Genomics of Corona – Help in Vaccine
Genomics (Part 12)
What is known?
There have been no documented cases of SARS-CoV-2 prior to December 2019.
Preliminary genomic analyses indicate that the first human cases of SARS-CoV-2 appeared between
10/19/2019 and 12/17/2019.1-3
The mutation rate of SARS-CoV-2 is estimated to be similar to that of other RNA viruses (such as SARS,
Ebola, Zika), and is currently estimated as 1.04×10-3substitutions per site per year (N = 116
genomes).4
Preliminary phylogenetic analysis identified a very close genetic similarity between SARS-CoV-2 and a
Bat coronavirus (RaTG13) that was isolated from Yunnan Province, China. It has suggested that SARS-
CoV-2 originated from bats.5
Pangolin coronaviruses are also closely related to both SARS-CoV-2 and the closely related Bat
coronavirus (RaTG13). Phylogenetic analysis revealed that SARS-CoV-2 is of bat origin, but is closely
related to pangolin coronavirus.6,7
The Spike protein of SARS-CoV-2, known to mediate entry into host cells, and the major determinant of
host range, is very similar to the Spike protein of SARS-CoV.8 The rest of the genome is more closely
related to two separate bat8and pangolin7 coronavirus.
Analysis of SARS-CoV-2 sequences from Singapore identified a large nucleotide (382 bp) deletion in
ORF-8 that may give rise to an attenuated (less virulent) phenotype.9
What do we need to know?
Are there similar genomic differences in the progression of coronavirus strains from bat to
intermediate species to human?
Are there different strains or clades of circulating virus? If yes, do they differ in virulence?
References
Anderson, K., Estimates of the clock and TMRCA for 2019-nCoV based on 27 genomes.
http://virological.org/t/clock-and-tmrca-based-on-27-genomes/347(accessed 01/26/2020).
Bedford, T.; Neher, R., Genomic epidemiology of novel coronavirus (nCoV) using data from GISAID.
https://nextstrain.org/ncov.
Rambaut, A., Phylodynamic analysis of nCoV-2019 genomes – 27-Jan-2020.
http://virological.org/t/phylodynamic-analysis-of-ncov-2019-genomes-27-jan-2020/353.
Hill, V.; Rambaut, A., Phylodynamic analysis of SARS-CoV-2 | Update 2020-03-06. Virological: 2020.
Paraskevis, D.; Kostaki, E. G.; Magiorkinis, G.; Panayiotakopoulos, G.; Sourvinos, G.; Tsiodras, S.,
Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of
emergence as a result of a recent recombination event. Infect Genet Evol 2020, 79, 104212.
Liu, P.; Chen, W.; Chen, J.-P., Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of
Malayan Pangolins (Manis javanica). Viruses 2019, 11 (11), 979.
Liu, P.; Jiang, J.-Z.; Wan, X.-F.; Hua, Y.; Wang, X.; Hou, F.; Chen, J.; Zou, J.; Chen, J., Are
pangolins the intermediate host of the 2019 novel coronavirus (2019-nCoV) ? bioRxiv 2020,
2020.02.18.954628.
Lu, R.; Zhao, X.; Li, J.; Niu, P.; Yang, B.; Wu, H.; Wang, W.; Song, H.; Huang, B.; Zhu, N.; Bi, Y.;
Ma, X.; Zhan, F.; Wang, L.; Hu, T.; Zhou, H.; Hu, Z.; Zhou, W.; Zhao, L.; Chen, J.; Meng, Y.; Wang,
J.; Lin, Y.; Yuan, J.; Xie, Z.; Ma, J.; Liu, W. J.; Wang, D.; Xu, W.; Holmes, E. C.; Gao, G. F.; Wu,
G.; Chen, W.; Shi, W.; Tan, W., Genomic characterisation and epidemiology of 2019 novel coronavirus:
implications for virus origins and receptor binding. The Lancet 2020.
Su, Y. C.; Anderson, D. E.; Young, B. E.; Zhu, F.; Linster, M.; Kalimuddin, S.; Low, J. G.; Yan, Z.;
Jayakumar, J.; Sun, L.; Yan, G. Z.; Mendenhall, I. H.; Leo, Y.-S.; Lye, D. C.; Wang, L.-F.; Smith, G.
J., Discovery of a 382-nt deletion during the early evolution of SARS-CoV-2. bioRxiv 2020,
2020.03.11.987222
Thanks
DR AJAY GAMBHIR
President NNF (2015-16)
Delhi Medical Council (DMC)2010-2020
Board Member NABQP (Quality Council India)
NTAGI member & Ex Finance Sec (IMA HQ)
NTBN-National technical board Nutrition(Niti-Ayog)
Vice president(2007/8)& Jt Sec(15/16) CIAP