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.