Coronavirus Diversity, Phylogeny and Interspecies Jumping:
01 Oct 2009-Experimental Biology and Medicine (Exp Biol Med (Maywood))-Vol. 234, Iss: 10, pp 1117-1127
TL;DR: The present evidence supports that bat coronaviruses are the gene pools of group 1 and 2 coronaviraluses, whereas bird coronavirus are the genes of group 3 coronavIRuses.
Abstract: The SARS epidemic has boosted interest in research on coronavirus biodiversity and genomics. Before 2003, there were only 10 coronaviruses with complete genomes available. After the SARS epidemic, up to December 2008, there was an addition of 16 coronaviruses with complete genomes sequenced. These include two human coronaviruses (human coronavirus NL63 and human coronavirus HKU1), 10 other mammalian coronaviruses [bat SARS coronavirus, bat coronavirus (bat-CoV) HKU2, bat-CoV HKU4, bat-CoV HKU5, bat-CoV HKU8, bat-CoV HKU9, bat-CoV 512/2005, bat-CoV 1A, equine coronavirus, and beluga whale coronavirus] and four avian coronaviruses (turkey coronavirus, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13). Two novel subgroups in group 2 coronavirus (groups 2c and 2d) and two novel subgroups in group 3 coronavirus (groups 3b and 3c) have been proposed. The diversity of coronaviruses is a result of the infidelity of RNA-dependent RNA polymerase, high frequency of homologous RNA recombination, and the large genomes of coronaviruses. Among all hosts, the diversity of coronaviruses is most evidenced in bats and birds, which may be a result of their species diversity, ability to fly, environmental pressures, and habits of roosting and flocking. The present evidence supports that bat coronaviruses are the gene pools of group 1 and 2 coronaviruses, whereas bird coronaviruses are the gene pools of group 3 coronaviruses. With the increasing number of coronaviruses, more and more closely related coronaviruses from distantly related animals have been observed, which were results of recent interspecies jumping and may be the cause of disastrous outbreaks of zoonotic diseases.
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TL;DR: The viral factors that enabled the emergence of diseases such as severe acute respiratory syndrome and Middle East respiratory syndrome are explored and the diversity and potential of bat-borne coronaviruses are highlighted.
Abstract: Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are two highly transmissible and pathogenic viruses that emerged in humans at the beginning of the 21st century. Both viruses likely originated in bats, and genetically diverse coronaviruses that are related to SARS-CoV and MERS-CoV were discovered in bats worldwide. In this Review, we summarize the current knowledge on the origin and evolution of these two pathogenic coronaviruses and discuss their receptor usage; we also highlight the diversity and potential of spillover of bat-borne coronaviruses, as evidenced by the recent spillover of swine acute diarrhoea syndrome coronavirus (SADS-CoV) to pigs. Coronaviruses have a broad host range and distribution, and some highly pathogenic lineages have spilled over to humans and animals. Here, Cui, Li and Shi explore the viral factors that enabled the emergence of diseases such as severe acute respiratory syndrome and Middle East respiratory syndrome.
3,970 citations
Shuo Su1, Gary Wong2, Weifeng Shi, Jun Liu3, Jun Liu2, Alexander Lai4, Jiyong Zhou1, Wenjun Liu2, Yuhai Bi2, George F. Gao •
TL;DR: This review aims to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans.
2,268 citations
TL;DR: Data shows that E is involved in critical aspects of the viral life cycle and that CoVs lacking E make promising vaccine candidates, which can aid in the production of effective anti-coronaviral agents for both human CoVs and enzootic CoVs.
Abstract: Coronaviruses (CoVs) primarily cause enzootic infections in birds and mammals but, in the last few decades, have shown to be capable of infecting humans as well. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and, more recently, Middle-East respiratory syndrome (MERS) has demonstrated the lethality of CoVs when they cross the species barrier and infect humans. A renewed interest in coronaviral research has led to the discovery of several novel human CoVs and since then much progress has been made in understanding the CoV life cycle. The CoV envelope (E) protein is a small, integral membrane protein involved in several aspects of the virus’ life cycle, such as assembly, budding, envelope formation, and pathogenesis. Recent studies have expanded on its structural motifs and topology, its functions as an ion-channelling viroporin, and its interactions with both other CoV proteins and host cell proteins. This review aims to establish the current knowledge on CoV E by highlighting the recent progress that has been made and comparing it to previous knowledge. It also compares E to other viral proteins of a similar nature to speculate the relevance of these new findings. Good progress has been made but much still remains unknown and this review has identified some gaps in the current knowledge and made suggestions for consideration in future research. The most progress has been made on SARS-CoV E, highlighting specific structural requirements for its functions in the CoV life cycle as well as mechanisms behind its pathogenesis. Data shows that E is involved in critical aspects of the viral life cycle and that CoVs lacking E make promising vaccine candidates. The high mortality rate of certain CoVs, along with their ease of transmission, underpins the need for more research into CoV molecular biology which can aid in the production of effective anti-coronaviral agents for both human CoVs and enzootic CoVs.
1,502 citations
TL;DR: The epidemiology, virology, clinical features and current treatment strategies of SARS and MERS are summarized, and the discovery and development of new virus-based and host-based therapeutic options for CoV infections are discussed.
Abstract: Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which are caused by coronaviruses, have attracted substantial attention owing to their high mortality rates and potential to cause epidemics. Yuen and colleagues discuss progress with treatment options for these syndromes, including virus- and host-targeted drugs, and the challenges that need to be overcome in their further development. In humans, infections with the human coronavirus (HCoV) strains HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1 usually result in mild, self-limiting upper respiratory tract infections, such as the common cold. By contrast, the CoVs responsible for severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), which were discovered in Hong Kong, China, in 2003, and in Saudi Arabia in 2012, respectively, have received global attention over the past 12 years owing to their ability to cause community and health-care-associated outbreaks of severe infections in human populations. These two viruses pose major challenges to clinical management because there are no specific antiviral drugs available. In this Review, we summarize the epidemiology, virology, clinical features and current treatment strategies of SARS and MERS, and discuss the discovery and development of new virus-based and host-based therapeutic options for CoV infections.
1,388 citations
TL;DR: It appears that bats and birds, the warm blooded flying vertebrates, are ideal hosts for the coronavirus gene source and birds for Gammacoronavirus and Deltacor onavirus, to fuel coronav virus evolution and dissemination.
Abstract: Recently, we reported the discovery of three novel coronaviruses, bulbul coronavirus HKU11, thrush coronavirus HKU12, and munia coronavirus HKU13, which were identified as representatives of a novel genus, Deltacoronavirus, in the subfamily Coronavirinae. In this territory-wide molecular epidemiology study involving 3,137 mammals and 3,298 birds, we discovered seven additional novel deltacoronaviruses in pigs and birds, which we named porcine coronavirus HKU15, white-eye coronavirus HKU16, sparrow coronavirus HKU17, magpie robin coronavirus HKU18, night heron coronavirus HKU19, wigeon coronavirus HKU20, and common moorhen coronavirus HKU21. Complete genome sequencing and comparative genome analysis showed that the avian and mammalian deltacoronaviruses have similar genome characteristics and structures. They all have relatively small genomes (25.421 to 26.674 kb), the smallest among all coronaviruses. They all have a single papain-like protease domain in the nsp3 gene; an accessory gene, NS6 open reading frame (ORF), located between the M and N genes; and a variable number of accessory genes (up to four) downstream of the N gene. Moreover, they all have the same putative transcription regulatory sequence of ACACCA. Molecular clock analysis showed that the most recent common ancestor of all coronaviruses was estimated at approximately 8100 BC, and those of Alphacoronavirus, Betacoronavirus, Gammacoronavirus, and Deltacoronavirus were at approximately 2400 BC, 3300 BC, 2800 BC, and 3000 BC, respectively. From our studies, it appears that bats and birds, the warm blooded flying vertebrates, are ideal hosts for the coronavirus gene source, bats for Alphacoronavirus and Betacoronavirus and birds for Gammacoronavirus and Deltacoronavirus, to fuel coronavirus evolution and dissemination.
1,212 citations
Additional excerpts
...This phenomenon of host specificity is similar to that observed in bats, in which different genera are hosts of different CoVs (26, 45, 51, 52)....
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References
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TL;DR: It is found that a soluble form of ACE2, but not of the related enzyme ACE1, blocked association of the S1 domain with Vero E6 cells, indicating that ACE2 is a functional receptor for SARS-CoV.
Abstract: Spike (S) proteins of coronaviruses, including the coronavirus that causes severe acute respiratory syndrome (SARS), associate with cellular receptors to mediate infection of their target cells Here we identify a metallopeptidase, angiotensin-converting enzyme 2 (ACE2), isolated from SARS coronavirus (SARS-CoV)-permissive Vero E6 cells, that efficiently binds the S1 domain of the SARS-CoV S protein We found that a soluble form of ACE2, but not of the related enzyme ACE1, blocked association of the S1 domain with Vero E6 cells 293T cells transfected with ACE2, but not those transfected with human immunodeficiency virus-1 receptors, formed multinucleated syncytia with cells expressing S protein Furthermore, SARS-CoV replicated efficiently on ACE2-transfected but not mock-transfected 293T cells Finally, anti-ACE2 but not anti-ACE1 antibody blocked viral replication on Vero E6 cells Together our data indicate that ACE2 is a functional receptor for SARS-CoV
5,149 citations
"Coronavirus Diversity, Phylogeny an..." refers background in this paper
...It is also noteworthy that at least one member of group 1b, HCoV-NL63, also uses ACE2 as the receptor for cell entry, as in the case of SARS-CoV, though the site of binding on ACE2 is different (52, 53)....
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Paul A. Rota1, M. Steven Oberste1, Stephan S. Monroe1, W. Allan Nix1, Ray Campagnoli1, Joseph P. Icenogle1, Silvia Peñaranda1, Bettina Bankamp1, Kaija Maher1, Min hsin Chen1, Suxiong Tong1, Azaibi Tamin1, Luis Lowe1, Michael Frace1, Joseph L. DeRisi2, Qi Chen1, David Wang2, Dean D. Erdman1, Teresa C. T. Peret1, Cara C. Burns1, Thomas G. Ksiazek1, Pierre E. Rollin1, Anthony Sanchez1, Stephanie L. Liffick1, Brian P. Holloway1, Josef Limor1, Karen A. McCaustland1, Mellissa Olsen-Rasmussen1, Ron A. M. Fouchier3, Stephan Günther4, Albert Osterhaus3, Christian Drosten4, Mark A. Pallansch1, Larry J. Anderson1, William J. Bellini1 •
TL;DR: Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closelyrelated to any of the previouslycharacterized coronaviruses.
Abstract: In March 2003, a novel coronavirus (SARS-CoV) was discovered in association with cases of severe acute respiratory syndrome (SARS). The sequence of the complete genome of SARS-CoV was determined, and the initial characterization of the viral genome is presented in this report. The genome of SARS-CoV is 29,727 nucleotides in length and has 11 open reading frames, and its genome organization is similar to that of other coronaviruses. Phylogenetic analyses and sequence comparisons showed that SARS-CoV is not closely related to any of the previously characterized coronaviruses.
2,420 citations
"Coronavirus Diversity, Phylogeny an..." refers background or methods in this paper
...When SARS-CoV was first identified and its genome sequenced, it was proposed that it constituted a fourth group of coronavirus (48, 49)....
[...]
...For the E gene, TRS is present in group 2b, 2c, and 2d, but not group 2a, coronaviruses, in which an internal ribosomal entry site is used for their translation (33, 48, 49, 57)....
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TL;DR: It is reported that species of bats are a natural host of coronaviruses closely related to those responsible for the SARS outbreak, and these viruses display greater genetic variation than SARS-CoV isolated from humans or from civets.
Abstract: Severe acute respiratory syndrome (SARS) emerged in 2002 to 2003 in southern China. The origin of its etiological agent, the SARS coronavirus (SARS-CoV), remains elusive. Here we report that species of bats are a natural host of coronaviruses closely related to those responsible for the SARS outbreak. These viruses, termed SARS-like coronaviruses (SL-CoVs), display greater genetic variation than SARS-CoV isolated from humans or from civets. The human and civet isolates of SARS-CoV nestle phylogenetically within the spectrum of SL-CoVs, indicating that the virus responsible for the SARS outbreak was a member of this coronavirus group.
2,263 citations
"Coronavirus Diversity, Phylogeny an..." refers background in this paper
...The discovery of bat-SARS-CoV has marked the beginning of the race of coronavirus hunting in bats (31, 34)....
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...In 2005, we and others described the discovery of SARS-CoV–like viruses from at least four species of horseshoe bats in Hong Kong (Rhinolophus sinicus) and mainland China (Rhinolophus ferrumequinum, Rhinolophus macrotis, and Rhinolophus pearsoni) (31, 34)....
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Marco A. Marra, Steven J.M. Jones, Caroline R. Astell, Robert A. Holt, Angela Brooks-Wilson, Yaron S.N. Butterfield, Jaswinder Khattra, Jennifer Asano, Sarah Barber, Susanna Y. Chan, Alison Cloutier, Shaun M. Coughlin, Doug Freeman, Noreen Girn, Obi L. Griffith, Stephen Leach, Michael Mayo, Helen McDonald, Stephen B. Montgomery, Pawan Pandoh, Anca Petrescu, A. Gordon Robertson, Jacqueline E. Schein, Asim Siddiqui, Duane E. Smailus, Jeff M. Stott, George S. Yang, Francis A. Plummer, Anton Andonov, Harvey Artsob, Nathalie Bastien, Kathy Bernard, Timothy F. Booth, Donnie Bowness, Martin Czub, Michael Drebot, Lisa Fernando, Ramon Flick, Michael Garbutt, Michael Gray, Allen Grolla, Steven M. Jones, Heinz Feldmann, Adrienne Meyers, Amin Kabani, Yan Li, Susan Normand, Ute Ströher, Graham A. Tipples, Shaun Tyler, Robert Vogrig, Diane M. Ward, Brynn Watson, Robert C. Brunham, Mel Krajden, Martin Petric, Danuta M. Skowronski, Chris Upton, Rachel L. Roper
TL;DR: The genome sequence reveals that the severe acute respiratory syndrome–associated coronavirus known as the Tor2 isolate is only moderately related to other known coronaviruses, andylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronavirs.
Abstract: We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.
2,056 citations
"Coronavirus Diversity, Phylogeny an..." refers background or methods in this paper
...When SARS-CoV was first identified and its genome sequenced, it was proposed that it constituted a fourth group of coronavirus (48, 49)....
[...]
...For the E gene, TRS is present in group 2b, 2c, and 2d, but not group 2a, coronaviruses, in which an internal ribosomal entry site is used for their translation (33, 48, 49, 57)....
[...]
TL;DR: A new group 1 coronavirus, HCoV-NL63, was identified in a 7-month-old child suffering from bronchiolitis and conjunctivitis as discussed by the authors.
Abstract: Three human coronaviruses are known to exist: human coronavirus 229E (HCoV-229E), HCoV-OC43 and severe acute respiratory syndrome (SARS)-associated coronavirus (SARS-CoV). Here we report the identification of a fourth human coronavirus, HCoV-NL63, using a new method of virus discovery. The virus was isolated from a 7-month-old child suffering from bronchiolitis and conjunctivitis. The complete genome sequence indicates that this virus is not a recombinant, but rather a new group 1 coronavirus. The in vitro host cell range of HCoV-NL63 is notable because it replicates on tertiary monkey kidney cells and the monkey kidney LLC-MK2 cell line. The viral genome contains distinctive features, including a unique N-terminal fragment within the spike protein. Screening of clinical specimens from individuals suffering from respiratory illness identified seven additional HCoV-NL63-infected individuals, indicating that the virus was widely spread within the human population.
1,496 citations
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