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bioRxiv · 10.1101/2020.08.04.234153

SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic

Ghanchi, N. K.·Masood, K. I.·Nasir, A.·Khan, W.·Abidi, S. H.·Shahid, S.·Mahmood, S. F.·Kanji, A. R.·Razzak, S. A.·Ansar, Z.·Islam, N.·Dharejo, M. B.·Hasan, Z.·Hasan, R.
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Abstract

ObjectivesPakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country. MethodsWe performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May. ResultsStrains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions. ConclusionsThis data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease severity will be important to understand virus transmission patterns and host related determinants of COVID-19 in Pakistan.

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Ghanchi, N. K., Masood, K. I., Nasir, A., Khan, W., Abidi, S. H., Shahid, S., Mahmood, S. F., Kanji, A. R., Razzak, S. A., Ansar, Z., Islam, N., Dharejo, M. B., Hasan, Z., Hasan, R.. 2020-08-04. SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic. https://doi.org/10.1101/2020.08.04.234153

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