Genomic and evolutionary study from SARS-CoV-2 virus isolates from Bangladesh during the early stage of pandemic strongly correlate with European origin and not with China

Mohammad Fazle Alam Rabbi; Mala Khan; Mamudul Hasan Razu; Md Imran Khan; Saam Hasan; Mauricio Chalita; Kazi Nadim Hasan; Abu Sufian; Md Bayejid Hosen; Mohammed Nafiz Imtiaz Polol; Jannatun Naima; Kihyun Lee; Yeong Ouk Kim; Md Mizanur Rahman; Jongsik Chun; Md Abdul Khaleque; Zabed Bin Ahmed; Nur A Hasan; Rita R Colwell; Sharif Akhteruzzaman

doi:10.1016/j.ygeno.2022.110497

Genomic and evolutionary study from SARS-CoV-2 virus isolates from Bangladesh during the early stage of pandemic strongly correlate with European origin and not with China

Genomics. 2022 Nov;114(6):110497. doi: 10.1016/j.ygeno.2022.110497. Epub 2022 Sep 28.

Authors

Mohammad Fazle Alam Rabbi¹, Mala Khan², Mamudul Hasan Razu³, Md Imran Khan⁴, Saam Hasan⁴, Mauricio Chalita⁵, Kazi Nadim Hasan⁶, Abu Sufian⁷, Md Bayejid Hosen⁸, Mohammed Nafiz Imtiaz Polol⁴, Jannatun Naima⁴, Kihyun Lee⁵, Yeong Ouk Kim⁵, Md Mizanur Rahman⁹, Jongsik Chun⁵, Md Abdul Khaleque⁶, Zabed Bin Ahmed³, Nur A Hasan¹⁰, Rita R Colwell¹¹, Sharif Akhteruzzaman¹²

Affiliations

¹ NGS Lab, DNA Solution Limited, Dhaka, Bangladesh; Department of Soil, Water and Environment, University of Dhaka, Dhaka, Bangladesh.
² Bangladesh Reference Institute for Chemical Measurements, BRiCM, Dhaka, Bangladesh. Electronic address: bricmdg@yahoo.com.
³ Bangladesh Reference Institute for Chemical Measurements, BRiCM, Dhaka, Bangladesh.
⁴ NGS Lab, DNA Solution Limited, Dhaka, Bangladesh.
⁵ ChunLab Inc., Seoul, South Korea.
⁶ Department of Biochemistry and Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh.
⁷ NGS Lab, DNA Solution Limited, Dhaka, Bangladesh; National Forensic DNA Profiling Laboratory, Dhaka Medical College, Dhaka, Bangladesh.
⁸ National Forensic DNA Profiling Laboratory, Dhaka Medical College, Dhaka, Bangladesh.
⁹ NGS Lab, DNA Solution Limited, Dhaka, Bangladesh; NIPRO JMI Pharma, Dhaka, Bangladesh.
¹⁰ EzBiome Inc, Gaithersburg, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA.
¹¹ Center for Bioinformatics and Computational Biology, University of Maryland, College Park, USA.
¹² NGS Lab, DNA Solution Limited, Dhaka, Bangladesh; Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh. Electronic address: sharif_akhteruzzaman@yahoo.com.

Abstract

The goal of this study was to identify the genomic variants and determine molecular epidemiology of SARS-CoV-2 virus during the early pandemic stage in Bangladesh. Viral RNA was extracted, converted to cDNA, and amplified using Ion AmpliSeq™ SARS-CoV-2 Research Panel. 413 unique mutants from 151 viral isolates were identified. 80% of cases belongs to 8 mutants: 241C toT, 1163A toT, 3037C toT, 14408C toT, 23403A toG, 28881G toA, 28,882 G toA, and 28883G toC. Observed dominance of GR clade variants that have strong presence in Europe, suggesting European channel a possible entry route. Among 37 genomic mutants significantly associated with clinical symptoms, 3916CtoT (associated with sore-throat), 14408C to T (associated with cough-protection), 28881G to A, 28882G to A, and 28883G to C (associated with chest pain) were notable. These findings may inform future research platforms for disease management and epidemiological study.

Keywords: COVID-19; GISAID; Pandemic; Phylogeny; SARS-CoV-2; Whole genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / epidemiology
China
Genomics
Humans
SARS-CoV-2* / genetics