Introduction
The SARS-CoV-2 ssRNA virus was initially detected in December 2019 within China’s Hubei province and its associated COVID-19 pandemic is currently ongoing, with a global toll of over 5 million infections and 333 thousand deaths so far (WHO, Corona virus disease (COVID-19) situation report-124, published on 23rd May, 2020). North American and European nations have already suffered a crippling blow from this pandemic, and the infection numbers within Southeast Asian, South American and African nations are growing. However, the number of infections in resource-poor, low-income countries may be underestimated due to their limited test facilities and skilled personnel. A number of earlier studies indicated that high temperatures and high humidity could decrease the spread parameter of the virus (Demongeot, Flet-Berliac & Seligmann, 2020; Sajadi et al., 2020; Wang, Tang, Feng, & Lv, 2020). Despite having such climate conditions, COVID-19 cases are increasing at an alarming rate in relatively hot and humid subtropical Southeast Asian countries. As of 22nd May, a total of 182,278 cases of SARS-CoV-2 infected cases were identified in Southeast Asia, with a death toll of over 5,500 (WHO, Corona virus disease (COVID-19) situation report-124, published on 23rd May, 2020).
Scientists from all over the world are making an unprecedented effort to expose the genomic profiles, and characterize the mutation variants, of the circulating virus to get insight into its evolutionary patterns and driving force. Tang, X.L. et al. analyzed 103 genomic sequences and indicated that the circulating SARS-CoV-2 strains have two major lineages, one with a synonymous mutation (NSP4_S75S) and the other with a non-synonymous mutation (NS8_L84S) (Tang et al., 2020). In another study, Forster, Peter et al. found 3 central variants by analyzing 160 sequences and claimed that B type viruses (with amino acid substitution, NS8_L84S) were common in East Asia, whereas A type (ancestral lineage) and C type (NS3_G251V variant) were prevalent in Europe and North America (Forster, Forster, Renfrew, & Forster, 2020). Changchuan Yin analyzed 558 genome sequences and found 15 high frequency single SNP genotypes (Yin, 2020). He suggested four major groups with either single or co-evolving mutations; group 1 with NSP6_L37F, group 2 with NS3_G251V, group 3 with co-evolving mutation at 2 sites (NSP4_S75S and NS8_L84S) and group 4 with co-evolving mutations at 4 sites (241C > T- leader sequence, NSP3_F105F, NSP12_P323L and spike_D614G). In addition, GISAID differentiated COVID-19 into three major clades; Clade S (prevalent in North America), Clade V (prevalent in Asia and Europe) and Clade G (prevalent in Europe), having non-synonymous mutations with amino acid substitutions at NS8_L84S, NS3_G251V and spike_D614G respectively (Fuertes et al., 2020). Finally, based on genomic data available from the GISAID, Nextstrain’s SARS-CoV-2 global genomic epidemiology analysis show 10 major clades for this virus. In this study, we investigated 60 sequenced genomes of SARS-CoV-2 available from Southeast Asia to provide a proximate insight into the genomic divergence, phylogeny and recurrent mutations in this region.