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. 2021;4(3):533-541.
doi: 10.1007/s42398-020-00123-z. Epub 2020 Sep 18.

Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

Anand Prakash Maurya #  1 , Rupesh V Chikhale #  2 , Piyush Pandey  1
Affiliations

Transmission of SARS-CoV-2 in South Asian countries: molecular evolutionary model based phylogenetic and mutation analysis

Anand Prakash Maurya et al. Environ Sustain (Singap). 2021.

Abstract

The on-going coronavirus disease 19 (COVID-19) pandemic has caused a very high number of infections and deaths around the globe. The absence of vaccine/drugs to counter COVID-19 has scrambled scientific communities to repurpose available medicines/vaccines. As the virus is known to mutate, using the whole genome sequences, the transmission dynamics and molecular evolutionary models were evaluated for South Asian countries to determine the evolutionary rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Phylogenetic analyses were done using the data available on National Center for Biotechnology Information (NCBI). Different nucleotide substitution models and molecular evolutionary models were analyzed to see how SARS-CoV-2 was transmitted in the populations. Models for the viral 'S' and 'N' protein from selected strains were constructed, validated, and analyzed to determine the mutations and discover the potential therapeutics against this deadly viral disease. We found that the Hasegawa-Kishino-Yano (HKY) nucleotide substitution model was the best model with the lowest Bayesian information criterion (BIC) scores. Molecular clock RelTime analysis showed the evolutionary rate of SARS-CoV-2 substitutions in the genome was at 95% confidence interval, and heterogeneity was observed. Several mutations in the viral S-protein were found with one in the receptor-binding domain concerning SARS-CoV-2/Wuhan-1/S-Protein. Nucleocapsid protein also showed mutations in the strains from India and Sri Lanka. Our analysis suggests that SARS-CoV-2 is evolving at a diverse rate. The mutation leading to substitution in the nucleotide sequence occurred in the genome during the transmission of COVID-19 among individuals in the South Asian countries.

Keywords: COVID-19; Coronavirus; Genetic variability; Human mobility; Pandemic; Receptor binding domain (RBD).

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Conflict of interest statement

Conflict of interestAuthors declare no conflict of interest.

Figures

Fig. 1
Fig. 1
Phylogenetic tree of SARS-CoV-2 genomes with the highest log likelihood indicating spread of COVID-19. Tree(s) for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Tamura-Nei model, and then selecting the topology with superior log likelihood value
Fig. 2
Fig. 2
Minimum evolution (ME) time tree of SARS-CoV-2 genomes: Origin and transmission dynamics at different rate and time intervals. (Each node represents 95% confidence intervals)
Fig. 3
Fig. 3
a Multiple Sequence Alignment of 11 SARS-CoV-2 spike protein sequences. b The trimeric SARS-CoV-2 spike protein with surface and ribbon representation and one single spike protein with receptor binding domain (RBD) towards the top and tail region at bottom. c The highlighted box show homology models of 11 sequences in superposed representation, Ile407 mutation in green colour and the surrounding residues superposed on rest of the modelled spike protein along with the SARS-CoV-2 spike protein crystal structure (PDB: 6vyb)
Fig. 4
Fig. 4
a Multiple sequence alignment of 11 SARS-CoV-2 nucleocapsid protein sequences. b The trimeric SARS-CoV-2 nucleocapsid protein receptor binding domain (RBD) in ribbon form. c Superposed homology model for 11 SARS-CoV-2 nucleocapsid protein receptor binding domain (RBD) showing high structural similarity
Fig. 5
Fig. 5
a The SARS-CoV-2 spike protein with receptor binding domain as red coloured region. b mutations in the spike proteins SARS-CoV-2/human/IND/29/2020(Gap Val143-Tyr144), c SARS-CoV-2/human/IND/GBRC1/2020/S-Protein (Arg271), d SARS-CoV-2/human/IND/166/2020 (Val930), e SARS-CoV-2/human/LKA/COV53/2020 and SARS-CoV-2/human/IND/GBRC1/2020/S-Protein (Glu614)
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