Shiloh
Editor, Senior Moderator
Source: https://www.thedailystar.net/opinion/news/mystery-sars-cov-2-genome-isolated-bangladesh-1903186
...Lead by me at the Department of Genetic Engineering and Biotechnology, University of Dhaka, the Epigenetic and Bioinformatics team on nCoV research has done basic analysis of the genome. My team member Mr Abdullah Al Kamran Khan was with me in this analysis. We compared the sequence with that of the first reported coronavirus genome sequence from Wuhan, China—which is globally considered as "reference". Strikingly, we have found that this genome is very similar (99.7 percent similarity) to that of reference SARS-CoV-2 isolated from Wuhan. There are changes only in nine places and these changes are single nucleotide change (SNP). There are no deletion or insertion/addition of any large sequence compared to the original reference.
However, with great surprise, we observed that this genome has acquired two new mutations which have not been seen among the viruses reported so far and that we have observed closely. At position 1163 (genes orf1ab) a new mutation from A to T has been detected. Previously at the same position nucleotide A to C in one virus and nucleotide A to G changed in another genome reported. Also, there is a brand new mutation position at 17019 detected in our Bangladeshi isolated virus which has not been reported so far. This means that these are the new changes that the virus has acquired after entering into Bangladesh. Out of nine, seven other mutations were very common among the sequenced viruses so far. We can further study what trouble or benefit these new mutations have brought us.
Very interestingly, of these nine mutations, it contains a mutation (Single Nucleotide Mutation or SNP) in its Spike protein. There is non-silent (non-synonymous), amino acid changing (Aspartate to Glycine) mutation at the 614th position of the Spike protein (D614G). This is of particular interest because it is probably due to this mutation that the virus could spread quickly among the European and American populations compared to the original virus from China. This creates an additional serine protease (Elastase) cleavage site near the Open Reading Frame (ORF) S1 and S2 junction of the Spike protein.
The interesting aspect is that in human, a single nucleotide mutation (deletion of C nucleotide, delC) (rs35074065 variant site) in the TMPRSS2 receptor gene facilitates the entry of SARS-CoV-2 with D614G mutation to the cell very effectively. Dr Hemayet Ullah from Howard University, USA, also informed us that this delC mutation is very common in the American and European population but very rare in the East Asian/Asian populations—hence the change of amino acid aspartic acid to glycine in the S protein of the virus may be helpful for Asian countries but more infectious in the American and European populations. We do see a less severe effect in Asian countries compared to that in Europe and America. Any deleterious mutation from the perspective of an organism gets lost through natural selection and we hope more virulent mutation does not appear in Asian countries later on. Several research papers are also available on this mutation...
...Lead by me at the Department of Genetic Engineering and Biotechnology, University of Dhaka, the Epigenetic and Bioinformatics team on nCoV research has done basic analysis of the genome. My team member Mr Abdullah Al Kamran Khan was with me in this analysis. We compared the sequence with that of the first reported coronavirus genome sequence from Wuhan, China—which is globally considered as "reference". Strikingly, we have found that this genome is very similar (99.7 percent similarity) to that of reference SARS-CoV-2 isolated from Wuhan. There are changes only in nine places and these changes are single nucleotide change (SNP). There are no deletion or insertion/addition of any large sequence compared to the original reference.
However, with great surprise, we observed that this genome has acquired two new mutations which have not been seen among the viruses reported so far and that we have observed closely. At position 1163 (genes orf1ab) a new mutation from A to T has been detected. Previously at the same position nucleotide A to C in one virus and nucleotide A to G changed in another genome reported. Also, there is a brand new mutation position at 17019 detected in our Bangladeshi isolated virus which has not been reported so far. This means that these are the new changes that the virus has acquired after entering into Bangladesh. Out of nine, seven other mutations were very common among the sequenced viruses so far. We can further study what trouble or benefit these new mutations have brought us.
Very interestingly, of these nine mutations, it contains a mutation (Single Nucleotide Mutation or SNP) in its Spike protein. There is non-silent (non-synonymous), amino acid changing (Aspartate to Glycine) mutation at the 614th position of the Spike protein (D614G). This is of particular interest because it is probably due to this mutation that the virus could spread quickly among the European and American populations compared to the original virus from China. This creates an additional serine protease (Elastase) cleavage site near the Open Reading Frame (ORF) S1 and S2 junction of the Spike protein.
The interesting aspect is that in human, a single nucleotide mutation (deletion of C nucleotide, delC) (rs35074065 variant site) in the TMPRSS2 receptor gene facilitates the entry of SARS-CoV-2 with D614G mutation to the cell very effectively. Dr Hemayet Ullah from Howard University, USA, also informed us that this delC mutation is very common in the American and European population but very rare in the East Asian/Asian populations—hence the change of amino acid aspartic acid to glycine in the S protein of the virus may be helpful for Asian countries but more infectious in the American and European populations. We do see a less severe effect in Asian countries compared to that in Europe and America. Any deleterious mutation from the perspective of an organism gets lost through natural selection and we hope more virulent mutation does not appear in Asian countries later on. Several research papers are also available on this mutation...