Covid-19: natural or anthropic origin?

Abstract

<jats:title>Abstract</jats:title><jats:p>Viruses similar to the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been discovered in bats of the genus <jats:italic>Rhinolophus</jats:italic> and in the Sunda pangolin, <jats:italic>Manis javanica</jats:italic> Desmarest, 1822, suggesting that these animals have played a key role in the emergence of the Covid-19 outbreak in the city of Wuhan, China. In this paper, we review the available data for sarbecoviruses (viruses related to SARS-CoV [2002–2003 outbreak] and SARS-CoV-2) to propose all possible hypotheses on the origin of Covid-19, i. e., involving direct transmission from horseshoe bats to humans, indirect transmission via the pangolin or another animal, with interspecies contamination between either wild animals or animals kept in cage. Present evidence indicates that <jats:italic>Rhinolophus</jats:italic> bats are the natural reservoir of all sarbecoviruses, and that two divergent SARS-CoV-2-like viruses have circulated in southern China (at least in Guangxi and Guangdong provinces) between August 2017 and March 2019 in captive pangolins destined for sale in wildlife markets. We performed a genetic analysis of seven seized pangolins found to be positive for SARS-CoV-2-like virus using mitochondrial DNA sequences extracted from Sequence Reads Archive data. The results reveal that the same SARS-CoV-2-like virus can be found in animals with distinct haplotypes, which means that they were probably captured in different Southeast Asian regions. Our interpretation is that some pangolins were contaminated in captivity (by other pangolins or by another species to be determined), suggesting that illegal trade of living wild mammals is at the origin of the Covid-19 outbreak. To definitely validate this hypothesis, it is however necessary to discover a virus almost identical to SARS CoV-2 (at least 99% of identity) in animals sold in wet markets. Although pangolins are good candidates, other mammals, such as small carnivores, should not be overlooked.</jats:p>

The Ecological Niche of SARS-CoV-2-like Viruses in Bats, as Inferred from Phylogeographic Analyses of Rhinolophus Species

“…Further substantiating this hypothesis, the geographic distribution of Manis javanica [28] overlaps the ecological niche here predicted for bat SARS-CoV-2 viruses (Figures 4a and 4b), and SARS-CoV-2 neutralizing antibodies have been recently detected in a Sunda pangolin collected in eastern Thailand [8]. Collectively, these data strengthen the hypothesis that pangolin trafficking is responsible for multiple exports of SARS-CoV-2-like viruses to China [3].…”

“…More recently, several viruses showing between 96.2 and 91.8 % of genome identity with SARS-CoV-2 were identified from fecal samples of four horseshoe bat species: the RaTG13 virus was isolated from a Rhinolophus affinis bat collected in Yunnan in 2013 [1]; the RmYN02 virus was found in a Rhinolophus malayanus bat sampled in Yunnan in 2019 [6]; two variants of the same virus RshSTT200 (other variant: RshSTT182) were detected in two Rhinolophus shameli bats caught in northern Cambodia in 2010 [7]; and five variants of the same virus RacCS203 (other variants: RacCS224, RacCS253, RacCS264, and RacCS271) were sequenced from five Rhinolophus acuminatus bats collected in eastern Thailand in 2020 [8]. These data confirmed that the genus Rhinolophus is the natural reservoir host of all viruses of the subgenus Sarbecovirus [3,5]. The bat species Rhinolophus acuminatus and Rhinolophus shameli are endemic to Southeast Asia whereas the two other bat species, Rhinolophus affinis and Rhinolophus malayanus, are distributed in both Southeast Asia and China ( Figure 1), suggesting that Southeast Asia is the main region where bat SARS-CoV-2-like viruses diversified.…”

“…Even if the viruses sequenced in pangolins are not that close to SARS-CoV-2 (one was 85% identical and the other 90%), they indicate that at least two sarbecoviruses could have been imported into China well before the emergence of Covid-19 epidemic. Indeed, it has been shown that Sunda pangolins collected from different Southeast Asian regions have contaminated each other while in captivity on Chinese territory [3]. The question remained on how the Sunda pangolins became infected initially.…”

“…After 15 months, the coronavirus disease 2019 (Covid-19) pandemic has affected more than 112 million of people around the world, claiming over 2.49 million lives [2]. The origin of SARS-CoV-2 remains enigmatic and many hypotheses have been advanced to explain the first animal-to-human transmission [3].…”

Assessing the SARS-CoV-2 threat to wildlife: Potential risk to a broad range of mammals

“…Many authors argue that humans favored this pandemic, because anthropogenic activities enhance conditions to cross the species barrier from wild animals to humans ( Hassanin et al, 2020 , Volpato et al, 2020 ). The main causes were encroaching into natural areas, the increased demand and market of bushmeat and, a synergy with globalization that promoted its rapid dissemination ( Volpato et al, 2020 ).…”