Comparative Analysis of Twelve Genomes of Three Novel Group 2c and Group 2d Coronaviruses Reveals Unique Group and Subgroup Features

Abstract

Twelve complete genomes of three novel coronaviruses-bat coronavirus HKU4 (bat-CoV HKU4), bat-CoV HKU5 (putative group 2c), and bat-CoV HKU9 (putative group 2d)-were sequenced. Comparative genome analysis showed that the various open reading frames (ORFs) of the genomes of the three coronaviruses had significantly higher amino acid identities to those of other group 2 coronaviruses than group 1 and 3 coronaviruses. Phylogenetic trees constructed using chymotrypsin-like protease, RNA-dependent RNA polymerase, helicase, spike, and nucleocapsid all showed that the group 2a and 2b and putative group 2c and 2d coronaviruses are more closely related to each other than to group 1 and 3 coronaviruses. Unique genomic features distinguishing between these four subgroups, including the number of papain-like proteases, the presence or absence of hemagglutinin esterase, small ORFs between the membrane and nucleocapsid genes and ORFs (NS7a and NS7b), bulged stem-loop and pseudoknot structures downstream of the nucleocapsid gene, transcription regulatory sequence, and ribosomal recognition signal for the envelope gene, were also observed. This is the first time that NS7a and NS7b downstream of the nucleocapsid gene has been found in a group 2 coronavirus. The high Ka/Ks ratio of NS7a and NS7b in bat-CoV HKU9 implies that these two group 2d-specific genes are under high selective pressure and hence are rapidly evolving. The four subgroups of group 2 coronaviruses probably originated from a common ancestor. Further molecular epidemiological studies on coronaviruses in the bats of other countries, as well as in other animals, and complete genome sequencing will shed more light on coronavirus diversity and their evolutionary histories.

Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae

“…Two genomes each of TV1, TV2 and TV3 were amplified and sequenced using strategies we previously used for complete genome sequencing of other picornaviruses and coronaviruses, with the RNA extracted from the alimentary specimens as templates Woo et al, 2005Woo et al, , 2006aWoo et al, , 2007aWoo et al, , 2009. The RNA was converted to cDNA by a combined randompriming and oligo(dT)-priming strategy.…”

‘One Health’ for the people of Hong Kong and the world

“…Ten years after the identification of the SARS coronavirus, many other groups that jumped into the field after the outbreak of SARS have left, while the teams at the University of Hong Kong continued to make major contributions to the field. The recently identified group 2c human coronavirus EMC associated with one severe and two fatal cases of respiratory syndrome in Saudi Arabia was most closely related to two bat coronaviruses identified by Hong Kong scientists in 2007 (Woo et al, 2007;Zaki et al, 2012). Thus, the findings obtained by scientists at the University of Hong Kong have shaped the field of coronavirus research for years to come.…”

Detection of a respiratory coronavirus from tissues archived during a pneumonia epizootic in free-ranging Pacific harbor seals Phoca vitulina richardsii

“…Dis Aquat Org 90: [113][114][115][116][117][118][119][120] 2010 crochiropteran bat hosts; and Group 2d, from megachiropteran bat hosts (Woo et al 2007). It has been proposed that Group 3 be divided as follows: Groups 3a, from avian hosts; Group 3b, which contains a coronavirus from a beluga whale Delphinapterus leucas, the only coronavirus identified in a marine mammal to date; and Group 3c, which contains viruses from diverse avian hosts as well as one from an Asian leopard cat Prionailurus bengalensis that may represent recent host switching (Woo et al 2009).…”

“…The genus Coronavirus has been divided into 3 groups (González et al 2003). It has been proposed that Group I be subdivided into Groups 1a and 1b (Woo et al 2007); Group 1a has only been found in laurasiatherian mammal hosts, primarily those from the Carnivora, whereas Group 1b has been found in both laurasiatherian and euarchontoglire mammal hosts. It has been proposed that Group 2 be divided into the following groups: Group 2a, which has been found in both laurasiatherian and euarchontoglire mammal hosts; Group 2b, which contains SARS and viruses from microchiropteran bats; Group 2c, from mi-crochiropteran bat hosts; and Group 2d, from megachiropteran bat hosts (Woo et al 2007).…”

“…It has been proposed that Group I be subdivided into Groups 1a and 1b (Woo et al 2007); Group 1a has only been found in laurasiatherian mammal hosts, primarily those from the Carnivora, whereas Group 1b has been found in both laurasiatherian and euarchontoglire mammal hosts. It has been proposed that Group 2 be divided into the following groups: Group 2a, which has been found in both laurasiatherian and euarchontoglire mammal hosts; Group 2b, which contains SARS and viruses from microchiropteran bats; Group 2c, from mi-crochiropteran bat hosts; and Group 2d, from megachiropteran bat hosts (Woo et al 2007). It has been proposed that Group 3 be divided as follows: Groups 3a, from avian hosts; Group 3b, which contains a coronavirus from a beluga whale Delphinapterus leucas, the only coronavirus identified in a marine mammal to date; and Group 3c, which contains viruses from diverse avian hosts as well as one from an Asian leopard cat Prionailurus bengalensis that may represent recent host switching (Woo et al 2009).…”