The genome variants of SARS-COV-2 strain from Bangladesh
The first complete genome sequence of SARS-CoV-2 (CHRF_nCoV19_0001) from a Bangladeshi isolate was submitted to the GISAID database on 12 May 2020. Bangladesh based Child Health Research Foundation conducted the sequencing project [38]. As of July 17, genome sequencing of 222 samples from Bangladeshi SARS-CoV-2 isolates was submitted on the GISAID database, of which 173 samples were sequenced by the Bangladesh Council of Scientific and Industrial Research (BCSIR) [39]. Jashore University of Science and Technology had announced on 24 June 2020 that they had sequenced the complete genome of another three SARS-CoV-2 strain that is responsible for the respiratory infections in the southern part of the country [40]. A comparative study of the Bangladeshi strain and other strains around the world revealed that there were 9 single-nucleotide variants in the Bangladeshi strain, mostly in the ORF1ab gene and also a sequence containing 3 successive variants in the N protein which probably reflects a weaker strain of SARS-CoV-2 and explain the reason of low mortality rate in Bangladesh [41]. Phylogenetic analysis elucidated that there is sequence homology among the Bangladeshi strains and strains from Taiwan, Greece and Kazakhstan which implicates that the virus strains found in these countries were descendent from a weaker strain of the same origin, probably Michigan or Arizona in the United States [41]. Another investigation of 184 genome samples of SARS-CoV-2 across the country found 634 mutations located in the whole genome that results in 274 nonsynonymous substitutions in 22 different proteins. Among the spike protein variants circulating across the country, G614 is most prevalent followed by L323 (94%) in RNA- dependent RNA polymerase (RdRp), K203 (82%) and R204 (82%) in nucleocapsid, and F120 (78%) in NSP2. These mutations implicated a close homology with a European haplotype of SARS-CoV-2. These sequencing data will help to predict prognosis and develop an effective vaccine for the treatment of COVID-19 patients in Bangladesh.