Discussion
In this study, the full length genome of SARS-CoV-2 strain Bangladesh is completely analyzed and compared with the viral genome sequence of the COVID-19 patient in Wuhan [5] and some neighboring countries as well as Western countries (https://www.gisaid.org/). Phylogenetic analysis consistently placed the Bangladeshi patient’s strain in a distinct cluster from the neighboring country India and also the Wuhan patient’s strain. The strain of Bangladeshi patient grouped in this small study with 33 sequences within mostly Asian countries like Japan, Kuwait, Russia and also European country, Spain. In comparison with the Wuhan patient’s strain a total of 9 SNPs were observed [5]. This is consistent with the other reports published recently where India reported their isolated strains with 15 mutations while Italy reported 11 mutations compare to the Wuhan strains. Such variations reflects the various kind of mutations that are common to the most RNA viruses [11, 12, 13, 14]. This strain of Bangladeshi female patient also showed at least SARS-CoV-2 strain 10 SNPs when compared with the Indian strains. Again it clearly is very much diverse as the viral outbreak might be initiated by the people who visited the hotspots or migrated from those areas. And Bangladeshi and Indian people are working across the globe in Europe, America and Middle Eastern countries being the being the dominant countries. While trading relationship is also very high for these countries to diverse overseas countries.
The sequence data of Bangladesh revealed 2 novel SNPs. Among them, Mutation NSP13 E261D already occurred 2 times (0.01% of all samples with NSP13 sequence) in 2 countries including Bangladesh. The first strain with this mutation, collected in March 2020, was hCoV-19/Austria/CeMM0004/2020. The mutation most recently occurred in strain hCoV-19/Bangladesh/CHRF_nCOV19_0001/2020, collected in April 2020. This finding is very important as it only occurred second time. Even the NCBI database revealed this as first time for Bangladesh, but it matched with Austrian strain when we analyzed with the GISAID database. There is at least 1 SNP that was observed in Bangladeshi Patient’s sequence that is completely novel. It is the mutation in NSP3 region nucleotide 1162 which is T for Bangladeshi strain, but A for Wuhan strain. This is for the amino acid Iso leucine (I) is replaced by Phenyl alanine (F). It would be very interesting to analyze the protein function more details of NSP3. However, initial analysis performed by i-tesser didn’t show significant differences. The mutations should be further investigated to understand whether they may affect virus characteristics. During this analysis, the lack of epidemiological information available with most sequences deposited in the database and the number of incomplete genomes available made difficulties in the strain selections. Nevertheless, these data provides valuable insights about SARS-CoV-2 strain in Bangladesh and may be useful to understand the dynamics of the local transmission of SARS-CoV-2 in the coming days.