PT  - JOURNAL ARTICLE
AU  - Najia Karim Ghanchi
AU  - Kiran Iqbal Masood
AU  - Asghar Nasir
AU  - Waqasuddin Khan
AU  - Syed Hani Abidi
AU  - Saba Shahid
AU  - Syed Faisal Mahmood
AU  - Akbar Kanji
AU  - Safina Razzak
AU  - Zeeshan Ansar
AU  - Nazneen Islam
AU  - M. B. Dharejo
AU  - Zahra Hasan
AU  - Rumina Hasan
TI  - SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic
AID  - 10.1101/2020.08.04.234153
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.08.04.234153
4099  - http://biorxiv.org/content/early/2020/08/04/2020.08.04.234153.short
4100  - http://biorxiv.org/content/early/2020/08/04/2020.08.04.234153.full
AB  - Objectives Pakistan 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.Methods We performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May.Results Strains 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.Conclusions This 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.Competing Interest StatementThe authors have declared no competing interest.