The document discusses the phylogenetic relationship between SARS CoV1, MERS CoV, and SARS CoV2 based on their spike proteins. It provides information on coronaviruses in general and describes the three virus types - SARS CoV, MERS CoV, and SARS CoV2. For each virus type, it discusses symptoms, transmission, prevention, and their respective spike protein sequences. It also briefly discusses COVID-19 vaccines such as Covaxin, Pfizer, and Moderna.

1. THE PHYLOGENETIC RELATIONSHIP BETWEEN SARS
CoV1, MERS CoV AND SARS CoV2 ON THE BASIS OF
THEIR SPIKES PROTEIN.
By.
Sumit Singh
Biotechnology Engineer

2. OBJECTIVE
Coronavirus
Types of coronavirus
SARS CoV
MERS CoV
SARS CoV2
Vaccines
Important guidelines
Relation between SARS CoV, MERS CoV & SARS CoV2 on the basis of
their spike protein

3. CORONAVIRUSES
Coronaviruses (CoV) are a large family of viruses that cause illness ranging from
the common cold to more severe diseases such as Middle East Respiratory
Syndrome (MERS-CoV) and Severe Acute Respiratory Syndrome (SARS-CoV). A
novel coronavirus (nCoV) is a new strain that has not been previously identified in
humans.
Coronaviruses are zoonotic, meaning they are transmitted between animals and
people. Detailed investigations found that SARS-CoV was transmitted from civet
cats to humans and MERS-CoV from dromedary camels to humans. Several known
coronaviruses are circulating in animals that have not yet infected humans.
Coronaviruses are single-stranded RNA viruses, about 120 nanometers
in diameter. They are susceptible to mutation and recombination and
are therefore highly diverse.
The corona-like appearance of coronaviruses is caused by so-called
spike glycoproteins, or peplomers, which are necessary for the viruses
to enter host cells.

5. TYPES OF CORONAVIRUSES
Coronaviruses are three types:-
SARS CoV
MERS CoV
SARS CoV2

6. SARS CoV
Severe acute respiratory syndrome (SARS) is a contagious and sometimes fatal respiratory
illness.
It was first identified at the end of February 2003 during an outbreak that
emerged in China and spread to 4 other countries.
SARS-CoV was transmitted from civet cats to humans.
SARS is an airborne virus and can spread through small droplets of saliva in a
similar way to the cold and influenza.
It was the first severe and readily transmissible new disease to emerge in the
21st century and showed a clear capacity to spread along the routes of
international air travel.
Symptoms
SARS usually begins with flu-like signs and symptoms — fever, chills, muscle aches,
headache and occasionally diarrhea. After about a week, signs and symptoms include:
❖ Fever of 100.5 F (38 C) or higherDry
❖ cough
❖ Shortness of breath

7. How SARS spreads
◈ spread through droplets that enter the air when someone with the disease coughs, sneezes
or talks.
◈ Most experts think SARS spreads mainly through close personal contact, such as caring
for someone with SARS.
◈ The virus may also be spread on contaminated objects — such as doorknobs, telephones
and elevator buttons
Complications
◈ Many people with SARS develop pneumonia, and breathing problems can become so
severe that a mechanical respirator is needed. SARS is fatal in some cases, often due to
respiratory failure.
◈ Other possible complications include heart and liver failure . People older than 60 —
especially those with underlying conditions such as diabetes or hepatitis — are at the
highest risk of serious complications.
Prevention
❖ Wash your hands
❖ Wear disposable gloves.
❖ Wear a surgical mask
❖ Wash personal item.
❖ Disinfect surface

8. MERS CoV
Coronaviruses are a large family of viruses that can cause diseases ranging from the
common cold to Severe Acute Respiratory Syndrome (SARS)
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. 27 countries have reported cases of MERS
MERS-CoV from dromedary camels to humans. Several known coronaviruses are
circulating in animals that have not yet infected humans.
Symptoms
fever, cough and shortness of breath. Pneumonia is a common finding, but not always
present.
Gastrointestinal symptoms, including diarrhoea, have also been reported.
Severe illness can cause respiratory failure that requires mechanical ventilation and
support in an intensive care unit.
The virus appears to cause more severe disease in older people, people with weakened
immune systems, and those with chronic diseases such as renal disease, cancer, chronic
lung disease, and diabetes.
Source of virus
MERS-CoV is a zoonotic virus, which means it is a virus that is transmitted
between animals and people.

9. that humans are infected through direct or indirect contact with infected dromedary
camels
MERS-CoV has been identified in dromedaries in several countries in the Middle
East, Africa and South Asia.
Transmission
Non-human to human transmission: The route of transmission from
animals to humans is not fully understood, but dromedary camels are
the major reservoir host for MERS-CoV and an animal source of
infection in humans.
Strains of MERS-CoV that are identical to human strains have been
isolated from dromedaries in several countries, including Egypt, Oman,
Qatar, and Saudi Arabia.
Prevention and treatment
No vaccine or specific treatment is currently available, however several
MERS-CoV specific vaccines and treatments are in development.
Treatment is supportive and based on the patient’s clinical condition.
Until more is understood about MERS-CoV, people with diabetes, renal
failure, chronic lung disease, and immune compromised persons are
considered to be at high risk of severe disease from MERS-CoV
infection. These people should avoid contact with camels, drinking raw
camel milk or camel urine

10. SARS CoV2 (COVID-19)
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the
virus that causes coronavirus disease 2019 (COVID-19).
SARS-CoV-2 is a positive-sense single-stranded RNA virus (and hence
Baltimore class IV) that is contagious in humans. As described by the US
National Institutes of Health.
The World Health Organization declared the outbreak a Public Health
Emergency of International Concern on 30 January 2020, and a
pandemic on 11 March 2020.
Structural biology
Each SARS-CoV-2 virion is 50–200 nanometres in diameter. Like other
coronaviruses.
SARS-CoV-2 has four structural proteins, known as the S (spike), E
(envelope), M (membrane), and N (nucleocapsid) proteins.
the N protein holds the RNA genome, and the S, E, and M proteins
together create the viral envelope.
SARS-CoV-2 virus binds to ACE2, it prevents ACE2 from performing its normal
function to regulate ANG II signaling.
After fusion, an endosome forms around the virion, separating it from
the rest of the host cell.

11. The virion escapes when the pH of the endosome drops or when cathepsin, a
host cysteine protease, cleaves it. The virion then releases RNA into the cell
and forces the cell to produce and disseminate copies of the virus, which
infect more cells.
Symptoms
Common signs and symptoms can include:
Fever
Cough
Tiredness
Early symptoms of COVID-19 may include a loss of taste or smell.
Other symptoms can include:
Shortness of breath or difficulty breathing
Muscle aches
Chills
Sore throat
Runny nose
Headache
Chest pain
Pink eye

12. Risk factors
Risk factors for COVID-19 appear to include:
Close contact (within 6 feet, or 2 meters) with someone who has COVID-19
Being coughed or sneezed on by an infected person
Prevention
The U.S. Food and Drug Administration (FDA) has given emergency use
authorization for two COVID-19 vaccines, the Pfizer/Bio.Tech COVID-19 vaccine
and the Modern COVID-19 vaccine.
Avoid close contact (within about 6 feet, or 2 meters) with anyone who
is sick or has symptoms.
Keep distance between yourself and others (within about 6 feet, or 2
meters). This is especially important if you have a higher risk of serious
illness. Keep in mind some people may have COVID-19 and spread it to
others, even if they don't have symptoms or don't know they have
COVID-19.
Wash your hands often with soap and water for at least 20 seconds, or
use an alcohol-based hand sanitizer that contains at least 60% alcohol.

13. Vaccines
There are three main approaches to designing a vaccine.
use a whole virus or bacterium;
just the parts of the germ that triggers the immune system;
just the genetic material that provides the instructions for making
specific proteins and not the whole virus
◈

14. COVAXINTM
- (Bharat Biotech)
COVAXINTM
, India's indigenous COVID-19 vaccine by Bharat Biotech is
developed in collaboration with the Indian Council of Medical Research (ICMR) -
National Institute of Virology (NIV).
The indigenous, inactivated vaccine is developed and manufactured in Bharat
Biotech's BSL-3 (Bio-Safety Level 3) high containment facility.
The vaccine is developed using Whole-Virion Inactivated Vero Cell derived
platform technology. Inactivated vaccines do not replicate and are therefore unlikely
to revert and cause pathological effects.
They contain dead virus, incapable of infecting people but still able to instruct the
immune system to mount a defensive reaction against an infection
COVAXINTM is included along with immune-potentiators, also known as vaccine
adjuvants, which are added to the vaccine to increase and boost its immunogenicity.
It is a 2-dose vaccination regimen given 28 days apart.
It is a vaccine with no sub-zero storage, no reconstitution requirement, and ready to
use liquid presentation in multi-dose vials, stable at 2-8oC.

15. Comimaty (Pfizer)
VACCINE NAME: Comirnaty (also known as tozinameran or BNT162b2 )
EFFICACY: 95%
DOSE: 2 doses, 3 weeks apart
TYPE: Muscle injection
STORAGE: Freezer storage only at –94°F (–70°C)
mRNA-1273 (Moderna)
VACCINE NAME: mRNA-1273
EFFICACY: 94.5%
DOSE: 2 doses, 4 weeks apart
TYPE: Muscle injection
STORAGE: 30 days with refrigeration, 6 months at –4°F (–20°C)
CVnCoV (CureVac)
VACCINE NAME: CVnCoV
EFFICACY: Unknown
DOSE: 2 doses, four weeks apart
TYPE: Muscle injection
STORAGE: Stable at least 3 months at 36–46°F (2–8°C)

16. Important Guidelines

17. Spike protein of SARS CoV
◈ MFIFLLFLTLTSGSDLDRCTTFDDVQAPNYTQHTSSMRGVYYPDEIFRSDTLYLTQDLFL
◈ PFYSNVTGFHTINHTFGNPVIPFKDGIYFAATEKSNVVRGWVFGSTMNNKSQSVIIINNS
◈ TNVVIRACNFELCDNPFFAVSKPMGTQTHTMIFDNAFNCTFEYISDAFSLDVSEKSGNFK
◈ HLREFVFKNKDGFLYVYKGYQPIDVVRDLPSGFNTLKPIFKLPLGINITNFRAILTAFSP
◈ AQDIWGTSAAAYFVGYLKPTTFMLKYDENGTITDAVDCSQNPLAELKCSVKSFEIDKGIY
◈ QTSNFRVVPSGDVVRFPNITNLCPFGEVFNATKFPSVYAWERKKISNCVADYSVLYNSTF
◈ FSTFKCYGVSATKLNDLCFSNVYADSFVVKGDDVRQIAPGQTGVIADYNYKLPDDFMGCV
◈ LAWNTRNIDATSTGNYNYKYRYLRHGKLRPFERDISNVPFSPDGKPCTPPALNCYWPLND
◈ YGFYTTTGIGYQPYRVVVLSFELLNAPATVCGPKLSTDLIKNQCVNFNFNGLTGTGVLTP
◈ SSKRFQPFQQFGRDVSDFTDSVRDPKTSEILDISPCSFGGVSVITPGTNASSEVAVLYQD
◈ VNCTDVSTAIHADQLTPAWRIYSTGNNVFQTQAGCLIGAEHVDTSYECDIPIGAGICASY
◈ HTVSLLRSTSQKSIVAYTMSLGADSSIAYSNNTIAIPTNFSISITTEVMPVSMAKTSVDC
◈ NMYICGDSTECANLLLQYGSFCTQLNRALSGIAAEQDRNTREVFAQVKQMYKTPTLKYFG
◈ GFNFSQILPDPLKPTKRSFIEDLLFNKVTLADAGFMKQYGECLGDINARDLICAQKFNGL
◈ TVLPPLLTDDMIAAYTAALVSGTATAGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYE
◈ NQKQIANQFNKAISQIQESLTTTSTALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLN
◈ DILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSK
◈ RVDFCGKGYHLMSFPQAAPHGVVFLHVTYVPSQERNFTTAPAICHEGKAYFPREGVFVFN
◈ GTSWFITQRNFFSPQIITTDNTFVSGNCDVVIGIINNTVYDPLQPELDSFKEELDKYFKN
◈ HTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKWPWYVWL
◈ GFIAGLIAIVMVTILLCCMTSCCSCLKGACSCGSCCKFDEDDSEPVLKGVKLHYT
◈ Spike protein of MERS CoV
◈ >MERS1 Spike Protein
◈ MIHSVFLLMFLLTPTESYVDVGPDSVKSACIEVDIQQTFFDKTWPRPIDVSKADGIIYPQ
◈ GRTYSNITITYQGLFPYQGDHGDMYVYSAGHATGTTPQKLFVANYSQDVKQFANGFVVRI
◈ GAAANSTGTVIISPSTSATIRKIYPAFMLGSSVGNFSDGKMGRFFNHTLVLLPDGCGTLL
◈ RAFYCILEPRSGNHCPAGNSYTSFATYHTPATDCSDGNYNRNASLNSFKEYFNLRNCTFM
◈ YTYNITEDEILEWFGITQTAQGVHLFSSRYVDLYGGNMFQFATLPVYDTIKYYSIIPHSI
◈ RSIQSDRKAWAAFYVYKLQPLTFLLDFSVDGYIRRAIDCGFNDLSQLHCSYESFDVESGV
◈ YSVSSFEAKPSGSVVEQAEGVECDFSPLLSGTPPQVYNFKRLVFTNCNYNLTKLLSLFSV

18. ◈ NDFTCSQISPAAIASNCYSSLILDYFSYPLSMKSDLSVSSAGPISQFNYKQSFSNPTCLI
◈ LATVPHNLTTITKPLKYSYINKCSRFLSDDRTEVPQLVNANQYSPCVSIVPSTVWEDGDY
◈ YRKQLSPLEGGGWLVASGSTVAMTEQLQMGFGITVQYGTDTNSVCPKLEFANDTKIASQL
◈ GNCVEYSLYGVSGRGVFQNCTAVGVRQQRFVYDAYQNLVGYYSDDGNYYCLRACVSVPVS
◈ VIYDKETKTHATLFGSVACEHISSTMSQYSRSTRSMLKRRDSTYGPLQTPVGCVLGLVNS
◈ SLFVEDCKLPLGQSLCALPDTPSTLTPRSVRSVPGEMRLASIAFNHPIQVDQLNSSYFKL
◈ SIPTNFSFGVTQEYIQTTIQKVTVDCKQYVCNGFQKCEQLLREYGQFCSKINQALHGANL
◈ RQDDSVRNLFASVKSSQSSPIIPGFGGDFNLTLLEPVSISTGSRSARSAIEDLLFDKVTI
◈ ADPGYMQGYDDCMQQGPASARDLICAQYVAGYKVLPPLMDVNMEAAYTSSLLGSIAGVGW
◈ TAGLSSFAAIPFAQSIFYRLNGVGITQQVLSENQKLIANKFNQALGAMQTGFTTTNEAFH
◈ KVQDAVNNNAQALSKLASELSNTFGAISASIGDIIQRLDVLEQDAQIDRLINGRLTTLNA
◈ FVAQQLVRSESAALSAQLAKDKVNECVKAQSKRSGFCGQGTHIVSFVVNAPNGLYFMHVG
◈ YYPSNHIEVVSAYGLCDAANPTNCIAPVNGYFIKTNNTRIVDEWSYTGSSFYAPEPITSL
◈ NTKYVAPQVTYQNISTNLPPPLLGNSTGIDFQDELDEFFKNVSTSIPNFGSLTQINTTLL
◈ DLTYEMLSLQQVVKALNESYIDLKELGNYTYYNKWPWYIWLGFIAGLVALALCVFFILCC
◈ TGCGTNCMGKLKCNRCCDRYEEYDLEPHKVHVH
◈ Spike protein of SARS CoV
◈ >COVID19 Spike Protein
◈ MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFS
◈ NVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIV
◈ NNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLE
◈ GKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT
◈ LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETK
◈ CTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISN
◈ CVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIAD
◈ YNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC
◈ NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVN
◈ FNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITP
◈ GTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSY
◈ ECDIPIGAGICASYQTQTNSPRRARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTI
◈ SVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQE
◈ VFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDC
◈ LGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAM
◈ QMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALN
◈ TLVKQLSSNFGAISSVLNDILSRLDKVEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRA
◈ SANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPA
◈ ICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDP
◈ LQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDL
◈ QELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDD
◈ SEPVLKGVKLHYT
◈

19. Phylogenetic relation between SARS CoV,
MERS CoV & SARS CoV2 on the basis of
their spike protein

20. • By the observation of phylogenetic tree of SARS CoV1,MERS CoV & SARS
CoV2 (COVID 19) on the basis of their Spikes protein. We observe that
SARS CoV2 (COVID 19) Spikes protein match with SARS CoV1.Both
viruses match with 932.00 and 932.00 spikes protein out of their 2118
spike protein. So we can use SARS CoV1 as a model for better
understanding SARS CoV2 (COVID 19)
Virus

21. THANK YOU..