Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera‐hosted coronaviruses: SARS‐CoV, MERS‐CoV and SARS‐CoV‐2

Abstract

The severe acute respiratory syndrome coronavirus (SARS‐CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS‐CoV, many argue that Carnivora‐hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS‐CoV) in 2012 also involves Chiroptera‐hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS‐CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS‐CoV‐2, causative agent of coronavirus disease 2019 (COVID‐19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae . We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera‐hosted viruses are the sister group of SARS‐CoV, SARS‐CoV‐2 and MERS‐related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS‐CoV‐2 genomes dataset to elucidate the phylogenetic relationship between SARS‐CoV‐2 and Chiroptera‐hosted coronaviruses.

Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions

“…45,52,53 Despite a confusing array of reports confirming [54][55][56] and denying 57 the origin of SARS-CoV-2 from pangolin (Manis javanica) hosts, pangolins are not involved in the lineage of SARS-CoV-2 that infected humans. 49 This finding is similar to the emergence of SARS-CoV, 9 which also infected humans from bat-hosted viruses without any need for intermediate hosts, including Himalayan palm civets (Parguma larvata) and raccoon dogs (Nyctereutes procyonoides).…”

“…47,48 Third, what is the natural source of SARS-CoV-2? The most comprehensive phylogenomic analysis of coronavirus 49 (Fig. 3b) addressed the fundamental evolution of HCoVs (Fig.…”

Heat efficiently inactivates coronaviruses inside vehicles

“…The placement of the BCoV-Mebus strain within the phylogeny of Orthocoronavirinae (including alpha, beta, gamma, and delta coronaviruses) was based on the most comprehensive evolutionary study of this virus subfamily to date. 18 The phylogenetic tree was constructed from 2,006 complete and unique genomes of coronaviruses (12 deltacoronavirus, 265 gammacoronaviruses, 630 alphacoronaviruses, and 1,099 betacoronaviruses) downloaded from NCBI and GISAID. In order to avoid common errors that were identified in leading publications of the evolution of viruses, 19,20 we used several techniques including: 1) successive outgroup expansion, 21 2) genome annotation and multiple sequence alignment (using MAFFT v7.453 22,23 ) of homologous gene partitions (for the polyprotein 1ab, spike, membrane, envelope, and nucleoprotein genes).…”

“…Additional details on the data and methodological procedures used for phylogenetic analyses have been previously described. 30 Results Selection of a Surrogate Coronavirus. Worldwide, Bovine coronavirus is a causative agent of diarrhea in newborn calves, winter dysentery in adult cattle, and respiratory tract illnesses.…”

“…33,34 Standard reference strains of BCoV include the Quebec and Mebus (GenBank accession numbers AF220295.1 and U00735.2, respectively) strains. 35 The most recent and comprehensive phylogenetic analysis of coronaviruses 18 counts with 2,006 unique genomes of all Orthocoronavirinae genera (Deltacoronavirus, Gammacoronavirus, Alphacoronavirus, and Betacoronavirus). That analysis unequivocally places BCoV strain Mebus within a clade that includes human coronaviruses (HCoVs) such as HCoV-HKU1, HCoV-0C43, and HCoV-4408 (Figure 1).…”