8.1. Routes
The relative importance of the larger respiratory droplets and the smaller aerosol particles
(airborne transmission) is unknown. There has been extensive debate around the traditional
distinction between the two forms of transmission, with the UK Government and a review
combining them into one "respiratory route". Regardless of whether droplets or aerosols are
the dominant route, the risk is always lower outside and with good ventilation.
1.8.2. Respiratory droplets
The main route of transmission of COVID-19 is respiratory
droplets expelled from the mouth and nose when a
person sneezes, coughs, or speaks.
The virus spreads through respiratory droplets produced
when an infected person breathes, coughs, sneezes, or
talks. These droplets can land in the mouths or noses of
Figure 4: Transmission through droplets.
Source: Wikipedia

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people who are nearby, or possibly be inhaled into the lungs. Spread is more likely when
people are in close contact within about 6 feet (1.8 m).
"Close contact" is variously defined. The U.S. Centers for Disease Control and Prevention
(CDC) defines it as "within 6 feet (1.8 m) of an infected person for a cumulative total of 15
minutes or more over a 24-hour period." The European Centre for Disease Prevention and
Control states that close proximity is "usually less than 1 meter (3.3 ft) apart." The Australian
Health Department defines it as sharing an enclosed space for a prolonged period such as two
hours.
Social distancing and the wearing of cloth face masks, surgical masks, respirators, or other
face coverings are controls for droplet transmission. The World Health Organization
recommends 1 meter (3.3 ft) of social distance; the U.S. Centers for Disease Control and
Prevention recommends 6 feet (1.8 m).
1.8.3. Aerosols
Airborne transmission of COVID-19 has been shown to occur through aerosols containing
residual of droplets, that are able to stay suspended in the air for longer periods of time.
Airborne transmission is able to occur, particularly indoors, such as in restaurants, choir
practices, fitness classes, nightclubs, offices, and religious venues, often when they are
crowded or less ventilated. It also occurs in healthcare settings, often when aerosol-
generating medical procedures performed on COVID-19 patients. Long distance dispersal of
virus particles has been detected in ventilation systems of a hospital, indicating the possibility
of long range aerosol transmission.
1.8.4. Respiratory
Multiple outbreaks have been reported in indoor locations where infected persons spend long
periods of time, such as restaurants and nightclubs. This has particularly shown how the virus
can spread through the airborne route. There are several well documented examples where
COVID-19 has transmitted despite there not being the close proximity required for droplet
transmission, including choir practice in Washington, a restaurant in Guangzhou, and a tour
bus in Hunan.
The US CDC11 states that airborne transmission occurs under special circumstances, however
they "appear uncommon"; whereas ECDC12 states that the relative importance is unclear, the
UK government combines the methods into one “respiratory route” involving large and small
droplets, and the Public Health Agency of Canada states that the relative importance is not
clear.
11
The Centers for Disease Control and Prevention, formed in 1946, is the leading national public health
institute of the United States.
12
The European Centre for Disease Prevention and Control (ECDC) is an agency of the European Union
(EU) whose mission is to strengthen Europe's defences against infectious diseases.

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1.8.5. Medical
Although long distance dispersal of virus particles has been observed in hospital environment,
it is not considered to be as highly airborne as measles or chickenpox.
Some medical procedures performed on COVID-19 patients in health facilities are aerosol-
generating. WHO recommends the use of filtering face piece respirators such as N9513 masks
or FFP214 masks in settings where aerosol-generating procedures are performed, while CDC
and the European Centre for Disease Prevention and Control recommend these controls in all
situations involving the care of COVID-19 patients (other than during crisis shortages), as
respirators are designed to protect the wearer, whereas surgical masks are designed to
protect the patient.
1.8.6. Toilet
There has been concern that toilet aerosols generated by flushing contaminated toilets may
spread the COVID-19 virus. WHO recommends that people suspected or confirmed with
COVID-19 should use their own toilet, and while flushing the toilet lid should be down to block
both droplets and aerosol clouds.
1.8.7. Controversy
Aerosol transmission of the COVID-19 virus outside of medical facilities has been the subject
of controversy, with the WHO initially considering it insignificant, which led to widespread
criticism from scientists. In July 2020, the WHO changed its guidance, saying that short-range
aerosol transmission cannot be ruled out in these situations. In October 2020, it then further
changed its guidance, recognizing that although current evidence suggests respiratory
droplets is the main method, airborne transmission is occurring, particularly in high risk
indoor settings, where there is crowding and less ventilation. It states to avoid the "Three C"s
- crowded places, close contact settings, and confined and enclosed spaces.
The U.S. CDC has also been criticized for delays in informing the public about airborne
transmission, with John Allan from Harvard University's School of Public Health writing "many
scientists have known that airborne transmission of the virus was happening since February.
The CDC somehow failed to recognize the accumulating evidence that airborne transmission
is important and therefore failed to alert the public."
In Canada, the controversy has been attributed to complexities involving the N-95 mask
supply chain, and fears that it may run out. The Public Health Agency of Canada recognised
13
The N95 mask filter was invented by Taiwanese-American Peter Tsai and his team, and received its U.S.
patent in 1995.
14
FFP2 refers to the least filtering of the three masks with an aerosol filtration of at least 80% for 0.3 μm
particles, and is mainly used as an effective inhalation protection device.

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airborne transmission in November 2020, stating the relative importance between airborne
transmission and large droplet transmission is unknown.
In Australia the controversy involves PPE guidelines, with the Australian Medical Association
accusing Professor Lyn Gilbert, chair of the Infection Control Expert Group, of disparaging
frontline healthcare workers, accusing them of poor habits and being apathetic. She argues
that provision of N-95 masks gives clinicians a false sense of security, and they are unable to
be trained to use them properly, placing them more at risk. She also claims that washing
hands after touching contaminated surfaces is more important than use of a respirator, which
is recommended for only extraordinary circumstances.
1.8.8. Direct contact
Physical intimacy
The virus spreads through saliva and mucus, and kissing can easily transmit COVID-19. It is
possible that direct contact with feces including anilingus may also lead to virus transmission.
However, as of July 2020 there have been no published reports of COVID-19 transmission
through feces or urine. While COVID-19 is not a sexually transmitted infection, physical
intimacy carries a high risk of transmission due to close proximity.
Hand washing is a control against direct contact transmission. Others include avoiding kissing
and avoiding casual sex. During physical intimacy, barriers such as face masks, condoms, or
dental dams can be used, and socially distanced intimacy.
Mother to child
As of July 2020, there were no cases of transmission from mother to baby during pregnancy.
Studies have found no viable virus in breast milk. The WHO recommends that mothers with
suspected or confirmed COVID-19 should be encouraged to initiate or continue to breastfeed.
1.8.9. Indirect contact
Objects and surfaces
Surfaces that are often touched such as door handles may transmit COVID-19, although is not
thought to be the main way the virus spreads.
It may be possible that a person can get COVID-19 by touching a surface or object that has
the virus on it (called a fomite), and then touching their own mouth, nose, or possibly their
eyes. This is not thought to be the main way the virus spreads. Viable virus or RNA has been
detected on contaminated surfaces for periods ranging from hours to days, depending on
environmental conditions. As of July 2020, there were no specific reports which directly
demonstrated transmission via fomites, although fomite transmission is hard to distinguish
from transmission from the infectious person themselves, and fomite transmission was still
considered a likely mode of transmission.

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On surfaces the amount of viable active virus decreases over time until it can no longer cause
infection. One study indicated that the virus can be detected for up to four hours on copper,
up to one day on cardboard, and up to three days on plastic (polypropylene) and stainless
steel (AISI 304). In October 2020, medical researchers concluded the COVID-19 virus can
remain on common surfaces for up to 28 days.
Hand washing and periodic cleaning of surfaces are controls against indirect contact
transmission through fomites. Surfaces are easily decontaminated with household
disinfectants which destroy the virus outside the human body. Disinfectants or bleach are not
a treatment for COVID-19, and cause health problems when not used properly, such as when
used on or inside the human body.
Food and water
There is currently no evidence to support transmission of COVID-19 associated with food.
While virus RNA has been found in untreated wastewater, as of May 2020 there is little
evidence of infectious virus in wastewater or drinking water.
After COVID-19 outbreak in Beijing in June, food transmission evidence has been disclosed in
China early July 2020 by the detection of SARS-CoV-2 on frozen foods, including their
packaging materials and storage environments. On Oct 17, China CDC reports that they
separated out live SARS-CoV-2 virus from packaging of cold chain imported food, during
investigation of another outbreak in Qingdao in October. As of October, there is no direct
evidence of general public contracting the virus from contaminated food packaging.
Animal vectors
Humans appear to be capable of spreading the virus to some other animals, a type of disease
transmission referred to as zooanthroponosis. A domestic cat in Liège, Belgium, tested
positive after it started showing symptoms (diarrhoea, vomiting, and shortness of breath) a
week later than its owner, who was also positive. Tigers and lions at the Bronx Zoo in New
York, United States, tested positive for the virus and showed symptoms of COVID-19,
including a dry cough and loss of appetite. Minks at two farms in the Netherlands also tested
positive for COVID-19. In Denmark, as of October 31, 2020, 175 mink farms had seen COVID-
19 infection in mink, and also USA; Finland, Sweden and Spain have seen infections in mink.

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A study on domesticated animals inoculated with the virus found that cats and ferrets appear
to be "highly susceptible" to the disease, while dogs appear to be less susceptible, with lower
levels of viral replication. The study failed to find evidence of viral replication in pigs, ducks,
and chickens. It is known that other great ape species can be infected with COVID-19. Many
primate sanctuaries presume transmission from humans to other apes is possible, as it is for
other respiratory viruses.
As of August 2020, dozens of domestic cats and dogs had tested positive, though according
to the U.S. CDC, there was no evidence they transmitted the virus to humans. CDC guidance
recommends potentially infected people avoid close contact with pets.
On 4 November 2020, Prime Minister of Denmark Mette Frederiksen stated that a mutated
coronavirus was being transmitted to humans via minks, tied primarily to mink farms in
Northern Jutland.
There are a small number of cases of spread from people to pets, including cats and dogs.
Other cases include lions and tigers at a New York zoo, and minks on farms in the Netherlands.
In a laboratory settings, animals shown to be infected include ferrets, cats, golden Syrian
hamsters, rhesus macaques, cynomolgus macaques, grivets, common marmosets, and dogs.
By contrast, mice, pigs, chickens, and ducks do not seem to become infected or spread the
infection. There is no evidence that insect disease vectors such as mosquitoes or ticks spread
COVID-19.
CDC recommends that pet owners limit their pet's interaction with people outside their
household. Face coverings are not recommended on pets because covering a pet's face could
harm them, and they should not be disinfected with cleaning products not approved for
animal use. People sick with COVID-19 should avoid contact with pets and other animals.
The risk of COVID-19 spreading from animals to people is considered to be low. Although the
virus likely originated in bats, the pandemic is sustained through human-to-human spread.
Pets do not appear to play a role in spreading COVID-19, but there are reports from infected
mink farms indicating transmission to humans is a possibility.
1.9. Reproduction number
It transmits very easily and sustainably, however the number of people generally infected by
one infected person varies. Many people do not transmit the virus, but some transmit to
many people; therefore the virus is considered to be "over dispersed". As of September 2020
it was estimated that, on average, one infected person will infect between two and three
other people. This is more infectious than influenza, but less so than measles.

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Estimates of the number of people infected by one person with COVID-19, the R0
15, have
varied. The WHO's initial estimates of R0 were 1.4–2.5 (average 1.95); however an early April
2020 review found the median R0 to be 5.7.
It often spreads in clusters, where infections can be traced back to an index case or
geographical location. There is a major role of "super-spreading events", where many people
are infected by one person. These generally occur usually indoors, where groups of people
remain in poor ventilation for longer periods. It transmits via aerosols particularly in these
crowded and confined indoor spaces, which are particularly effective for transmitting the
virus, such as restaurants, nightclubs or choirs. Another important site for transmission is
between members of the same household.
1.10. Duration of transmissibility
People are most infectious when they show symptoms, even if mild or non-specific, but may
be infectious for up to two days before symptoms appear. They remain infectious an
estimated seven to twelve days in moderate cases and an average of two weeks in severe
cases. Research has indicated that viral load peaks around the day of symptom onset and
declines after, as measured by RNA16 studies.
The possibility of transmission for completely asymptomatic cases is unclear. A systematic
review estimated that the proportion of truly asymptomatic cases ranges from 6% to 41%,
with some limitations ("asymptomatic" was not very well defined). Another study with a clear
definition of asymptomatic infections estimated a proportion of 23%.
1.11. Reinfection
In October 2020, medical scientists reported evidence, for the first time in the U.S. and fifth
worldwide, of reinfection.
1.12. Pathophysiology
COVID-19 can affect the upper respiratory tract (sinuses, nose, and throat) and the lower
respiratory tract (windpipe and lungs). The lungs are the organs most affected by COVID-19
because the virus accesses host cells via the enzyme angiotensin-converting enzyme 2
(ACE2)17, which is most abundant in type II alveolar cells of the lungs. The virus uses a special
surface glycoprotein called a "spike" (peplomer) to connect to ACE2 and enter the host cell.
The density of ACE2 in each tissue correlates with the severity of the disease in that tissue
and decreasing ACE2 activity might be protective, though another view is that increasing ACE2
15
A very important number for describing whether a disease can become an epidemic or not is R0,
pronounced "R naught" or "R zero". It refers to how many people a person who has this disease is expected
to infect on average.
16
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding,
regulation and expression of genes.
17
Angiotensin-converting enzyme 2 (ACE2) is an enzyme attached to the cell membranes of cells located in
the lungs, arteries, heart, kidney, and intestines.

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using angiotensin II receptor blocker medications could be protective. As the alveolar disease
progresses, respiratory failure might develop and death may follow.
Whether SARS-CoV-2 is able to invade the nervous system remains unknown. The virus is not
detected in the CNS of the majority of COVID-19 people with neurological issues. However,
SARS-CoV-2 has been detected at low levels in the brains of those who have died from COVID-
19, but these results need to be confirmed. SARS-CoV-2 may cause respiratory failure through
affecting the brain stem as other coronaviruses have been found to invade the CNS18. While
virus has been detected in cerebrospinal fluid of autopsies, the exact mechanism by which it
invades the CNS remains unclear and may first involve invasion of peripheral nerves given the
low levels of ACE2 in the brain. The virus may also enter the bloodstream from the lungs and
cross the blood-brain barrier to gain access to the CNS, possibly within an infected white blood
cell.
The virus also affects gastrointestinal organs as ACE2 is abundantly expressed in the glandular
cells of gastric, duodenal and rectal epithelium as well as endothelial cells and enterocytes of
the small intestine.
The virus can cause acute myocardial injury and chronic damage to the cardiovascular system.
An acute cardiac injury was found in 12% of infected people admitted to the hospital in
Wuhan, China, and is more frequent in severe disease. Rates of cardiovascular symptoms are
high, owing to the systemic inflammatory response and immune system disorders during
disease progression, but acute myocardial injuries may also be related to ACE2 receptors in
the heart. ACE2 receptors are highly expressed in the heart and are involved in heart function.
A high incidence of thrombosis and venous thromboembolism have been found people
transferred to intensive care unit (ICU) with COVID-19 infections, and may be related to poor
prognosis. Blood vessel dysfunction and clot formation (as suggested by high D-dimer levels
caused by blood clots) are thought to play a significant role in mortality, incidences of clots
leading to pulmonary embolisms, and ischaemic events within the brain have been noted as
complications leading to death in people infected with SARS-CoV-2. Infection appears to set
off a chain of vasoconstrictive responses within the body, constriction of blood vessels within
the pulmonary circulation has also been posited as a mechanism in which oxygenation19
decreases alongside the presentation of viral pneumonia. Furthermore, microvascular blood
vessel damage has been reported in a small number of tissue samples of the brains – without
detected SARS-CoV-2 – and the olfactory bulbs from those who have died from COVID-19.
Another common cause of death is complications related to the kidneys. Early reports show
that up to 30% of hospitalized patients both in China and in New York have experienced some
injury to their kidneys, including some persons with no previous kidney problems.
18
The central nervous system (CNS) is the part of the nervous system consisting primarily of the brain and
spinal cord.
19
The process by which concentrations of oxygen increase within a tissue

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Autopsies of people who died of COVID-19 have found diffuse alveolar damage, and
lymphocyte-containing inflammatory infiltrates within the lung.
1.13. Immunopathology
Key components of the adaptive immune response to SARS-CoV-2.
Although SARS-CoV-2 has a tropism for ACE2-expressing epithelial cells of the respiratory
tract, people with severe COVID-19 have symptoms of systemic hyperinflammation. Clinical
laboratory findings of elevated IL-2, IL-7, IL-6, granulocyte-macrophage colony-stimulating
factor (GM-CSF)20, interferon-γ inducible protein 10 (IP-10)21, monocyte chemoattractant
protein 1 (MCP-1)22, macrophage inflammatory protein 1-α (MIP-1α)23, and tumour necrosis
factor-α (TNF-α)24 indicative of cytokine release syndrome (CRS)25 suggest an underlying
immunopathology.
Additionally, people with COVID-19 and acute respiratory distress syndrome (ARDS)26 have
classical serum biomarkers of CRS, including elevated C-reactive protein (CRP), lactate
dehydrogenase (LDH)27, D-dimer28, and ferritin29.
Systemic inflammation results in vasodilation, allowing inflammatory lymphocytic and
monocytic infiltration of the lung and the heart. In particular, pathogenic GM-CSF-secreting
T-cells were shown to correlate with the recruitment of inflammatory IL-6-secreting
20
Granulocyte-macrophage colony-stimulating factor (GM-CSF), also known as colony-stimulating factor
2 (CSF2), is a monomeric glycoprotein secreted by macrophages, T cells, mast cells, natural killer cells,
endothelial cells and fibroblasts that functions as a cytokine.
21
IP-10 is Interferon gamma (INF-γ) inducible protein 10. It is a chemokine, and important for recruiting
natural killer cells to the myocardium, and for limiting viral duplication in murine (mice/rodent)
coxsackievirus infection.
22
The monocyte chemoattractant protein-1 (MCP-1/CCL2) is a member of the C-C chemokine family, and
a potent chemotactic factor for monocytes.
23
Macrophage Inflammatory Proteins (MIP) belong to the family of chemotactic cytokines known as
chemokines. In humans, there are two major forms, MIP-1α and MIP-1β that are now (according to the
new nomenclature) officially named CCL3 and CCL4, respectively.
24
umor necrosis factor (TNF, cachexin, or cachectin; often called tumor necrosis factor alpha or TNF-α) is
a cytokine, i.e. a small protein used by the immune system for cell signaling. If macrophages (certain white
blood cells) detect an infection, they release TNF in order to alert other cells of the immune system as well
as cells of other tissues, leading to inflammation.
25
Cytokine release syndrome (CRS) is a form of systemic inflammatory response syndrome (SIRS) that
can be triggered by a variety of factors such as infections and certain drugs.
26
Acute respiratory distress syndrome (ARDS) is a type of respiratory failure characterized by rapid onset
of widespread inflammation in the lungs.
27
Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells. LDH catalyzes the
conversion of lactate to pyruvate and back, as it converts NAD+
to NADH and back. A dehydrogenase is an
enzyme that transfers a hydride from one molecule to another.
28
D-dimer (or D dimer) is a fibrin degradation product (or FDP), a small protein fragment present in the
blood after a blood clot is degraded by fibrinolysis.
29
Ferritin is a universal intracellular protein that stores iron and releases it in a controlled fashion.

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monocytes and severe lung pathology in people with COVID-19 . Lymphocytic infiltrates have
also been reported at autopsy.
1.14. Viral and host factors
1.14.1. Virus proteins
Multiple viral and host factors affect the pathogenesis of the virus. The S-protein, otherwise
known as the spike protein30, is the viral component that attaches to the host receptor via
the ACE2 receptors. It includes two subunits: S1 and S2. S1 determines the virus host range
and cellular tropism via the receptor binding domain. S2 mediates the membrane fusion of
the virus to its potential cell host via the H1 and HR2, which are heptad repeat regions. Studies
have shown that S1 domain induced IgG and IgA antibody levels at a much higher capacity. It
is the focus spike proteins expression that are involved in many effective COVID-19 vaccines.
The M protein is the viral protein responsible for the transmembrane transport of nutrients.
It is the cause of the bud release and the formation of the viral envelope. The N and E protein
are accessory proteins that interfere with the host's immune response.
1.14.2. Host factors
Human angiotensin converting enzyme 2 (hACE2)31 is the host factor that SARS-COV2 virus
targets causing COVID-19. Theoretically the usage of angiotensin receptor blockers (ARB)32
and ACE inhibitors up regulating ACE2 expression might increase morbidity with COVID-19,
though animal data suggest some potential protective effect of ARB. However no clinical
studies have proven susceptibility or outcomes. Until further data is available, guidelines and
recommendations for hypertensive patients remain.
The virus' effect on ACE2 cell surfaces leads to leukocytic infiltration, increased blood vessel
permeability, alveolar wall permeability, as well as decreased secretion of lung surfactants.
These effects cause the majority of the respiratory symptoms. However, the aggravation of
local inflammation causes a cytokine storm eventually leading to a systemic inflammatory
response syndrome.
1.14.3. Host cytokine response
The severity of the inflammation can be attributed to the severity of what is known as the
cytokine storm. Levels of interleukin 1B, interferon-gamma, interferon-inducible protein 10,
30
The spike protein, which has been imaged at the atomic level using cryogenic electron microscopy, is the
protein responsible for allowing the virus to attach to its complementary host cell receptor.
31
Angiotensin-converting enzyme 2 (ACE2) is an enzyme attached to the cell membranes of cells located in
the lungs, arteries, heart, kidney, and intestines.
32
Angiotensin II receptor blockers (ARBs), formally angiotensin II receptor type 1 (AT1) antagonists, also
known as angiotensin receptor blockers, angiotensin II receptor antagonists, or AT1 receptor antagonists,
are a group of pharmaceuticals that bind to and inhibit the angiotensin II receptor type 1 (AT) and thereby
block the arteriolar contraction and sodium retention effects of renin–angiotensin system.

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and monocyte chemo attractant protein 1 were all associated with COVID-19 disease severity.
Treatment has been proposed to combat the cytokine storm as it remains to be one of the
leading causes of morbidity and mortality in COVID-19 disease.
A cytokine storm is due to an acute hyper inflammatory response that is responsible for
clinical illness in an array of diseases but in COVID-19, it is related to worse prognosis and
increased fatality. The storm causes the acute respiratory distress syndrome, blood clotting
events such as strokes, myocardial infarction, encephalitis, acute kidney injury, and vasculitis.
The production of IL-1, IL-2, IL-6, TNF-alpha, and interferon-gamma, all crucial components of
normal immune responses, inadvertently become the causes of a cytokine storm. The cells of
the central nervous system, the microglia, neurons, and astrocytes, are also be involved in the
release of pro-inflammatory cytokines affecting the nervous system, and effects of cytokine
storms toward the CNS are not uncommon.

Covid-19 Pandemic. Uganda in blackets

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