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An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India.

ABSTRACT: The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the 689 SARS-CoV-2 clinical samples revealed GH and GR to be the predominant clades circulating in different states in India. The northern part of India largely reported the 'GH' clade, whereas the southern part reported the 'GR', with a few exceptions. These sequences also revealed the presence of single independent mutations-E484Q and N440K-from Maharashtra (first observed in March 2020) and Southern Indian States (first observed in May 2020), respectively. Furthermore, this study indicates that the SARS-CoV-2 variant (VOC, VUI, variant of high consequence and double mutant) was not observed during the early phase of virus transmission (January-August). This increased number of variations observed within a short timeframe across the globe suggests virus evolution, which can be a step towards enhanced host adaptation.

SUBMITTER: Yadav PD

PROVIDER: S-EPMC8156686 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature

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An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India.

Yadav Pragya D PD Nyayanit Dimpal A DA Majumdar Triparna T Patil Savita S Kaur Harmanmeet H Gupta Nivedita N Shete Anita M AM Pandit Priyanka P Kumar Abhinendra A Aggarwal Neeraj N Narayan Jitendra J Vijay Neetu N Kalawat Usha U Sugunan Attayur P AP Munivenkatappa Ashok A Sharma Tara T Devi Sulochna S Majumdar Tapan T Jaryal Subhash S Bakshi Rupinder R Joshi Yash Y Sahay Rima R Shastri Jayanti J Singh Mini M Kumar Manoj M Rawat Vinita V Dutta Shanta S Yadav Sarita S Krishnasamy Kaveri K Raut Sharmila S Biswas Debasis D Borkakoty Biswajyoti B Verma Santwana S Rani Sudha S Deval Hirawati H Patel Disha D Turuk Jyotirmayee J Malhotra Bharti B Fomda Bashir B Nag Vijaylakshmi V Jain Amita A Bhargava Anudita A Potdar Varsha V Cherian Sarah S Abraham Priya P Gopal Anjani A Panda Samiran S Bhargava Balram B

Viruses 20210517 5

The number of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) cases is increasing in India. This study looks upon the geographic distribution of the virus clades and variants circulating in different parts of India between January and August 2020. The NPS/OPS from representative positive cases from different states and union territories in India were collected every month through the VRDLs in the country and analyzed using next-generation sequencing. Epidemiological analysis of the ...[more]

PMID: 34067745

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Project description:BackgroundEmergence of the new SARS-CoV-2 variant B.1.1.529 worried health policy makers worldwide due to a large number of mutations in its genomic sequence, especially in the spike protein region. The World Health Organization (WHO) designated this variant as a global variant of concern (VOC), which was named "Omicron." Following Omicron's emergence, a surge of new COVID-19 cases was reported globally, primarily in South Africa.ObjectiveThe aim of this study was to understand whether Omicron had an epidemiological advantage over existing variants.MethodsWe performed an in silico analysis of the complete genomic sequences of Omicron available on the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyze the functional impact of the mutations present in this variant on virus-host interactions in terms of viral transmissibility, virulence/lethality, and immune escape. In addition, we performed a correlation analysis of the relative proportion of the genomic sequences of specific SARS-CoV-2 variants (in the period from October 1 to November 29, 2021) with matched epidemiological data (new COVID-19 cases and deaths) from South Africa.ResultsCompared with the current list of global VOCs/variants of interest (VOIs), as per the WHO, Omicron bears more sequence variation, specifically in the spike protein and host receptor-binding motif (RBM). Omicron showed the closest nucleotide and protein sequence homology with the Alpha variant for the complete sequence and the RBM. The mutations were found to be primarily condensed in the spike region (n=28-48) of the virus. Further mutational analysis showed enrichment for the mutations decreasing binding affinity to angiotensin-converting enzyme 2 receptor and receptor-binding domain protein expression, and for increasing the propensity of immune escape. An inverse correlation of Omicron with the Delta variant was noted (r=-0.99, P<.001; 95% CI -0.99 to -0.97) in the sequences reported from South Africa postemergence of the new variant, subsequently showing a decrease. There was a steep rise in new COVID-19 cases in parallel with the increase in the proportion of Omicron isolates since the report of the first case (74%-100%). By contrast, the incidence of new deaths did not increase (r=-0.04, P>.05; 95% CI -0.52 to 0.58).ConclusionsIn silico analysis of viral genomic sequences suggests that the Omicron variant has more remarkable immune-escape ability than existing VOCs/VOIs, including Delta, but reduced virulence/lethality than other reported variants. The higher power for immune escape for Omicron was a likely reason for the resurgence in COVID-19 cases and its rapid rise as the globally dominant strain. Being more infectious but less lethal than the existing variants, Omicron could have plausibly led to widespread unnoticed new, repeated, and vaccine breakthrough infections, raising the population-level immunity barrier against the emergence of new lethal variants. The Omicron variant could have thus paved the way for the end of the pandemic.

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An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India.

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An Epidemiological Analysis of SARS-CoV-2 Genomic Sequences from Different Regions of India.

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