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The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. We present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and declassifying virus lineages that become unobserved and hence are likely inactive. By focusing on active virus lineages and those spreading to new locations this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.

Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5= and 3= ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination "hot spot" in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances.IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.KEYWORDS Africa, bats, coronavirus, HCoV-229E, HCoV-NL63, recombination, zoonoses C oronaviruses (CoVs) (subfamily Coronavirinae, family Coronaviridae, order Nidovirales) are common infectious agents that infect a wide range of hosts, including humans, causing respiratory, gastrointestinal, liver, and neurologic diseases, and that possess the largest genomes of any RNA viruses described to date (1). The subfamily Coronavirinae is currently classified into four genera: Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus (2). The alphacoronaviruses (alpha-CoVs) and

27The ongoing outbreak of viral pneumonia in China and beyond is associated with a novel 28 coronavirus, provisionally termed 2019-nCoV. This outbreak has been tentatively associated 29 with a seafood market in Wuhan, China, where the sale of wild animals may be the source of 30 zoonotic infection. Although bats are likely reservoir hosts for 2019-nCoV, the identity of 31 any intermediate host facilitating transfer to humans is unknown. Here, we report the 32 identification of 2019-nCoV related coronaviruses in pangolins (Manis javanica) seized in 33 anti-smuggling operations in southern China. Metagenomic sequencing identified pangolin 34 associated CoVs that belong to two sub-lineages of 2019-nCoV related coronaviruses, 35 including one very closely related to 2019-nCoV in the receptor-binding domain. The 36 discovery of multiple lineages of pangolin coronavirus and their similarity to 2019-nCoV 37 suggests that pangolins should be considered as possible intermediate hosts for this novel 38 human virus and should be removed from wet markets to prevent zoonotic transmission.

In the Acknowledgements section of this Article, the grant number 'SQ2019FY010009' should have been '2019FY101500'; this has been corrected online.