Evolutionary dynamics and geographic dispersal of beta coronaviruses in African bats

Abstract

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 (βCoV) 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 × 10^-3, HPD (1.064 × 10^-3-1.434 × 10^-3) subs/site/year. The African strains diversified into three main subgenera, Norbecovirus, Hibecovirus and Merbecovirus. The time to most common recent ancestor for Norbecovirus strains was 1973, and 2007, for the African Merbecovirus 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 βCoV 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.

Keywords: Africa; BtCoV; Evolutionary dynamics; Phylogeography.

Figure 1. Maximum Likelihood Phylogenetic tree, of Bat βCoV from this study.

The grey colored clade indicates alpha CoV from bats, green colored lines indicate lineage D (Norbecovirus) βCoV. The clade in red represents lineage B (Sabecovirus) Bat βCoV, while the blue colored clade represents lineage C (Merbecovirus) Bat βCoV. The orange colored labels represent Lineage E (Embecovirus), while the violet colored labels represent the Hibercovirus sub-genus. Bootstrap values are indicated as circles on the branches of the tree, the legend represents the value of the bootstrap where 1 is equivalent to 100%, 0.75 represents 75% 0.25 represents 25%.

Figure 2. Time scaled Maximum clade credibility tree (MCC) of partial RdrP gene region of African Bt-βCoV.

Branch lengths are proportional to time in years, while branch colors are indicative of country of origin as shown in the legend. The blue horizontal bar represents Lineage D/Norbecovirus strains, while red represents Lineage C/Merbecovirus. The black arrow indicates Hibercovirus (formally under lineage B) strains.

Figure 3. Time scaled Maximum clade credibility tree (MCC) of partial RdrP gene region of Bt-βCoV from Africa and other global strains.

Time scaled Maximum clade credibility tree (MCC) with Bayesian phylogeographic reconstruction of partial RdrP gene region of Bt-βCoV. Branch lengths are proportional to time in years, while branch colors are indicative of country of origin as shown in the legend. Names of bat species of CoV isolation are shown in the tip labels. The blue horizontal bar represents Lineage D/Norbecovirus strains, green represents Lineage B/Sabecovirus, while red represents Lineage C/Merbecovirus.

Figure 4. Spaciotemporal diffusion of BtCoV, showing genetic spread of BtCoV across the world.

Spaciotemporal diffusion of BtβCoV, the names of the countries of isolation are written in the map. The diameter of the pink circles is proportional to the number of maximum clade credibility branches (MCC). Concave lines (upward curving) show a clockwise spread movement between two points, while the convex bending (downward curving) lines depict anticlockwise movement between the points. The black arrows indicate the direction of the movements.

Figure 5. Bayesian Skygrid plot of Afr Bt-βCoV.

Bayesian Skygrid plot showing effective virus population size estimates over time of Afr Bt-βCoV. The solid blue line represents the median population size, while the upper and lower blue lines represent the 95% high posterior density intervals (95% HPD) for the population.