Full-genome sequences of the first two SARS-CoV-2 viruses from India

Yadav, Pragya D; Potdar, Varsha; Choudhary, Manohar Lal; Nyayanit, Dimpal A; Agrawal, Megha; Jadhav, Santosh; Majumdar, Triparna; Shete-Aich, Anita; Basu, Atanu; Abraham, Priya; Cherian, Sarah

doi:10.4103/ijmr.ijmr_663_20

Cited by 117 publications

(70 citation statements)

References 22 publications

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“…The Arg407 has mutated to Ile407 (Fig. 3c) in the RBD domain in the SARS-CoV-2/human/ IND/29/2020 sequence when compared to other strains from this region (Yadav et al 2020). Other mutations were found in the SARS-CoV-2/human/IND/29/2020 (Gap Val143-Tyr144), SARS-CoV-2/human/IND/GBRC1/2020/S-Protein (Arg271), SARS-CoV-2/human/IND/166/2020 (Val930), SARS-CoV-2/human/LKA/COV53/2020 and SARS-CoV-2/ human/IND/GBRC1/2020/S-Protein (Glu614) concerning the Wuhan sequence ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

Maurya

Chikhale

Pandey

2020

Environmental Sustainability

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The ongoing coronavirus disease 19 (COVID-19) pandemic has caused a very high number of infections and deaths around the globe. The absence of vaccine/drugs to counter COVID-19 has scrambled scientific communities to repurpose available medicines/vaccines. As the virus is known to mutate, using the whole genome sequences, the transmission dynamics and molecular evolutionary models were evaluated for South Asian countries to determine the evolutionary rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Phylogenetic analyses were done using the data available on National Center for Biotechnology Information (NCBI). Different nucleotide substitution models and molecular evolutionary models were analyzed to see how SARS-CoV-2 was transmitted in the populations. Models for the viral 'S' and 'N' protein from selected strains were constructed, validated, and analyzed to determine the mutations and discover the potential therapeutics against this deadly viral disease. We found that the Hasegawa-Kishino-Yano (HKY) nucleotide substitution model was the best model with the lowest Bayesian information criterion (BIC) scores. Molecular clock RelTime analysis showed the evolutionary rate of SARS-CoV-2 substitutions in the genome was at 95% confidence interval, and heterogeneity was observed. Several mutations in the viral S-protein were found with one in the receptor-binding domain concerning SARS-CoV-2/ Wuhan-1/S-Protein. Nucleocapsid protein also showed mutations in the strains from India and Sri Lanka. Our analysis suggests that SARS-CoV-2 is evolving at a diverse rate. The mutation leading to substitution in the nucleotide sequence occurred in the genome during the transmission of COVID-19 among individuals in the South Asian countries.

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Section: Discussionmentioning

confidence: 99%

Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

Maurya

Chikhale

Pandey

2020

Environmental Sustainability

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“…MERS-CoV and SARS-CoV, which have had significant impacts with regard to human health, also belong to the same genus. The SARS-CoV-2 genome is approximately 29.9 kilobases in length (Yadav et al, 2020) and encodes four structural proteins, viz. spike protein (S), envelope protein (E), membrane protein (M), and Nucleoprotein (N), apart from sixteen non-structural proteins, including RNA-Dependent RNA Polymerase (Rabaan et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

CRISPR-Cas System: An Approach With Potentials for COVID-19 Diagnosis and Therapeutics

Kumar

Malik

Ganesh

et al. 2020

Front. Cell. Infect. Microbiol.

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COVID-19, the human coronavirus disease caused by SARS-CoV-2, was reported for the first time in Wuhan, China in late 2019. COVID-19 has no preventive vaccine or proven standard pharmacological treatment, and consequently, the outbreak swiftly became a pandemic affecting more than 215 countries around the world. For the diagnosis of COVID-19, the only reliable diagnostics is a qPCR assay. Among other diagnostic tools, the CRISPR-Cas system is being investigated for rapid and specific diagnosis of COVID-19. The CRISPR-Cas-based methods diagnose the SARS-CoV-2 infections within an hour. Apart from its diagnostic ability, CRISPR-Cas system is also being assessed for antiviral therapy development; however, till date, no CRISPR-based therapy has been approved for human use. The Prophylactic Antiviral CRISPR in huMAN cells (PAC-MAN), which is Cas 13 based strategy, has been developed against coronavirus. Although this strategy has the potential to be developed as a therapeutic modality, it may face significant challenges for approval in human clinical trials. This review is focused on describing potential use and challenges of CRISPR-Cas based approaches for the development of rapid and accurate diagnostic technique and/or a possible therapeutic alternative for combating COVID-19. The assessment of potential risks associated with use of CRISPR will be important for future clinical advancements.

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“…The first three cases from India were reported in Kerala during January 2020 having travel history to Wuhan [3]; subsequently 69,597 active cases, 51,783 recovered cases and 3720 deaths have been officially recorded in India as on 23 rd May, 2020, 08:00 IST GMT+5:30 [4]. Inspite of high population density, poor hygiene conditions and overburdened health care system, death rate due to SARS-COV-2 is lower in India compared to USA or European countries [5].…”

Section: Introductionmentioning

confidence: 99%

The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020

Banerjee

Sarkar

Mitra

et al. 2020

Preprint

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18Background: This is a comprehensive analysis of 46 Indian SARS-CoV-2 genome sequences available from 19 the NCBI and GISAID repository during early 2020. Evolutionary dynamics, gene-specific phylogeny and 20 emergence of the novel co-evolving mutations in nine structural and non-structural genes among circulating 21 SARS-CoV-2 strains in ten states of India have been assessed. 22Materials and methods: 46 SARS-CoV-2 nucleotide sequences submitted from India were downloaded from 23 the GISAID (39/46) or from NCBI (7/46) database. Phylogenetic study and analyses of mutation were based on 24 the nine structural and non-structural genes of SARS-CoV-2 strains. Secondary structure of RdRP/NSP12 25 protein was predicted with respect to the novel A97V mutation. 26Results: Phylogenetic analyses revealed the evolution of "genome-type clusters" and adaptive selection of "L" 27 type SARS-CoV-2 strains with genetic closeness to the bat SARS-like coronaviruses than pangolin or MERS- 28CoVs. With regards to the novel co-evolving mutations, 2 groups are seen to circulate in India at present: the 29 "major group" (52.2%) and the "minor group" (30.4%), harboring four and five co-existing mutations, 30 respectively. The "major group" mutations fall in the A2a clade. All the minor group mutations, except 31 11083G>T (L37F, NSP6) were unique to the Indian isolates. 32 Conclusion: The study highlights rapidly evolving SARS-CoV-2 virus and co-circulation of multiple clades 33 and sub-clades, driving this pandemic worldwide. This comprehensive study is a potential resource for 34 monitoring the novel mutations in the viral genome, changes in viral pathogenesis, for designing vaccines and 35 other therapeutics. 36 37 38the Indian strains has been deciphered with respect to other isolates reported from Europe, USA and China 62 along with Coronavirus strains belonging to other genera infecting humans and other animal hosts. The novel 63 co-evolving mutations among the Indian SARS-CoV-2 strains have also been analyzed. 64Through this genome-analyses and phylogenetic approach we would throw light on the natural evolution of 65 SARS-CoV-2 from its existing ancestors in zoonotic reservoirs. Furthermore, analyzing the novel mutations 66 accumulated in the viral genome over the period of time with reference to Wuhan strains (clade O) may shed 67 light on their impact on protein structure and function. 68 2. Material and Methods 69 2.1. Sequence mining 70 46 SARS-CoV-2 nucleotide sequences submitted from India were downloaded either from the GISAID (39/46) 71 or from NCBI (7/46) database for phylogenetic analyses. Several other reference gene sequences of SARS-72 CoV-2 as well as other types of Coronaviruses were downloaded from NCBI submitted from other countries, 73 for dendrogram construction and further lineage analyses. 7 sequences from Karnataka (India) were excluded 74 for RdRP/NSP12 gene analysis due to low nucleotide sequence coverage.75 76 Nine phylogenetic dendrograms were constructed with respect to 2 structural genes (Spike an...

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Full-genome sequences of the first two SARS-CoV-2 viruses from India

Cited by 117 publications

References 22 publications

Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

CRISPR-Cas System: An Approach With Potentials for COVID-19 Diagnosis and Therapeutics

The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020

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