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.