> 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.