Full-genome sequences of the first two SARS-CoV-2 viruses from India.
Betacoronavirus
/ genetics
COVID-19
Coronavirus Infections
Epitopes, B-Lymphocyte
/ genetics
Epitopes, T-Lymphocyte
/ genetics
Genome, Viral
Humans
India
Models, Molecular
Pandemics
Phylogeny
Pneumonia, Viral
Protein Structure, Tertiary
RNA, Viral
/ genetics
Reverse Transcriptase Polymerase Chain Reaction
SARS-CoV-2
Spike Glycoprotein, Coronavirus
/ genetics
India
Kerala
genomes
next-generation sequencing
phylogeny
real-time reverse transcription-polymerase chain reaction
severe acute respiratory syndrome coronavirus 2
Epitope
Journal
The Indian journal of medical research
ISSN: 0971-5916
Titre abrégé: Indian J Med Res
Pays: India
ID NLM: 0374701
Informations de publication
Date de publication:
Historique:
pubmed:
4
4
2020
medline:
7
5
2020
entrez:
4
4
2020
Statut:
ppublish
Résumé
Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020. Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken. Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population. The two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.
Sections du résumé
Background & objectives
Since December 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has globally affected 195 countries. In India, suspected cases were screened for SARS-CoV-2 as per the advisory of the Ministry of Health and Family Welfare. The objective of this study was to characterize SARS-CoV-2 sequences from three identified positive cases as on February 29, 2020.
Methods
Throat swab/nasal swab specimens for a total of 881 suspected cases were screened by E gene and confirmed by RdRp (1), RdRp (2) and N gene real-time reverse transcription-polymerase chain reactions and next-generation sequencing. Phylogenetic analysis, molecular characterization and prediction of B- and T-cell epitopes for Indian SARS-CoV-2 sequences were undertaken.
Results
Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood market pneumonia virus (accession number: NC 045512). Phylogenetic analysis showed that the Indian sequences belonged to different clusters. Predicted linear B-cell epitopes were found to be concentrated in the S1 domain of spike protein, and a conformational epitope was identified in the receptor-binding domain. The predicted T-cell epitopes showed broad human leucocyte antigen allele coverage of A and B supertypes predominant in the Indian population.
Interpretation & conclusions
The two SARS-CoV-2 sequences obtained from India represent two different introductions into the country. The genetic heterogeneity is as noted globally. The identified B- and T-cell epitopes may be considered suitable for future experiments towards the design of vaccines and diagnostics. Continuous monitoring and analysis of the sequences of new cases from India and the other affected countries would be vital to understand the genetic evolution and rates of substitution of the SARS-CoV-2.
Identifiants
pubmed: 32242873
pii: 281471
doi: 10.4103/ijmr.IJMR_663_20
pmc: PMC7258756
doi:
Substances chimiques
Epitopes, B-Lymphocyte
0
Epitopes, T-Lymphocyte
0
RNA, Viral
0
Spike Glycoprotein, Coronavirus
0
spike protein, SARS-CoV-2
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
200-209Déclaration de conflit d'intérêts
None
Références
J Immunol. 1999 Jan 15;162(2):791-8
pubmed: 9916700
N Engl J Med. 2020 Feb 20;382(8):727-733
pubmed: 31978945
J Virol. 2019 Jun 14;93(13):
pubmed: 30971476
J Med Virol. 2020 Apr;92(4):401-402
pubmed: 31950516
Lancet Infect Dis. 2020 Apr;20(4):411-412
pubmed: 32105638
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9804-9
pubmed: 15210961
Emerg Infect Dis. 2018 May;24(5):898-901
pubmed: 29664366
Nat Microbiol. 2020 Apr;5(4):562-569
pubmed: 32094589
Emerg Microbes Infect. 2012 Sep;1(9):e23
pubmed: 26038429
Nat Microbiol. 2020 Apr;5(4):536-544
pubmed: 32123347
Infect Genet Evol. 2020 Apr;79:104212
pubmed: 32004758
Microbiol Mol Biol Rev. 2005 Dec;69(4):635-64
pubmed: 16339739
Lancet. 2020 Feb 22;395(10224):565-574
pubmed: 32007145
Nat Commun. 2019 May 28;10(1):2342
pubmed: 31138817
J Virol. 2020 Mar 17;94(7):
pubmed: 31996437
Clin Infect Dis. 2020 Feb 12;:
pubmed: 32047895
Nat Rev Microbiol. 2019 Mar;17(3):181-192
pubmed: 30531947
Science. 2005 Sep 16;309(5742):1864-8
pubmed: 16166518
Glob Chall. 2017 Jan 10;1(1):33-46
pubmed: 31565258
J Med Virol. 2020 May;92(5):495-500
pubmed: 32022276
Lancet. 2020 Feb 15;395(10223):507-513
pubmed: 32007143
Mol Biol Evol. 2016 Jul;33(7):1870-4
pubmed: 27004904