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Emergence of European and North American mutant variants of SARS-CoV-2 in Southeast Asia
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  • Ovinu Islam,
  • Hassan Al-emran,
  • Md. Hasan,
  • Azraf Anwar,
  • Md. Jahid,
  • M. Hossain
Ovinu Islam
Jashore University of Science & Technology
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Hassan Al-emran
Jashore University of Science and Technology
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Md. Hasan
Jashore University of Science & Technology
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Azraf Anwar
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Md. Jahid
Jashore University of Science & Technology
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M. Hossain
University of Dhaka
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Peer review status:IN REVISION

31 May 2020Submitted to Transboundary and Emerging Diseases
02 Jun 2020Assigned to Editor
02 Jun 2020Submission Checks Completed
06 Jun 2020Reviewer(s) Assigned
28 Jun 2020Peer Review Completed
29 Jun 2020Editorial Decision: Revise Major

Abstract

The SARS-CoV-2 strain of the coronavirus is responsible for the current COVID-19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this strain is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID-19 is increasing at an alarming pace within subtropical Southeast Asian nations with high temperatures and humidity. To understand this spread, we analyzed 60 genome sequences of SARS-CoV-2 available in GISAID platform from 6 Southeast Asian countries. Multiple sequence alignments and maximum likelihood phylogenetic analyses were performed to analyze and characterize the non-synonymous mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in Australia and Saudi Arabia indicate possible transmission routes. Unique spike protein and non-structural protein mutations were observed circulating within a localized area. We divided the circulating viral strains into 4 major groups and 2 sub-groups on the basis of the most frequent non-synonymous mutations. Strains with a unique set of 4 co-evolving mutations were found to be circulating at a high frequency within India, specifically, group 2 strains characterized by two co-evolving NS mutants which alter in RdRp (P323L) and spike protein (D614G) common in Europe and North America. These European and North American variants (Nextstrain clade A2) have rapidly emerged as dominant strains within Southeast Asia, increasing from a 0% presence in January to an 85% presence by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present the largest threat to Southeast Asia for the coming winter.