key: cord-0789132-cyqld91z authors: Banerjee, Arinjay; Doxey, Andrew C.; Mossman, Karen; Irving, Aaron T. title: Unravelling the zoonotic origin and transmission of SARS-CoV-2 date: 2020-12-13 journal: Trends Ecol Evol DOI: 10.1016/j.tree.2020.12.002 sha: bfbce362586797c0cdd0bad0cab8467636f34f0c doc_id: 789132 cord_uid: cyqld91z The origin and zoonotic transmission route of SARS-CoV-2 remains speculative. Here we discuss scenarios for the zoonotic emergence of SARS-CoV-2, along with exploring missing evidence and ecological considerations that are required to confidently identify the origin and transmission route of SARS-CoV-2 and to prevent future pandemics of zoonotic viruses. In December 2019, a human outbreak of pneumonia, later named coronavirus disease (COVID-19) began spreading across the planet, infecting millions of people. The causative agent of COVID-19 was quickly identified as a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Some of the earliest cases of COVID-19 in Wuhan clustered around a local seafood market, giving rise to speculations about an animal origin for the virus, with the possibility that it may have crossed the species barrier to infect humans (zoonotic event) in the market [1] . Earlier this year, researchers in China isolated and sequenced the genome of SARS-CoV-2 [1, 2] . On comparison with other CoV sequences, two bat SARS-related coronaviruses (SARSr-CoV), RaTG13 and RmYN02 have been identified as the closest known ancestors of SARS-CoV-2. RaTG13, identified in intermediate horseshoe bats (Rhinolophus affinis) in Yunnan, China exhibits 96.2% identity to SARS-CoV-2 at the whole genome level and clusters with SARS-CoV-2 in phylogenetic analysis [1] . RmYN02, identified in Malayan horseshoe bats (Rhinolophus malayanus) from Yunnan is 93.3% identical to SARS-CoV-2 at the whole genome level [3] . These SARSr-CoVs in bats could represent the evolutionary source of SARS-CoV-2. Alternately, SARSr-CoVs detected in bats could represent a clade that may have evolved independently from a common ancestor of SARS-CoV-2. Here we discuss recent data that shed light on possible zoonotic origins of SARS-CoV-2, along with speculations on evolutionary and spillover scenarios that may have played a role in its emergence. J o u r n a l P r e -p r o o f While close evolutionary relationships to bat CoVs suggest a bat origin for SARS-CoV-2, our understanding is notably limited by the available sequenced CoV genomes. These genomes represent a mere fraction of the natural CoV diversity. So, there likely exist closer relatives to SARS-CoV-2 that have yet to be sequenced, which begs the question -is 96.2% genomic identity between strains sufficient to confidently identify a reservoir host? For example, palm civets (Paguma larvata), the likely animal source of the SARS outbreak in 2002-03, carried a SARS-CoV-related virus that was 99.8% identical to SARS-CoV [4] . Highly homologous CoVs to SARS-CoV-2 have not been identified in any animal host, yet and detection of SARS-CoV-2 in an animal species in the future could be confounded by the possibility of zooanthroponosis. bat-derived CoV between 1948 and 1982 [5] , suggesting that SARSr-CoVs have been circulating in selected bat species for some time. The order Chiroptera represents over 1400 species of bats and emerging theoretical and experimental data suggest that not all bat species may support SARS-CoV-2 replication [6] . It is also possible that a SARSr-CoV evolved into SARS-CoV-2 in humans after spilling over from an animal source, followed by rapid transmission of this humanadapted strain [7] . Theories on lab-escape of existing SARSr-CoVs have no valid supportive evidence. In spite of these speculations, the transmission route of SARS-CoV-2 or SARSr-CoV from bats to humans, either directly or through an intermediate animal species remains elusive ( Figure 1 ). Two independent studies identified SARSr-CoVs in confiscated Malayan pangolins (Manis javanica), whereas confiscated Chinese pangolins (Manis pentadactyla) tested negative [8, 9] J o u r n a l P r e -p r o o f Journal Pre-proof (Table 1) . Both Lam and Xiao et al. isolated SARSr-CoVs from pangolins that were confiscated during illegal wildlife trade. Importantly, CoVs isolated from these pangolins were only 85.5 -92.4% similar to SARS-CoV-2 at the whole genome level [8] , but possess intriguing similarities to SARS-CoV-2 in regions that are critical for interaction with the human cellular receptor, angiotensin-converting enzyme 2 (ACE2). The receptor binding domain (RBD) within the CoV spike protein makes critical contacts with a human cellular receptor, ACE2 to facilitate viral entry. One pangolin SARSr-CoV RBD is 97.4% identical to SARS-CoV-2, suggesting that SARS-CoV-2 may have either acquired the RBD from pangolin CoVs via recombination or developed a similarity through convergent evolution [8, 9] ( Figure 1 ). CoVs are prone to recombination, however, a recent study reported the absence of any evidence of recombination in the spike proteins of CoVs within the lineage leading to SARS-CoV-2 and other related sarbecoviruses [5] . Thus, the origin of a pangolin SARSr-CoVlike RBD in SARS-CoV-2 remains a mystery (Figure 1 ). Intermediate hosts play an important role in the amplification and adaptation of zoonotic viruses. [11] . The sampled pangolins could have also been exposed to CoVs by other animal species or humans along the wildlife trade route [12] (Figure 1 Ecological factors may also promote the spillover of wildlife-borne viruses. For example, nutritional and reproductive stress are associated with increased Hendra virus replication in bats [15] . Factors such as urbanization, deforestation and forest fragmentation, mixed farming practices and other anthropogenic interference with wildlife habitats may indeed alter the delicate balance that reservoir species have evolved with their viruses. Additionally, animal stress from unsustainable livestock industries, wildlife trade and artificial co-housing of different animal species provides pathogens with the opportunity to find novel alternate hosts that are unlikely to occur in a natural setting. Indeed, investment in science with a One Health focus will tackle future emerging zoonosis, and closely monitor ecosystem health to limit human interference and minimize exposure across the human-wildlife interface. A pneumonia outbreak associated with a new coronavirus of probable bat origin A new coronavirus associated with human respiratory disease in China A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic Many bat species are not potential hosts of SARS-CoV and SARS-CoV-2: Evidence from ACE2 receptor usage A Genomic Perspective on the Origin and Emergence of SARS-CoV-2 Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins Isolation of SARS-CoV-2-related coronavirus from Malayan pangolins Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins (Manis javanica) Pangolins Harbor SARS-CoV-2-Related Coronaviruses No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia Pangolins and bats living together in underground burrows in Lope National Park, Gabon Due to factors yet unknown, bats may occasionally shed CoVs. Bat SARSr-CoVs may infect humans directly (5) or via an intermediate host (3 and 4), and select for human-adapted strains, such as SARS-CoV-2 through adaptive evolution (5; scenario A). A bat SARSr-CoV could have evolved into SARS Pangolins could have been infected with a bat SARSr-CoV, either directly (7) or via an undiscovered intermediate host (8), leading to recombination events between existing pangolin SARSr-CoVs and bat SARSr-CoVs to generate SARS-CoV-2 (scenario C). The recombined virus could have then spilled over into humans SARSr-CoV, severe acute respiratory syndrome-related coronavirus; ?, undiscovered intermediate host Adaptive evolution -the accumulation of advantageous mutations while propagating in a host Convergent evolution -the independent evolution of similar mutations or traits in different species Enzootic -presence of disease within animal populations in a region Koch's postulates -Four criteria