Abstract
Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.
Highlights
The rapid worldwide spread of a novel coronavirus following its first appearance in China has pressed the global community to take measures to flatten its transmission (Chan et al, 2020; Zhu et al, 2020)
Whole Genome Sequences (WGS) of SARS-CoV-2 suggest bat-CoV to be its closest progenitor with 96% homology but, the RNA binding domain (RBD) of its spike protein with an efficient binding to ACE-2, the receptor for SARS-CoV-2 in human cell seems to have been derived from PangolinCoVs (Wan et al, 2020, Andersen et al, 2020)
Generation sequencing (NGS) aided understanding of evolution of SARS-CoV-2 genomes and its transmission patterns after it enters a new population is proving to be an important step towards formulating strategies for management of this pandemic (Chen and Li et al, 2020)
Summary
The rapid worldwide spread of a novel coronavirus following its first appearance in China has pressed the global community to take measures to flatten its transmission (Chan et al, 2020; Zhu et al, 2020). WHO declared COVID-19 a Pandemic on 11th of March, 2020 based on the speed and scale of transmission with almost 4.7 million cases reported across the globe, so far (WHO, 18th May 2020). More severe symptoms can include pneumonia, severe acute respiratory syndrome, kidney failure and even death with coalescence of factors (Zhu et al, 2020, Youg et al, 2020). Many COVID-19 cases have been reported to be asymptomatic and may serve as carrier of SARS-CoV-2 (Xu et al, 2020; He et al, 2020). Generation sequencing (NGS) aided understanding of evolution of SARS-CoV-2 genomes and its transmission patterns after it enters a new population is proving to be an important step towards formulating strategies for management of this pandemic (Chen and Li et al, 2020)
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