RETRACTED ARTICLE: Origin and cross-species transmission of bat coronaviruses in China

Abstract

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha-than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and-genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.

Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses

“…S1b). This region of homology includes the RNA-dependent RNA polymerase (RdRp) (nsp12) and helicase (nsp13) which are known regions of high conservation across the coronaviruses, with the former frequently used as a taxonomic marker(34).…”

Epidemic trends of SARS-CoV-2 associated with immunity, race, and viral mutations

“…CD4 T lymphocytes against other common cold coronaviruses are known to cross-react with SARS-CoV-2. 21,44 It is likely that the regions of Southeast Asia and East Asia around China have long been exposed to Chinese bat-derived coronaviruses 45 and have accumulated a large number of memory CD4 T lymphocytes, explaining the low prevalence and CFR of SARS-CoV-2 in this area. In contrast to other regions, the D614G virus tends to lower CFR in Asia and Oceania.…”

Transitivity of COVID-19, based on parameters R_0 and R_((t)) in Pombos/PE municipality, Brazil

“…Coronaviruses are enveloped, consisting of a simple positive RNA strand that infects humans and extensive animal diversity (Velavan & Meyer, 2020). SARS-CoV-2 belongs to the beta-coronavirus subfamily and is closely related to the SARS-CoV virus emerging from mammals, particularly bats (Latinne et al, 2020;Li et al, 2005). SARS-CoV-2 genome, responsible for the COVID-19 pandemic, has several Open Reading Frames (ORFs), common to Coronaviruses and several other accessory genes (that is, genes not present in all strains of a species, considered as a flexible genome) (Zhou et al, 2020).…”

“…Considering the extensive genome size (the largest non-segmented RNA viral genome ever coded), high genomic plasticity (great capacity for genetic change), and frequent recombination (exchange of genes between homologous chromosomes during the meiosis stage), CoVs have predisposition to transmission between species, with the ability to quickly adapt to new hosts (Latinne et al, 2020). Thus, the rapid transmission and SARS-CoV-2 worldwide spread signalize concern points about adaptation and evolution of the viral genome, promoted by mutations, recombination and/or deletions; the proportion at which the virus Research, Society and Development, v. 9, n. 10, e1139108441, 2020 (CC BY 4.0) | ISSN 2525-3409 | DOI: http://dx.doi.org/10.33448/rsd-v9i10.8441 6 spreads globally, finding multiple immune responses in the hosts and several countermeasures (Islam et al, 2020).…”