Akinduti, P. A. | Search bioRxiv

bioRxiv2020

Evolution And Genetic Diversity Of SARSCoV-2 In Africa Using Whole Genome Sequences

The ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 x 10-4 high posterior density HPD (4.132 x 10-4 to 4.134 x 10-4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.

microbiology↗

bioRxiv2020

Evolutionary Dynamics And Geographic Dispersal Of Beta Coronaviruses In African Bats

Bats have been shown to serve as reservoir host of various viral agents including coronaviruses. They have also been associated with the novel coronavirus SARS-CoV-2. This has made them an all important agent for CoV evolution and transmission. Our objective in this study was to investigate the dispersal, phylogenomics and evolution of betacoronavirus ({beta}CoV) among African bats. We retrieved sequence data from established databases such as GenBank and Virus Pathogen Resource, covering the partial RNA dependent RNA polymerase (RdRP) gene of Bat coronaviruses from eight African, three Asian, five European, two South American countries and Australia. We analyzed for Phylogeographic information relating to genetic diversity and evolutionary dynamics. Our study revealed that majority of the African strains fell within Norbecovirus subgenera, with an Evolutionary rate of 1.301 x 10-3, HPD (1.064 x 10-3 - 1.434 x 10-3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Marbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1968, and 2010, for the African Marbecovirus strains. There was evidence of inter species transmission of Norbecovirus among bats in Cameroun and DRC. Phlylogeography showed that there were inter-continental spread of Bt-CoV from Europe, China and Hong Kong into Central and Southern Africa, highlighting the possibility of long distance transmission. Our study has elucidated the possible evolutionary origins of {beta}CoV among African bats, we therefore advocate for broader studies of whole genome sequences of BtCoV to further understand the drivers for their emergence and zoonotic spillovers into human population.

microbiology↗