3 ms·

Exploring the natural origins of SARS-CoV-2 in the light of recombination

2 points by lamontcg 5y ago

lamontcg 5y ago
> Summary > The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (Sarbecoviruses) have been identified,is fuelling speculation on the natural origins of SARS-CoV-2. We have comprehensively analysed phylogenetic relations between SARS-CoV-2, and the related bat and pangolin Sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Clustering of the inferred recombination events is non-random with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift in the ancestry of bat Sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm horseshoe bats, Rhinolophus, are the likely SARS-CoV-2 progenitor reservoir species. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and co-circulation of these viruses’ ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years or so. We confirm that a direct proximal ancestor to SARS-CoV-2 is yet to be sampled, since the closest relative shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for more wildlife sampling to (i) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, and (ii) survey the extent of the diversity in the related Sarbecoviruses’ phylogeny that present high risk for future spillover.
- lamontcg 5y ago
  > The two genetically closest relatives of SARS-CoV-2 that were identified shortly after its emergence were the bat Sarbecoviruses, RaTG13 and subsequently RmYN02, both from samples collected in Yunnan[3,4]. We find RmYN02 shares a most recent common ancestor with SARS-CoV-2 about 40 years ago and RaTG13 about 50 years ago (Figure 4A) consistent with previous estimates[11,12,19]. Although SARS-CoV-2 is most similar to RmYN02 across most of its genome, the region corresponding to the first half of the RmYN02 Spike ORF appears to have been derived through recombination from a parental sequence residing outside the nCoV clade[4](Figure 1A). Two more viruses very recently identified in Yunnan, RpYN066 and PrC318 are most closely related to RmYN02 for part of their genomes. In the portion of the genome corresponding to recombination breakpoint partitioned (RBP) regions 2 to 5, the three Yunnan viruses (RmYN02, RpYN06, PrC31) cluster with strong support in a sister clade to SARS-CoV-2 (Figure 2A, Figure S1). This pattern suggests that bat sampling efforts in Yunnan have uncovered a cluster of related viruses distinct to the likely viral population of SARS-CoV-2’s proximal ancestor. Molecular dating of the RBP region 5 phylogeny (Figure 4A) indicates that this “Yunnan cluster” shared a common ancestor with SARS-CoV-2 around 1982 (95% HPD: 1970-1994). This analysis further allows us to date the node between PrC31 and RmYN02 to 2005 (95% HPD: 1998-2010), which is one of the most recent nodes in the phylogeny (Figure 4A). > The recombination analysis, however, reveals a much more complex evolutionary history for the rest of the PrC31 genome. As seen in the consensus whole-genome phylogeny (Figure 1A), most of its genome clusters with viruses CoVZC45 and CoVZXC21 sampled in Zhejiang, a coastal province in East China[20,21]. Across the majority of their genomes (excluding segments of Orf1ab and Spike) these viruses are members of the nCoV clade and share a common ancestor with SARS-CoV-2 that existed before 1934 (95% HPD: 1907-1957) according to molecular dating of RBP region 5(Figure 4A). However, in RBP regions 8-12 the sequences of these viruses cluster outside the nCoV clade, being genetically most closely related to Zhejiang virus Longquan_140 and the HKU3 set of closely related bat Sarbecoviruses sampled in Hong Kong (bordering Guangdong province) (Figure 2A, Figure S1). The link between SARS-CoV-2’s closest relatives and viral populations in the southeast of South China becomes even more apparent in the phylogeny of RBP region 2 where Longquan_140 clusters within the nCoV clade along with CoVZC45 and CoVZXC21 (Figure 2A). These relationships indicate ancestral movement of the nCoV viruses across large geographic ranges in spanning Yunnan in southwestChina and Zhejiang on the east coast (Figure 3B). > As more countries initiate wildlife-infecting coronavirus sampling and sequencing efforts, the geographic range of the nCoV clade linked to bat host species will be further refined, evident from the recent reporting of bat sarbecoviruses closely related to SARS-CoV-2 from: i) two samples collected in Cambodia from R. shameli (RShSTT182 and RShSTT200) confirmed by whole-genome analysis[7], and ii) five bat samples from R. acuminatus collected in Thailand with one fully sequenced genome of virus RacCS2035. These viruses are, after the China sampled CoVs mentioned above, the next closest relatives to SARS-CoV-2 with common ancestor age estimates (using RBP region 5) around 1907 (95% HPD: 1873-1938) and 1883 (95% HPD: 1841-1921),respectively (Figure 4A). Similar to the other nCoV viruses, the recombination analysis uncovers more intricate phylogenetic relations for some parts of the genome. Notably, RShSTT182 and RShSTT200, despite being from Cambodia, cluster with RaTG13 for RBP regions 8 and 9 (Figure 2A, Figure S1), while in RBP region 4 of the genome RacCS203, from Thailand,c lusters together with SARS-CoV-2 within the Yunnan clade (Figure 2A). This indicates that co-circulation and recombination between these viruses in the last century is responsible for the observed patterns in their inferred evolutionary history, despite the current samples having been collected across a geographic range of at least 2,500km. This wide distribution of related viruses, including shared recombination breakpoints, highlights an important feature of bat species:their frequently overlapping/sympatric ranges will provide ample opportunities for transmissions of viral variants from one bat species (or sub-species) to another. > Consistent with the Spike S1 recombination hotspots revealed in the initial analysis (Figure 1B,C), most close relatives of SARS-CoV-2 presented here have non-nCoV derived recombinant sequences at the start of the Spike gene (Figure 2B). Despite one collected from Yunnan, China and the other from Cambodia, viruses RmYN02 and RacCS203 share a closely related non-nCoV sequence in RBP regions 15 and 16 (encompassing the Spike NTD and RBD respectively; Figure 2B) having a distinct RBD compared to that of SARS-CoV-24,[5]. On the other hand, viruses RpYN06, PrC31, CoVZC45 and CoVZXC21 cluster within the nCoV clade for region 15 but move into broadly the same non-nCoV cluster as RmYN02 and RacCS203 for region 16 (Figure 2B). We speculate that some of the apparent patterns of recombination-mediated exchange between nCoV and non-nCoV viruses can be partly explained by recombination “overprinting”. This will occur when annCoV virus has acquired a non-nCoV genomic sequence through ancestral recombination but its progenitors co-circulating with other nCoV viruses incurred subsequent recombination events that overlapped portions of the original non-nCoV recombinant sequence, producing the more complex “patchy”patterns we see in the currently sampled viruses. Note, overprinting of recombination regions will result in reduced confidence in the breakpoints at deeper nodes in the phylogeny. > The finding that Sunda (also known as Malayan) pangolins, Manis javanica, non-native to China, are the other mammal species from which nCoV Sarbecoviruses have been sampled in Guangxi and Guangdong provinces inSouth China[22,23], indicates these animals are likely being infected in this part of the country (Figure 3B). Pangolins are one of the most frequently trafficked animals with multiple smuggling routes leading to southern China[24]. The most common routes involve moving the animals from Southeast Asia (Myanmar, Malaysia, Laos, Indonesia, Vietnam) to Guangxi, Guangdong, and Yunnan. The most likely scenario that is consistent with both the respiratory distress that the sampled pangolins exhibited[23,25] and the lack of evidence of similar infections among Sunda pangolins in Malaysia[26], is that the viruses obtained from these animals infected them (presumably from bat sources)after they were trafficked into southernChina. > Although the recombination patterns evident in the pangolin-derived virus genomes seem to be less complex than those of the bat nCoV genomes, the Guangdong Pangolin-CoV has a Spike receptor binding domain that is most similar to that of SARS-CoV-2, likely due to recombination in the other sampled close relatives, e.g., RaTG1311(and reflected in region 17, Figure 2A). The susceptibility of pangolins to an apparently new human coronavirus is not surprising given the well-documented generalist nature of SARS-CoV-227, which has been found to readily transmit to multiple mammals with similar ACE2 receptors and poses a grave risk of reverse-zoonoses as has been most notably demonstrated with human to mink transmissions[28]. > Overlapping horseshoe bat ranges. Considering that almost all Sarbecoviruses have been sampled in related bat hosts, i.e.,the Rhinolophidae, horseshoe bats, which have ranges that span different regions where nCoV clade viruses have been collected(Figure 4B), should be prioritized for sampling. For example, the intermediate horseshoe bat species, R. affinis, is sufficiently dispersed across China to account for the geographical spread of i) bat Sarbecovirus recombinants in the West and East of China, ii) infected imported pangolins in the South, iii) bat Sarbecovirus recombinant links to southwest ofChina, and iv) SARS-CoV-2 emergence towards Hubei in Central China (Figure 3B). Strikingly, the ranges of multiple species including R. affinis,R. sinicus and R.pusillus overlap all the regions of China where the nCoVs have been collected (Figure 4B). Other horseshoe bat species that might harbour nCoVs have different ranges, for example,R. ferrumequinum, being absent from large parts of South Central China, andR. malayanus found predominantly in the western part of China and countries to the Southwest of China (Myanmar, Thailand, Cambodia, Laos, Viet Nam, and Peninsular Malaysia)[29]. RmYN02, RmYN05 and RmYN08 were sampled from R. malayanus in Yunnan[4,6](Figure 4B)indicating that the nCoVviruses are being exchanged between bat species in regions where ranges overlap such as Yunnan, linking hosts found predominantly in China with hosts in the Indochinese peninsula.
  - lamontcg 5y ago
    > The wide geographic ranges of R. pusillus and R. affinis and the fact that two of the closest known relatives of SARS-CoV-2, RpYN06 and RaTG13, have been sampled in these species flags them as prime suspects for the source of the SARS-CoV-2’s progenitor in China. Additionally, these two bat species are found in shared roosts with R. sinicus and R. ferrumequinum in Yunnan and with R. sinicus in Guangxi[30], providing opportunities for host switches, co-infections and thus recombination between the sarbecoviruses that these bat species carry. R. pusillusand R. affinisal so link more regions of China with bat species such as R. shameli, R. malayanusand R. acuminatus which are only found in Southeast Asia and southwest of China(Figure 4B). Latinne et al. (2020)[31] recently published a large-scale sampling expedition of coronaviruses across bats in China. Although only short RdRp fragments were sequenced, reconstructing the phylogeny for the novel viruses reveals a cluster of seven identical Sarbecovirus sequences sampled from R. affinis within the nCoV clade, that cluster close to SARS-CoV-2 (Figure S2). Still, the fact that viruses in the Yunnan clade (consisting of RmYN02, RpYN06 and PrC31) were sampled from three different Rhinolophus species supports the hypothesis that these viruses readily infect multiple different horseshoe bat species with overlapping geographical ranges. > Based on the analysis of the Sarbecovirus and host data presented here, we propose that horseshoe bat population sampling should focus on the known ranges of probable bat hosts. Specifically, samples should be collected in roosting environments spread across China with care being taken both to avoid a further spillover or reverse zoonosis and to protect the bat species[30]. Sampling strategies will also need to consider the distinct subspecies of Rhinolophus as the delineators of genetically meaningful host populations for coronaviruses. For example, there are two R. affinis sub-species on mainland China: himalayanus and macrurus[32]. Future sampling should also encompass a range of indigenous mammals other than bats that we now know can be infected by coronaviruses. Although highly endangered, it is possible that Chinese pangolins, given their susceptibility to infection and their geographical range across southern China[33], might be the “missing” intermediate host of the SARS-CoV-2 proximal ancestor[1]. > Conclusion > The currently available data, although sparse, illustrates a complex reticulate history involving the lineage of Sarbecoviruses SARS-CoV-2 emerged from, governed by co-circulation of related coronaviruses, over at least the last 100 years, across the bat populations in southern China, and into Southeast Asia with multiple recombination events imprinted on the genomes of these viruses. Considering the high frequency of recombination, it is expected that selection could preferentially favour exchanges of specific genome regions, in line with our detection of hotspots near the Spike gene (Figure 1B,C). Our analysis further illustrates the importance of accounting for recombination rather than using whole-genome pairwise similarity to determine the shared evolutionary history of these viruses. This is exemplified by RaTG13 which is often described as the “on average” closest Sarbecovirus to SARS-CoV-2 despite not being the closest virus once recombination history is accounted for in the othernCoV Sarbecoviruses (Figure 1A, 3A). > The evidence of recombination events between Sarbecoviruses sampled in different geographical regions and from different bat hosts, indicates recent extensive movement of the viruses between different regions and species (and presumably sub-species too) as a result of the different bat populations that carry them coming into contact with one another. Although very few nCoV viruses are known to be hosted by mammals other than horseshoe bats, the recombination patterns detected within the nCoV genomes imply the existence of one or a few primary reservoir hosts with a geographical range spanning Thailand from the Southwest and Zhejiang to the East, a distribution that is consistent with specific Chinese horseshoe bats being the primary reservoir hosts. Having presented evidence in support of R. affinis and R. pusillus’s potential significance as the reservoir species,it should be noted that at least 20 different Rhinolophus species are distributed across China (four being endemic to China), many of which have not yet been found hosting nCoVs. The generalist nature of Sarbecoviruses also means multiple wild or farmed animals (e.g., minks)[1] could have facilitated transmission of SARS-CoV-2 from bats to humans. > The risk of future emergence of a new SARS-CoV-2 like nCoV strain in humans is too high to restrict sampling strategies. Beyond the relatively rare detection of SARS-like antibodies in people from rural communities in China[34,35],SARS related coronaviruses have not, to our knowledge, seeded outbreaks in humans before. This indicates that there is limited human exposure to these viruses, suggesting ecological “barriers”to their emergence[36]. One possible recent disruption that caused widespread and unusual movements of animals in China and may have increased the permeability of this barrier, was the dramatic shortage of pork products in 2019[37] attributable to an African swine fever virus (ASFV) outbreak impacting 100s of millions of pigs in China[38]. Such a major disruption in the food supply chain will have potentially brought humans into increased contact with Sarbecovirus infected animals as i) exotic meats replaced pork, ii) animals from rural locations were brought to city markets and/or iii) by meat from infected animals being transported in cold chain processes. Further facilitating animal contacts,increased human encroachment into rural areas as a result of new and faster travel networks around and between metropolitan areas have also likely increased opportunities for Sarbecoviruses to spillover into humans.Given the reality of frequent human-animal contact, routine characterisation of respiratory infections would seem a sensible precaution to prevent future emergence of Sarbecoviruses. > The key and most urgent questions relating to the prevention of another emergence, is thus not how did SARS-CoV-2 get from Yunnan to Hubei, but rather which bat or other animal species are harbouring nCoV Sarbecoviruses and what are the risks of a future spillover? There is undoubtedly a virus highly related to SARS-CoV-2 still present somewhere most probably in a bat species in South China or towards Yunnan in the southwest. The best we can do is maximize the probability that future sampling efforts will uncover that host species or sub-species.

2 points by lamontcg 5y ago

> Summary > The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (Sarbecoviruses) have been identified,is fuelling speculation on the natural origins of SARS-CoV-2. We have comprehensively analysed phylogenetic relations between SARS-CoV-2, and the related bat and pangolin Sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Clustering of the inferred recombination events is non-random with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift in the ancestry of bat Sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm horseshoe bats, Rhinolophus, are the likely SARS-CoV-2 progenitor reservoir species. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and co-circulation of these viruses’ ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years or so. We confirm that a direct proximal ancestor to SARS-CoV-2 is yet to be sampled, since the closest relative shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for more wildlife sampling to (i) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, and (ii) survey the extent of the diversity in the related Sarbecoviruses’ phylogeny that present high risk for future spillover.

lamontcg 5y ago
> The two genetically closest relatives of SARS-CoV-2 that were identified shortly after its emergence were the bat Sarbecoviruses, RaTG13 and subsequently RmYN02, both from samples collected in Yunnan[3,4]. We find RmYN02 shares a most recent common ancestor with SARS-CoV-2 about 40 years ago and RaTG13 about 50 years ago (Figure 4A) consistent with previous estimates[11,12,19]. Although SARS-CoV-2 is most similar to RmYN02 across most of its genome, the region corresponding to the first half of the RmYN02 Spike ORF appears to have been derived through recombination from a parental sequence residing outside the nCoV clade[4](Figure 1A). Two more viruses very recently identified in Yunnan, RpYN066 and PrC318 are most closely related to RmYN02 for part of their genomes. In the portion of the genome corresponding to recombination breakpoint partitioned (RBP) regions 2 to 5, the three Yunnan viruses (RmYN02, RpYN06, PrC31) cluster with strong support in a sister clade to SARS-CoV-2 (Figure 2A, Figure S1). This pattern suggests that bat sampling efforts in Yunnan have uncovered a cluster of related viruses distinct to the likely viral population of SARS-CoV-2’s proximal ancestor. Molecular dating of the RBP region 5 phylogeny (Figure 4A) indicates that this “Yunnan cluster” shared a common ancestor with SARS-CoV-2 around 1982 (95% HPD: 1970-1994). This analysis further allows us to date the node between PrC31 and RmYN02 to 2005 (95% HPD: 1998-2010), which is one of the most recent nodes in the phylogeny (Figure 4A). > The recombination analysis, however, reveals a much more complex evolutionary history for the rest of the PrC31 genome. As seen in the consensus whole-genome phylogeny (Figure 1A), most of its genome clusters with viruses CoVZC45 and CoVZXC21 sampled in Zhejiang, a coastal province in East China[20,21]. Across the majority of their genomes (excluding segments of Orf1ab and Spike) these viruses are members of the nCoV clade and share a common ancestor with SARS-CoV-2 that existed before 1934 (95% HPD: 1907-1957) according to molecular dating of RBP region 5(Figure 4A). However, in RBP regions 8-12 the sequences of these viruses cluster outside the nCoV clade, being genetically most closely related to Zhejiang virus Longquan_140 and the HKU3 set of closely related bat Sarbecoviruses sampled in Hong Kong (bordering Guangdong province) (Figure 2A, Figure S1). The link between SARS-CoV-2’s closest relatives and viral populations in the southeast of South China becomes even more apparent in the phylogeny of RBP region 2 where Longquan_140 clusters within the nCoV clade along with CoVZC45 and CoVZXC21 (Figure 2A). These relationships indicate ancestral movement of the nCoV viruses across large geographic ranges in spanning Yunnan in southwestChina and Zhejiang on the east coast (Figure 3B). > As more countries initiate wildlife-infecting coronavirus sampling and sequencing efforts, the geographic range of the nCoV clade linked to bat host species will be further refined, evident from the recent reporting of bat sarbecoviruses closely related to SARS-CoV-2 from: i) two samples collected in Cambodia from R. shameli (RShSTT182 and RShSTT200) confirmed by whole-genome analysis[7], and ii) five bat samples from R. acuminatus collected in Thailand with one fully sequenced genome of virus RacCS2035. These viruses are, after the China sampled CoVs mentioned above, the next closest relatives to SARS-CoV-2 with common ancestor age estimates (using RBP region 5) around 1907 (95% HPD: 1873-1938) and 1883 (95% HPD: 1841-1921),respectively (Figure 4A). Similar to the other nCoV viruses, the recombination analysis uncovers more intricate phylogenetic relations for some parts of the genome. Notably, RShSTT182 and RShSTT200, despite being from Cambodia, cluster with RaTG13 for RBP regions 8 and 9 (Figure 2A, Figure S1), while in RBP region 4 of the genome RacCS203, from Thailand,c lusters together with SARS-CoV-2 within the Yunnan clade (Figure 2A). This indicates that co-circulation and recombination between these viruses in the last century is responsible for the observed patterns in their inferred evolutionary history, despite the current samples having been collected across a geographic range of at least 2,500km. This wide distribution of related viruses, including shared recombination breakpoints, highlights an important feature of bat species:their frequently overlapping/sympatric ranges will provide ample opportunities for transmissions of viral variants from one bat species (or sub-species) to another. > Consistent with the Spike S1 recombination hotspots revealed in the initial analysis (Figure 1B,C), most close relatives of SARS-CoV-2 presented here have non-nCoV derived recombinant sequences at the start of the Spike gene (Figure 2B). Despite one collected from Yunnan, China and the other from Cambodia, viruses RmYN02 and RacCS203 share a closely related non-nCoV sequence in RBP regions 15 and 16 (encompassing the Spike NTD and RBD respectively; Figure 2B) having a distinct RBD compared to that of SARS-CoV-24,[5]. On the other hand, viruses RpYN06, PrC31, CoVZC45 and CoVZXC21 cluster within the nCoV clade for region 15 but move into broadly the same non-nCoV cluster as RmYN02 and RacCS203 for region 16 (Figure 2B). We speculate that some of the apparent patterns of recombination-mediated exchange between nCoV and non-nCoV viruses can be partly explained by recombination “overprinting”. This will occur when annCoV virus has acquired a non-nCoV genomic sequence through ancestral recombination but its progenitors co-circulating with other nCoV viruses incurred subsequent recombination events that overlapped portions of the original non-nCoV recombinant sequence, producing the more complex “patchy”patterns we see in the currently sampled viruses. Note, overprinting of recombination regions will result in reduced confidence in the breakpoints at deeper nodes in the phylogeny. > The finding that Sunda (also known as Malayan) pangolins, Manis javanica, non-native to China, are the other mammal species from which nCoV Sarbecoviruses have been sampled in Guangxi and Guangdong provinces inSouth China[22,23], indicates these animals are likely being infected in this part of the country (Figure 3B). Pangolins are one of the most frequently trafficked animals with multiple smuggling routes leading to southern China[24]. The most common routes involve moving the animals from Southeast Asia (Myanmar, Malaysia, Laos, Indonesia, Vietnam) to Guangxi, Guangdong, and Yunnan. The most likely scenario that is consistent with both the respiratory distress that the sampled pangolins exhibited[23,25] and the lack of evidence of similar infections among Sunda pangolins in Malaysia[26], is that the viruses obtained from these animals infected them (presumably from bat sources)after they were trafficked into southernChina. > Although the recombination patterns evident in the pangolin-derived virus genomes seem to be less complex than those of the bat nCoV genomes, the Guangdong Pangolin-CoV has a Spike receptor binding domain that is most similar to that of SARS-CoV-2, likely due to recombination in the other sampled close relatives, e.g., RaTG1311(and reflected in region 17, Figure 2A). The susceptibility of pangolins to an apparently new human coronavirus is not surprising given the well-documented generalist nature of SARS-CoV-227, which has been found to readily transmit to multiple mammals with similar ACE2 receptors and poses a grave risk of reverse-zoonoses as has been most notably demonstrated with human to mink transmissions[28]. > Overlapping horseshoe bat ranges. Considering that almost all Sarbecoviruses have been sampled in related bat hosts, i.e.,the Rhinolophidae, horseshoe bats, which have ranges that span different regions where nCoV clade viruses have been collected(Figure 4B), should be prioritized for sampling. For example, the intermediate horseshoe bat species, R. affinis, is sufficiently dispersed across China to account for the geographical spread of i) bat Sarbecovirus recombinants in the West and East of China, ii) infected imported pangolins in the South, iii) bat Sarbecovirus recombinant links to southwest ofChina, and iv) SARS-CoV-2 emergence towards Hubei in Central China (Figure 3B). Strikingly, the ranges of multiple species including R. affinis,R. sinicus and R.pusillus overlap all the regions of China where the nCoVs have been collected (Figure 4B). Other horseshoe bat species that might harbour nCoVs have different ranges, for example,R. ferrumequinum, being absent from large parts of South Central China, andR. malayanus found predominantly in the western part of China and countries to the Southwest of China (Myanmar, Thailand, Cambodia, Laos, Viet Nam, and Peninsular Malaysia)[29]. RmYN02, RmYN05 and RmYN08 were sampled from R. malayanus in Yunnan[4,6](Figure 4B)indicating that the nCoVviruses are being exchanged between bat species in regions where ranges overlap such as Yunnan, linking hosts found predominantly in China with hosts in the Indochinese peninsula.
- lamontcg 5y ago
  > The wide geographic ranges of R. pusillus and R. affinis and the fact that two of the closest known relatives of SARS-CoV-2, RpYN06 and RaTG13, have been sampled in these species flags them as prime suspects for the source of the SARS-CoV-2’s progenitor in China. Additionally, these two bat species are found in shared roosts with R. sinicus and R. ferrumequinum in Yunnan and with R. sinicus in Guangxi[30], providing opportunities for host switches, co-infections and thus recombination between the sarbecoviruses that these bat species carry. R. pusillusand R. affinisal so link more regions of China with bat species such as R. shameli, R. malayanusand R. acuminatus which are only found in Southeast Asia and southwest of China(Figure 4B). Latinne et al. (2020)[31] recently published a large-scale sampling expedition of coronaviruses across bats in China. Although only short RdRp fragments were sequenced, reconstructing the phylogeny for the novel viruses reveals a cluster of seven identical Sarbecovirus sequences sampled from R. affinis within the nCoV clade, that cluster close to SARS-CoV-2 (Figure S2). Still, the fact that viruses in the Yunnan clade (consisting of RmYN02, RpYN06 and PrC31) were sampled from three different Rhinolophus species supports the hypothesis that these viruses readily infect multiple different horseshoe bat species with overlapping geographical ranges. > Based on the analysis of the Sarbecovirus and host data presented here, we propose that horseshoe bat population sampling should focus on the known ranges of probable bat hosts. Specifically, samples should be collected in roosting environments spread across China with care being taken both to avoid a further spillover or reverse zoonosis and to protect the bat species[30]. Sampling strategies will also need to consider the distinct subspecies of Rhinolophus as the delineators of genetically meaningful host populations for coronaviruses. For example, there are two R. affinis sub-species on mainland China: himalayanus and macrurus[32]. Future sampling should also encompass a range of indigenous mammals other than bats that we now know can be infected by coronaviruses. Although highly endangered, it is possible that Chinese pangolins, given their susceptibility to infection and their geographical range across southern China[33], might be the “missing” intermediate host of the SARS-CoV-2 proximal ancestor[1]. > Conclusion > The currently available data, although sparse, illustrates a complex reticulate history involving the lineage of Sarbecoviruses SARS-CoV-2 emerged from, governed by co-circulation of related coronaviruses, over at least the last 100 years, across the bat populations in southern China, and into Southeast Asia with multiple recombination events imprinted on the genomes of these viruses. Considering the high frequency of recombination, it is expected that selection could preferentially favour exchanges of specific genome regions, in line with our detection of hotspots near the Spike gene (Figure 1B,C). Our analysis further illustrates the importance of accounting for recombination rather than using whole-genome pairwise similarity to determine the shared evolutionary history of these viruses. This is exemplified by RaTG13 which is often described as the “on average” closest Sarbecovirus to SARS-CoV-2 despite not being the closest virus once recombination history is accounted for in the othernCoV Sarbecoviruses (Figure 1A, 3A). > The evidence of recombination events between Sarbecoviruses sampled in different geographical regions and from different bat hosts, indicates recent extensive movement of the viruses between different regions and species (and presumably sub-species too) as a result of the different bat populations that carry them coming into contact with one another. Although very few nCoV viruses are known to be hosted by mammals other than horseshoe bats, the recombination patterns detected within the nCoV genomes imply the existence of one or a few primary reservoir hosts with a geographical range spanning Thailand from the Southwest and Zhejiang to the East, a distribution that is consistent with specific Chinese horseshoe bats being the primary reservoir hosts. Having presented evidence in support of R. affinis and R. pusillus’s potential significance as the reservoir species,it should be noted that at least 20 different Rhinolophus species are distributed across China (four being endemic to China), many of which have not yet been found hosting nCoVs. The generalist nature of Sarbecoviruses also means multiple wild or farmed animals (e.g., minks)[1] could have facilitated transmission of SARS-CoV-2 from bats to humans. > The risk of future emergence of a new SARS-CoV-2 like nCoV strain in humans is too high to restrict sampling strategies. Beyond the relatively rare detection of SARS-like antibodies in people from rural communities in China[34,35],SARS related coronaviruses have not, to our knowledge, seeded outbreaks in humans before. This indicates that there is limited human exposure to these viruses, suggesting ecological “barriers”to their emergence[36]. One possible recent disruption that caused widespread and unusual movements of animals in China and may have increased the permeability of this barrier, was the dramatic shortage of pork products in 2019[37] attributable to an African swine fever virus (ASFV) outbreak impacting 100s of millions of pigs in China[38]. Such a major disruption in the food supply chain will have potentially brought humans into increased contact with Sarbecovirus infected animals as i) exotic meats replaced pork, ii) animals from rural locations were brought to city markets and/or iii) by meat from infected animals being transported in cold chain processes. Further facilitating animal contacts,increased human encroachment into rural areas as a result of new and faster travel networks around and between metropolitan areas have also likely increased opportunities for Sarbecoviruses to spillover into humans.Given the reality of frequent human-animal contact, routine characterisation of respiratory infections would seem a sensible precaution to prevent future emergence of Sarbecoviruses. > The key and most urgent questions relating to the prevention of another emergence, is thus not how did SARS-CoV-2 get from Yunnan to Hubei, but rather which bat or other animal species are harbouring nCoV Sarbecoviruses and what are the risks of a future spillover? There is undoubtedly a virus highly related to SARS-CoV-2 still present somewhere most probably in a bat species in South China or towards Yunnan in the southwest. The best we can do is maximize the probability that future sampling efforts will uncover that host species or sub-species.