This document summarizes information about COVID-19 and the SARS-CoV-2 virus. It describes coronaviruses and how a new strain was identified in Wuhan, China in December 2019. COVID-19 is the disease caused by the SARS-CoV-2 virus. Symptoms include fever, dry cough and shortness of breath. Testing methods like RT-PCR and serology tests are used to detect current and past infections. Genome sequencing of over 3,000 virus samples from around the world shows how the virus has spread and evolved into different strains.

1. Basic Biology of Coronavirus
Part-II
Dr. Rashmi Kumari
Department of Zoology
Assistant Professor
College of Commerce, Arts & Science
Patliputra University, Patna

2. What is novel coronavirus (COVID-19 and SARS-CoV-2)???
Coronaviruses (CoV) are a large family of viruses that cause a wide range of illness from the common cold to
more severe diseases. eg. Middle East Respiratory Syndrome [MERS]; Severe Acute Respiratory Syndrome [SARS].
A novel coronavirus (nCoV) is a new strain that has not been previously identified in humans.
On 31 December 2019, The WHO China office was informed of pneumonia cases of unknown cause in
Wuhan city, Hubei Province of China.
A novel coronavirus (nCoV-2) was isolated and identified as the causative virus of COVID-19 by Chinese authorities on 7th
January 2020.
COVID-19 is a disease caused by coronavirus called SARS-CoV-2.
Incubation period- current estimates of the incubation period of the virus range: 1-12.5 days (median 5-6 days)
Modes of transmission: droplets sprayed by affected individuals, contact with patient respiratory secretions, contaminated
surfaces and equipment.
Transmission from animals and human-to-human.
Currently, no available treatment or vaccination, supportive measures only. Source: World Health Organization (WHO)

3. COVID-19 signs and symptoms
Illness seems to start with a fever, followed by a
dry cough and then, after a week, leads to shortness
of breath and some patients needing hospital
treatment.
Source: World Health Organization (WHO)

4. Case definitions – (as of 04/02/2020) to be investigated
and tested
A. History of fever, cough, and requiring admission to hospital, (with no other etiology that fully explains the
clinical presentation)
AND
History of travel or residence in/to China in the 14 days prior to symptom onset
OR
B. Patient with any acute respiratory illness AND atleast one of the following during the 14 days prior to
symptom onset: Contact with a confirmed or suspected case of COVID-19 infection
OR
Worked in or attended a health care facility where patients with confirmed or probable COVID-19 acute
respiratory disease patients were being treated
Source: World Health Organization (WHO)

5. Characteristics of COVID-19 and SARS-CoV-2 & Testing
Viruses are completely dependent on hosts for replication
Many viruses like coronavirus use RNA (instead of DNA) as their genome
Redrawn from Fundamentals of virology, Acheson
How do we test for the coronavirus
infection?
1. RT-PCR Test
Reverse Transcription-Polymerase Chain
Reaction (Real-Time)
Measures RNA from the virus
Detects current Infections
2. Serology Test
Measures antibodies against the virus
Detects immune response to the current and
past infections.
RNA DNA
Virus Antibody

6. 3. CRISPR–Cas12-based detection of SARS-CoV-2
Genome map showing primers, probes and gRNAs. Visualization of primers and probes on the SARS-CoV-2
genome. RT–LAMP primers are indicated by black rectangles, the binding position of the F1c and B1c half of
the forward inner primer (FIP) (gray) is represented by a striped rectangle with dashed borders
The minimum equipment needed to run the protocol.
With appropriate biosafety level 2 requirements, the
minimum equipment required to run the protocol
following RNA extraction includes Eppendorf tubes
with reagents, heat blocks or water bath (37 °C and
62 °C), nuclease-free water, pipettes and tips and
lateral flow strips
(a)
(b)
Schematic of SARS-CoV-2 DETECTR workflow. Conventional RNA extraction can be used as an input to
DETECTR (LAMP preamplification and Cas12-based detection for E gene, N gene and RNase P), which is
visualized by a fluorescent reader or lateral flow strip
(c)
Broughton, J.P., Deng, X., Yu, G. et al. CRISPR–
Cas12-based detection of SARS-CoV-2. Nat
Biotechnol (2020). https://doi.org/10.1038/s41587-
020-0513-4.

7. How are we learning about the spread and different
strains of coronavirus??
Source: https://nextstrain.org/narratives/ncov/sit-rep/2020-04-10
Fig. Phylogeny of 1442 SARS-CoV-2 viruses collected between December 2019 and March 2020 colored by country of sampling as
shown in the map on the right. Viruses from China are shown in purple, viruses from Southeast Asia and Oceania in blue, viruses from
Europe in yellow/green, viruses from South America in orange, and viruses from North America in red. Virus genome data shared
through GISAID and phylogeny reconstructed by Nextstrain.
14/04/2020 1400 hr
3160 viral genomes

8. References:
1. World Health Organization (WHO) [https://www.who.int/emergencies/diseases/novel-coronavirus-
2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it].
2. Zuendorf, Ilse. (2007). Fundamentals of Molecular Virology. Von Nicholas H. Acheson. Pharmazie in
Unserer Zeit. 36. 479-479. 10.1002/pauz.200790112.
3. Broughton, J.P., Deng, X., Yu, G., Fasching, C. L., Servellita, V., Singh, J., Miao, X., Streithorst, J. A.,
Grandos, A., Sotomavor-Gonzalez, A., Zorn, K., Gopez, A., Hsu, E., Gu, W., Miller, S., Pan, C-Y., Guevara,
H., Wadford, D. A., Chen, J. S., & Chiu, C. Y. (2020). CRISPR–Cas12-based detection of SARS-CoV-
2. Nat Biotechnol. https://doi.org/10.1038/s41587-020-0513-4.
4. https://nextstrain.org/narratives/ncov/sit-rep/2020-04-10.
5. Google Images.