Animal Reservoirs and Hosts for Emerging Alpha- and Betacoronaviruses
Ria R. GhaiAnn CarpenterMeghan K. HerringKrystalyn MartinSusan I. GerberAron J. HallAmanda LiewJonathan M. SleemanSophie VonDobschuetzCasey Barton Behravesh
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The ongoing global pandemic caused by coronavirus disease 2019 (COVID-19) has once again demonstrated the significance of the Coronaviridae family in causing human disease outbreaks. As SARS-CoV-2 was first detected in December 2019, information on its tropism, host range, and clinical presentation in animals is limited. Given the limited information, data from other coronaviruses may be useful to inform scientific inquiry, risk assessment and decision-making. We review the endemic and emerging alpha- and betacoronavirus infections of wildlife, livestock, and companion animals, and provide information on the receptor usage, known hosts, and clinical signs associated with each host for 15 coronaviruses discovered in people and animals. This information can be used to guide implementation of a One Health approach that involves human health, animal health, environmental, and other relevant partners in developing strategies for preparedness, response, and control to current and future coronavirus disease threats.Keywords:
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The city of Wuhan, Hubei province, China, was the origin of a severe pneumonia outbreak in December 2019, attributed to a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]), causing a total of 2761 deaths and 81109 cases (25 February 2020). SARS-CoV-2 belongs to genus Betacoronavirus, subgenus Sarbecovirus. The polyprotein 1ab (pp1ab) remains unstudied thoroughly since it is similar to other sarbecoviruses. In this short communication, we performed phylogenetic-structural sequence analysis of pp1ab protein of SARS-CoV-2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was found in a virus isolated from a Japanese patient that did not display critical symptoms. While comparing pp1ab protein with other betacoronaviruses, we found a 42 amino acid signature that is only present in SARS-CoV-2 (AS-SCoV2). Members from clade 2 of sarbecoviruses have traces of this signature. The AS-SCoV2 located in the acidic-domain of papain-like protein of SARS-CoV-2 and bat-SL-CoV-RatG13 guided us to suggest that the novel 2019 coronavirus probably emerged by genetic drift from bat-SL-CoV-RaTG13. The implication of this amino acid signature in papain-like protein structure arrangement and function is something worth to be explored.
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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has reignited global interest in animal coronaviruses and their potential for human transmission. While bats are thought to be the wildlife reservoir of SARS-CoV and SARS-CoV-2, the widespread human coronavirus OC43 is thought to have originated in rodents. Here, we sampled 297 rodents and shrews, representing eight species, from three municipalities of southern China. We report coronavirus prevalences of 23.3% and 0.7% in Guangzhou and Guilin, respectively, with samples from urban areas having significantly higher coronavirus prevalences than those from rural areas. We obtained three coronavirus genome sequences from Rattus norvegicus, including a Betacoronavirus (rat coronavirus [RCoV] GCCDC3), an Alphacoronavirus (RCoV-GCCDC5), and a novel Betacoronavirus (RCoV-GCCDC4). Recombination analysis suggests that there was a potential recombination event involving RCoV-GCCDC4, murine hepatitis virus (MHV), and Longquan Rl rat coronavirus (LRLV). Furthermore, we uncovered a polybasic cleavage site, RARR, in the spike (S) protein of RCoV-GCCDC4, which is dominant in RCoV. These findings provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the value of a One Health approach to virus discovery. IMPORTANCE Surveillance of viruses among rodents in rural and urban areas of South China identified three rodent coronaviruses, RCoV-GCCDC3, RCoV-GCCDC4, and RCoV-GCCDC5, one of which was identified as a novel potentially recombinant coronavirus with a polybasic cleavage site in the spike (S) protein. Through reverse transcription-PCR (RT-PCR) screening of coronaviruses, we found that coronavirus prevalence in urban areas is much higher than that in rural areas. Subsequently, we obtained three coronavirus genome sequences by deep sequencing. After different method-based analyses, we found that RCoV-GCCDC4 was a novel potentially recombinant coronavirus with a polybasic cleavage site in the S protein, dominant in RCoV. This newly identified coronavirus RCoV-GCCDC4 with its potentially recombinant genome and polybasic cleavage site provides a new insight into the evolution of coronaviruses. Furthermore, our results provide further information on the potential for interspecies transmission of coronaviruses and demonstrate the necessity of a One Health approach for zoonotic disease surveillance.
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The 2019 novel Coronavirus (2019-nCoV) has caused the pneumonia outbreak in Wuhan (a city of China) In our previous study, the analytical results showed that both 2019-nCoV and SARS coronavirus belong to Betacoronavirus subgroup B (BB coronavirus), but have large differences, which are consistent with the differences in the clinical symptoms of two related diseases The most important finding was that the alternative translation of Nankai CDS could produce more than 17 putative proteins, which may be responsible for the host adaption The genotyping of 13 viruses using the 17 putative proteins revealed the high mutation rate and diversity of BB coronavirus The present study for the first time (on January 21st, 2020) reported a very important mutation in the Spike (S) proteins of Betacoronavirus By this mutation, 2019-nCoV acquired a cleavage site for furin enzyme in its S protein, which is not present in the S proteins of most other Betacoronavirus (e g SARS coronavirus) This cleavage site may increase the efficiency of virus infection into cells, making 2019-nCoV has significantly stronger transmissibility than SARS coronavirus The infection mechanism of 2019-nCoV may be changed to being more similar to those of MHV, HIV, Ebola virus (EBoV) and some avian influenza viruses, other than those of most other Betacoronavirus (e g SARS coronavirus) In addition, we unexpectedly found that some avian influenza viruses acquired a cleavage site for furin enzyme by the similar mutation as 2019-nCoV Therefore, the natural mutation can result in a short insertion to form a cleavage site for furin enzyme The cleavage site for furin enzyme in 2019-nCoV contains the CGGCGG sequence encoding two arginine (R) residues CGG, however, is a rare codon for human So we concluded that these two codons were present in the 2019-nCoV -like Betacoronavirus before they transmitted into human and the intermediate host (s) are mammals with a high relative frequency of usage We provide a relative frequency table of CGG usage in mammals to help identify the intermediate hosts of 2019-nCoV Future studies of this mutation will help to reveal the stronger transmissibility of 2019-nCoV and lay foundations for vaccine development and drug design of, but not limited to 2019-nCoV
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Coronaviruses are a class of RNA viruses that can cause respiratory and intestinal infections in animals and humans. SARS-CoV, MERS-CoV, and a novel coronavirus (SARS-CoV-2 [2019-nCoV]) belong to the family Coronaviridae and the genus Betacoronavirus. At present, the understanding of SARS-CoV-2 is getting deeper and deeper. In order to better prevent and treat SARS-CoV-2, this article compares the infectivity, pathogenicity, and related clinical characteristics of the three human pathogenic coronaviruses, SARS-CoV-2, SARS-CoV, and MERS-CoV to help us further understand the pathogenic characteristics of novel coronaviruses.
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A cluster of cases of pneumonia caused by a novel coronavirus, COVID-19, was first reported in Wuhan in the Hubei province in China in late December 2019. Since then, several thousand cases have been reported in mainland China, with spread to over two dozen countries. Although many comparisons to other coronavirus epidemics have been made, the potential impact of this coronavirus is uncertain. We seek to summarize what is known about COVID-19, compare this epidemic to prior coronavirus outbreaks, and provide a primer on novel coronaviruses for practicing clinicians. Coronaviruses are widespread among mammals and birds. The widest varieties of genotypes infect bats, but 2 subtypes infect humans: alpha and beta coronaviruses.1Chan J.F. Lau S.K. To K.K. Cheng V.C. Woo P.C. Yuen K.Y. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease.Clin Microbiol Rev. 2015; 28: 465-522Crossref PubMed Scopus (663) Google Scholar Beta coronaviruses include severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the coronavirus variant COVID-19 virus first described in Wuhan. In humans, these coronaviruses have short incubation periods, ranging from days for SARS-CoV and weeks for MERS-CoV, with the COVID-19 appearing to fall in between the two.2Imai N. Dorigatti I. Cori A. Riley S. Ferguson N.M. Estimating the potential total number of novel coronavirus (COVID-19) cases in Wuhan City, China. Imperial College London, London, UKJanuary 17, 2020Google Scholar,3World Health OrganizationNovel coronavirus (COVID-19). World Health Organization website.https://www.who.int/emergencies/diseases/novel-coronavirus-2019Date: Published 2020Date accessed: January 27, 2020Google Scholar Although information about the COVID-19 is emerging, SARS-CoV and MERS-CoV provide some context for understanding the public health significance of coronaviruses. SARS-CoV was first noted in the Guangdong province of China in November 2002.4Christian M.D. Poutanen S.M. Loutfy M.R. Muller M.P. Low D.E. Severe acute respiratory syndrome.Clin Infect Dis. 2004; 38: 1420-1427Crossref PubMed Scopus (184) Google Scholar,5Peiris J.S. Yuen K.Y. Osterhaus A.D. Stohr K. The severe acute respiratory syndrome.N Engl J Med. 2003; 349: 2431-2441Crossref PubMed Scopus (1025) Google Scholar The index case was a physician from that province who then traveled to Hong Kong and infected several others. Subsequently, SARS-CoV resulted in over 8000 cases and approximately 750 deaths occurred worldwide over the next several months. The outbreak finally ended in July 2003.4Christian M.D. Poutanen S.M. Loutfy M.R. Muller M.P. Low D.E. Severe acute respiratory syndrome.Clin Infect Dis. 2004; 38: 1420-1427Crossref PubMed Scopus (184) Google Scholar, 5Peiris J.S. Yuen K.Y. Osterhaus A.D. Stohr K. The severe acute respiratory syndrome.N Engl J Med. 2003; 349: 2431-2441Crossref PubMed Scopus (1025) Google Scholar, 6World Health Organization. Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003. World Health Organization website. http://www.who.int/csr/sars/country/table2004_04_21/en/index.html. Accessed January 27, 2020.Google Scholar Severe acute respiratory syndrome coronavirus typically presented with fever and symptoms of lower respiratory tract infection with radiographic evidence of pneumonia or acute respiratory distress syndrome (ARDS). SARS-CoV disproportionately impacted health care workers (HCWs) in countries with the most reported cases. However, in countries with relatively few cases, transmission was much rarer. This finding suggests that infection control measures are adequate to interrupt transmission to HCWs, but consistency is critical because the greater number of opportunities for lapses in the hardest hit centers likely led to more HCW infections.7Park B.J. Peck A.J. Kuehnert M.J. et al.Lack of SARS transmission among healthcare workers, United States.Emerg Infect Dis. 2004; 10: 244-248Crossref PubMed Scopus (64) Google Scholar The incubation period of SARS-CoV is between 2 and 10 days.8Sampathkumar P. Temesgen Z. Smith T.F. Thompson R.L. SARS: epidemiology, clinical presentation, management, and infection control measures.Mayo Clin Proc. 2003; 78: 882-890Abstract Full Text Full Text PDF PubMed Scopus (69) Google Scholar Diagnosis is based on polymerase chain reaction testing. Treatments attempted included corticosteroids and ribavirin, which were not found to be beneficial. Supportive care remains the cornerstone of care for SARS-CoV, although in vitro studies suggest that antivirals developed in the wake of the Ebola virus epidemic may inhibit SARS-CoV replication as well.9Agostini M.L. Andres E.L. Sims A.C. et al.Coronavirus susceptibility to the antiviral remdesivir (GS-5734) is mediated by the viral polymerase and the proofreading exoribonuclease.mBio. 2018; 9: e00221-e00228Crossref PubMed Scopus (1015) Google Scholar MERS-CoV was first reported in September 2012.10Zaki A.M. van Boheemen S. Bestebroer T.M. Osterhaus A.D. Fouchier R.A. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia [published correstion appears in N Engl J Med. 2013;369(4):394].N Engl J Med. 2012; 367: 1814-1820Crossref PubMed Scopus (4156) Google Scholar The virus was isolated from sputum of a man in Saudi Arabia hospitalized with a respiratory tract infection.10Zaki A.M. van Boheemen S. Bestebroer T.M. Osterhaus A.D. Fouchier R.A. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia [published correstion appears in N Engl J Med. 2013;369(4):394].N Engl J Med. 2012; 367: 1814-1820Crossref PubMed Scopus (4156) Google Scholar Since then, more than 2400 cases of MERS-CoV have been reported to the World Health Organization (WHO) in and around the Arabian Peninsula.11Sampathkumar P. Middle East respiratory syndrome: what clinicians need to know.Mayo Clin Proc. 2014; 89: 1153-1158Abstract Full Text Full Text PDF PubMed Scopus (18) Google Scholar Periodic infections and localized outbreaks have continued. Similar to SARS-CoV, presentation is typically fever with symptoms of lower respiratory tract infection and radiographic evidence of pneumonia or ARDS. Other manifestations might include renal failure, anorexia, nausea, vomiting, diarrhea, abdominal pain, and disseminated intravascular coagulation. Again, HCWs were disproportionately infected, although a large number of those cases were mild or asymptomatic.7Park B.J. Peck A.J. Kuehnert M.J. et al.Lack of SARS transmission among healthcare workers, United States.Emerg Infect Dis. 2004; 10: 244-248Crossref PubMed Scopus (64) Google Scholar The incubation period of MERS-CoV ranges from 1 to 14 days. Diagnosis is made by identifying the virus in respiratory samples by polymerase chain reaction testing. Treatment is largely supportive,11Sampathkumar P. Middle East respiratory syndrome: what clinicians need to know.Mayo Clin Proc. 2014; 89: 1153-1158Abstract Full Text Full Text PDF PubMed Scopus (18) Google Scholar focusing on management of complications of sepsis and ARDS in intensive care units. Antivirals such as ribavirin and interferon-based treatments have had questionable benefit, but the role for these treatments remains experimental.12Arabi Y.M. Balkhy H.H. Hayden F.G. et al.Middle East respiratory syndrome.N Engl J Med. 2017; 376: 584-594Crossref PubMed Scopus (313) Google Scholar Most recently, a novel strain of the coronavirus, COVID-19, was identified in Wuhan, a city in the Hubei province of China.3World Health OrganizationNovel coronavirus (COVID-19). World Health Organization website.https://www.who.int/emergencies/diseases/novel-coronavirus-2019Date: Published 2020Date accessed: January 27, 2020Google Scholar Initial cases were associated with a seafood market that also sold live animals.2Imai N. Dorigatti I. Cori A. Riley S. Ferguson N.M. Estimating the potential total number of novel coronavirus (COVID-19) cases in Wuhan City, China. Imperial College London, London, UKJanuary 17, 2020Google Scholar The seafood market was shut down and disinfected to contain what was thought to be a zoonotic infection, ie, one that is transmitted from animals to humans. Despite this intervention, the reported number of persons infected increased rapidly, and on January 21, 2020, Chinese health authorities first reported human-to-human transmission including transmission to HCWs. Since then, case counts have been increasing rapidly.13Centers for Disease Control and PreventionLesson 6: Investigating an outbreak. Centers for Disease Control and Prevention website.https://www.cdc.gov/csels/dsepd/ss1978/lesson6/section2.htmlDate accessed: January 27, 2020Google Scholar Cases have now been reported outside mainland China, with the spread of cases internationally to several countries in Asia, Europe, North America, and to Australia. Person to person transmission has been reported to family members, other close contacts, and to HCWs. Initial reports suggest an incubation period similar to the incubation period of SARS-CoV and MERS-CoV.2Imai N. Dorigatti I. Cori A. Riley S. Ferguson N.M. Estimating the potential total number of novel coronavirus (COVID-19) cases in Wuhan City, China. Imperial College London, London, UKJanuary 17, 2020Google Scholar The clinical features are also rather similar to these viruses: fever, cough, chest tightness, dyspnea, and difficulty breathing.14Huang C. Wang Y. Li X. et al.Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China [published online ahead of print January 24, 2020].https://doi.org/10.1016/S0140-6736(20)30183-5Google Scholar,15Zhu N. Zhang D. Wang W. et al.A novel coronavirus from patients with pneumonia in China, 2019 [published online ahead of print January 24, 2020].https://doi.org/10.1056/NEJMoa2001017Google Scholar Severe cases with ARDS have been reported, with this being a leading reason for admission to the intensive care unit.2Imai N. Dorigatti I. Cori A. Riley S. Ferguson N.M. Estimating the potential total number of novel coronavirus (COVID-19) cases in Wuhan City, China. Imperial College London, London, UKJanuary 17, 2020Google Scholar Gastrointestinal symptoms have been reported in 10% of cases, a higher proportion than seen with other coronaviruses. The novel coronavirus also is associated with fewer upper respiratory tract symptoms and lower respiratory symptoms than other coronaviruses.14Huang C. Wang Y. Li X. et al.Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China [published online ahead of print January 24, 2020].https://doi.org/10.1016/S0140-6736(20)30183-5Google Scholar Fever is a prominent symptom, present in 98.6% of cases.16Wang D. Hu B. Hu C. et al.Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. [published online ahead of print February 7, 2020].https://doi.org/10.1001/jama.2020.1585Google Scholar Between 20% and 25% require intensive care unit admission. Patients admitted to ICU had higher serum white blood cell counts, lower serum albumin, liver function test disorders, and higher D-dimer.14Huang C. Wang Y. Li X. et al.Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China [published online ahead of print January 24, 2020].https://doi.org/10.1016/S0140-6736(20)30183-5Google Scholar Significantly, severe cases appear to cluster in the elderly, and thus far, severe disease has not been widely reported in children.16Wang D. Hu B. Hu C. et al.Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. [published online ahead of print February 7, 2020].https://doi.org/10.1001/jama.2020.1585Google Scholar The Centers for Disease Control and Prevention (CDC) has issued interim guidance for HCWs.17Centers for Disease Control and Prevention2019 Novel coronavirus: interim guidance for healthcare professionals. Centers for Disease Control and Prevention website.https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-criteria.htmlGoogle Scholar Novel coronavirus should be suspected if patients meet the criteria described in Table 1. The WHO uses similar criteria for case identification.Table 1COVID-19 Diagnosis Criteria to Serve as Guidance for EvaluationAdapted from the Centers for Disease Control and Prevention.16Wang D. Hu B. Hu C. et al.Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in Wuhan, China. [published online ahead of print February 7, 2020].https://doi.org/10.1001/jama.2020.1585Google ScholarCOVID-19 Clinical featuresCOVID-19 Epidemiological riskFever AND symptoms of lower respiratory tract illness including, but not limited to, cough, difficulty breathing →AND any one of the following: (a) In the past 14 days (before symptom onset), a history of travel from Wuhan City, ChinaOR (b) In the past 14 days (before symptom onset), close contact with a person who is under investigation for COVID-19 while that person was illFever OR symptoms of lower respiratory tract illness including, but not limited to, cough, difficulty breathing →AND In the past 14 days (before symptom onset), close contact with an ill patient with laboratory-confirmed COVID-19COVID-19 = 2019 novel coronavirus. Open table in a new tab COVID-19 = 2019 novel coronavirus. The current approach includes early diagnosis and identification, prevention of spread, and management of complications.18World Health Organization Infection prevention and control. World Health Organization website.https://www.who.int/csr/disease/coronavirus_infections/prevention_control/en/Date: Published 2020Date accessed: January 27, 2020Google Scholar Optimal supportive care with appropriate isolation and infection control precautions are cornerstones of treatment. Health care professionals who encounter suspected cases should contact local infection control and public health offices regarding potential cases and appropriate next steps based on regional resources and protocols. Many unknowns remain regarding COVID-19. The exact mode of transmission has not been established. It appears that most transmission occurs by droplet spread, ie, large droplets that are generated when a patient coughs or sneezes. Protection against this type of transmission involves use of face masks with eye protection, gloves, gowns, and hand hygiene. There is concern that airborne transmission may also be playing a role. This possibility is more problematic because airborne infectious particles can remain suspended in the air for long periods, the infection can be transmitted to larger numbers of people including those not in close contact with the index case, and protective measures include wearing a respirator and patient placement in negative air pressure rooms that may not be available at all medical centers. At the present time, the CDC recommends a combination of airborne precautions (patient placement in a negative air pressure room, HCWs to wear respirators), contact precautions (HCWs to wear gloves and gowns for all patient contact), and use of eye protection for patients hospitalized with suspected COVID-19 infection. An initial report suggested transmission from an asymptomatic individual to several other people who attended business meetings with the index case. This has since been reported to be inaccurate.19Rothe C. Schunk M. Sothmann P. et al.Transmission of 2019-nCoV infection from an asymptomatic contact in Germany [published online ahead of print January 30, 2020].N Engl J Med. 2020; https://doi.org/10.1056/NEJMc2001468Crossref PubMed Scopus (2797) Google Scholar Table 2 presents a comparison of clinical symptoms of the 3 coronavirus strains that have caused worldwide outbreaks. As more cases are identified, the epidemiology and clinical characteristics of this disease will be better elucidated.Table 2Comparison of Clinical Symptoms and Public Health Characteristics of 3 Coronavirus StrainsCharacteristicSARS-CoV (2002-2003)MERS-CoV (2012-2013)COVID-19 (2019-2020)Clinical presentation(1) Fever(1) Pneumonia(1) Fever, cough, dyspnea(2) Symptoms of lower respiratory tract infection (cough, dyspnea, difficulty breathing)(2) Renal injury(2) Radiologic evidence of pneumonia(3) Radiologic evidence of pneumonia or ARDS(3) ARDS(3) ARDS(4) Diarrhea(5) VomitingIncubation period2-10 d1-14 d5-7 d (per initial reports)Geographic locationChinaArabian PeninsulaAustraliaHong KongUnited States (2 imported cases)BelgiumCanadaSouth Korea (MERS-CoV outbreak in 2015)CambodiaSingaporeCanadaVietnamChina (including Hong Kong and Macau)FinlandFranceGermanyIndiaItalyJapanMalaysiaNepalNepalSingaporeSouth KoreaSpainSri LankaSwedenTaiwanThailandUnited Arab EmiratesUnited KingdomUnited StatesVietnamCases8096246837,592aAs of February 9, 2020.Case fatality rate14%-15%20Yanan W. Moritsugu K. Human-to-human transmission confirmed in China coronavirus. AP News website.https://apnews.com/14d7dcffa205d9022fa9ea593bb2a8c5Google Scholar35%12Arabi Y.M. Balkhy H.H. Hayden F.G. et al.Middle East respiratory syndrome.N Engl J Med. 2017; 376: 584-594Crossref PubMed Scopus (313) Google Scholar2.2%aAs of February 9, 2020.ARDS = acute respiratory distress syndrome; MERS-CoV = Middle East respiratory syndrome coronavirus; COVID-19 = 2019 novel coronavirus; SARS-CoV = severe acute respiratory syndrome coronavirus.a As of February 9, 2020. Open table in a new tab ARDS = acute respiratory distress syndrome; MERS-CoV = Middle East respiratory syndrome coronavirus; COVID-19 = 2019 novel coronavirus; SARS-CoV = severe acute respiratory syndrome coronavirus. The release of the viral genome sequence has made it possible for the CDC to create a rapid molecular diagnostic test for COVID-19. The test received expedited approval from the FDA and the test is being made available to state health departments and selected commercial laboratories. At this time the test is only performed at the CDC but it is likely that the test will be made available at several state health departments in the near feature. The currently available diagnostic tests for other coronaviruses (eg, FilmArray Respiratory Panel [BioFire Diagnostics]) do not detect the COVID-19. Because of the potential for transmission to laboratory workers from patient specimens, the CDC recommends that laboratory workers use a class 2 biological safety cabinet and personal protective equipment when processing specimens with potential to generate fine particulate matter. Decontamination of work surfaces and equipment with Environmental Protection Agency–registered hospital disinfectant is of paramount importance.21Roos R. Estimates of SARS death rates revised upward. University of Minnesota Center for Infectious Disease Research and Policy website.http://www.cidrap.umn.edu/news-perspective/2003/05/estimates-sars-death-rates-revised-upwardGoogle Scholar When transporting suspected case specimens, the International Air Transport Association guidelines for dangerous goods must be followed.21Roos R. Estimates of SARS death rates revised upward. University of Minnesota Center for Infectious Disease Research and Policy website.http://www.cidrap.umn.edu/news-perspective/2003/05/estimates-sars-death-rates-revised-upwardGoogle Scholar Chinese officials closed the fish market initially suspected as the source of the virus on January 1, 2020. On January 20, China confirmed human to human transmission of this virus.22Centers for Disease Control and PreventionInterim laboratory biosafety guidelines for handling and processing specimens associated with 2019 novel coronavirus (COVID-19). Centers for Disease Control and Prevention website.https://www.cdc.gov/coronavirus/COVID-19/lab-biosafety-guidelines.htmlGoogle Scholar,23Wuhan Tianhe Airport was put into operation on April 15, 1995. CNHubei website.https://web.archive.org/web/20171107024254/http://www.cnhubei.com/xwzt/2008zt/hbgg30y/bhdss/tianhe/fazhan/200804/t287403.shtmlGoogle Scholar On January 23, the Chinese government suspended air, road, and rail travel in the area around Wuhan in an effort to limit the spread outside the city over the Chinese New Year, traditionally a very busy time to travel. In addition, public gatherings for New Year festivities were banned all over the country. Over the next few days, quarantine orders were extended to cover the entire province of Hubei. Despite these stringent measures, case counts continued to rise within China, and several countries including the United States reported imported cases. On January 30, the WHO declared that the COVID-19 outbreak was a public health emergency of international consequence (PHEIC). On January 31, the United States announced that it would bar entry of foreign nationals who had visited China and quarantine United States citizens arriving from China for 14 days. Simultaneously, several major United States airlines suspended flights to mainland China. Since then several other nations have imposed similar travel bans. However, at the time of this writing over 35,000 cases have been confirmed in 28 countries and there have been more than 800 deaths.24Civil Aviation Administration of ChinaStatistics of key performance indicators for China's civil aviation industry in October 2019. Civil Aviation Administration of China website.http://www.caac.gov.cn/en/HYYJ/SJ/201912/t20191223_199948.htmlGoogle Scholar, 25Coronavirus what airport measures are in place to detect sick passengers? The Guardian website.https://www.theguardian.com/world/2020/jan/18/coronavirus-what-airport-measures-are-in-place-to-detect-for-sick-passengersGoogle Scholar, 26Ahmed I. Roxburgh H. US confirms first case of China virus as death toll reaches six. International Business Times website.https://www.ibtimes.com/china-says-virus-spreading-between-humans-who-set-meet-2906266Google Scholar China was initially lauded for its efforts to control the outbreak, including the construction of a 1000 bed medical facility in less than 10 days. More recently, the death of a Chinese physician Li Wenlinag, who was reprimanded by Chinese authorities for sounding the alarm about a cluster of pneumonia in December, has rekindled misgivings about how China is handling the situation. At the time of this report, there have been more than 35,000 confirmed cases of COVID-19, with more than 800 confirmed deaths (Figure).27Visual and Data Journalism TeamCoronavirus: a visual guide to the outbreak. BBC News website.https://www.bbc.com/news/world-51235105Google Scholar,28Talmazan Y. Baculinao E. Chen L. Abbas M. China coronavirus death toll climbs to 106 as government scrambles to contain outbreak. NBC News website.https://www.nbcnews.com/news/world/china-coronavirus-death-toll-climbs-80-government-scrambles-contain-outbreak-n1123561Google Scholar Deaths appear to be occurring predominantly in the elderly, with a median age of 75 years in reported cases, but lately, younger patients have died as well. The COVID-19 has resulted in a large outbreak of febrile respiratory illness originating in mainland China. There are still many unknowns: mode of transmission, risk factors for infection and mortality, and whether there is a nonhuman reservoir that could cause additional outbreaks. China has taken unprecedented measures to contain the infection by quarantining large cities, imposing bans on mass gatherings, and canceling public events associated with the Chinese New Year. Travel bans imposed by several countries have slowed, but not completely eliminated, the spread outside of China. In addition to the suffering and loss of life, the impact on the global supply chain is likely to be very significant as China as a whole, and Wuhan in particular, are major manufacturing hubs.
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ABSTRACT We discovered a novel Betacoronavirus lineage A coronavirus, China Rattus coronavirus (ChRCoV) HKU24, from Norway rats in China. ChRCoV HKU24 occupied a deep branch at the root of members of Betacoronavirus 1 , being distinct from murine coronavirus and human coronavirus HKU1. Its unique putative cleavage sites between nonstructural proteins 1 and 2 and in the spike (S) protein and low sequence identities to other lineage A betacoronaviruses (βCoVs) in conserved replicase domains support ChRCoV HKU24 as a separate species. ChRCoV HKU24 possessed genome features that resemble those of both Betacoronavirus 1 and murine coronavirus, being closer to Betacoronavirus 1 in most predicted proteins but closer to murine coronavirus by G+C content, the presence of a single nonstructural protein (NS4), and an absent transcription regulatory sequence for the envelope (E) protein. Its N-terminal domain (NTD) demonstrated higher sequence identity to the bovine coronavirus (BCoV) NTD than to the mouse hepatitis virus (MHV) NTD, with 3 of 4 critical sugar-binding residues in BCoV and 2 of 14 contact residues at the MHV NTD/murine CEACAM1a interface being conserved. Molecular clock analysis dated the time of the most recent common ancestor of ChRCoV HKU24, Betacoronavirus 1 , and rabbit coronavirus HKU14 to about the year 1400. Cross-reactivities between other lineage A and B βCoVs and ChRCoV HKU24 nucleocapsid but not spike polypeptide were demonstrated. Using the spike polypeptide-based Western blot assay, we showed that only Norway rats and two oriental house rats from Guangzhou, China, were infected by ChRCoV HKU24. Other rats, including Norway rats from Hong Kong, possessed antibodies only against N protein and not against the spike polypeptide, suggesting infection by βCoVs different from ChRCoV HKU24. ChRCoV HKU24 may represent the murine origin of Betacoronavirus 1 , and rodents are likely an important reservoir for ancestors of lineage A βCoVs. IMPORTANCE While bats and birds are hosts for ancestors of most coronaviruses (CoVs), lineage A βCoVs have never been found in these animals and the origin of Betacoronavirus lineage A remains obscure. We discovered a novel lineage A βCoV, China Rattus coronavirus HKU24 (ChRCoV HKU24), from Norway rats in China with a high seroprevalence. The unique genome features and phylogenetic analysis supported the suggestion that ChRCoV HKU24 represents a novel CoV species, occupying a deep branch at the root of members of Betacoronavirus 1 and being distinct from murine coronavirus. Nevertheless, ChRCoV HKU24 possessed genome characteristics that resemble those of both Betacoronavirus 1 and murine coronavirus. Our data suggest that ChRCoV HKU24 represents the murine origin of Betacoronavirus 1 , with interspecies transmission from rodents to other mammals having occurred centuries ago, before the emergence of human coronavirus (HCoV) OC43 in the late 1800s. Rodents are likely an important reservoir for ancestors of lineage A βCoVs.
Betacoronavirus
Coronavirus
Bovine coronavirus
Mouse hepatitis virus
Coronaviridae
Lineage (genetic)
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因为 20022003 严重急性呼吸症候群(SARS ) 爆发为 SARS coronavirus 的自然水库推动了搜索，众多的 alpha- 和 betacoronaviruses 在全世界在蝙蝠被发现了。蝙蝠是可能的 alpha- 和 betacoronaviruses 的自然水库，并且由于富有的差异和蝙蝠的全球分发，蝙蝠 coronaviruses 的数字将多半增加。我们在 Mojiang 县在放弃的 mineshaft 在蝙蝠进行了 coronaviruses 的监视，云南省，中国，从 20122013。六蝙蝠种经常在洞被检测：Rhinolophus sinicus， Rhinolophus affinis， Hipposideros pomona， Miniopterus schreibersii， Miniopterus fuliginosus，和 Miniopterus fuscus。由定序 coronavirus 的 PCR 产品 RNA 依赖的 RNA 聚合酶基因(RdRp ) ，我们在 mineshaft 在不同蝙蝠种类由 coronaviruses 的一个多样的组发现了感染的高频率。定序的部分 RdRp 碎片与描绘得好的 Alphacoronavirus 种类有 80%99% nucleic 酸顺序身份，包括 BtCoV HKU2， BtCoV HKU8，和 BtCoV1，和未赋值的种类 BtCoV HKU7 和 BtCoV HKU10。另外，监视识别了二未分类的 betacoronaviruses，象 SARS 一样 coronavirus 的一个新种类，和一潜在地新的 betacoronavirus 种。而且， coronavirus 合作感染在所有六蝙蝠种被检测，促进再结合并且支持新奇病毒的出现的现象拉紧。我们的调查结果作为 coronaviruses 的自然水库强调蝙蝠的重要性并且潜在地病毒的病原体的 zoonotic 来源。
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Betacoronavirus
Coronaviridae
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In 2019, a new pandemic virus belonging to the betacoronavirus family emerged, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This new coronavirus appeared in Wuhan, China, and is responsible for severe respiratory pneumonia in humans, namely, coronavirus disease 2019 (COVID-19). Having infected almost 200 million people worldwide and caused more than 4.1 million deaths as of today, this new disease has raised a significant number of questions about its molecular mechanism of replication and, in particular, how infectious viral particles are produced. Although viral entry is well characterized, the full assembly steps of SARS-CoV-2 have still not been fully described. Coronaviruses, including SARS-CoV-2, have four main structural proteins, namely, the spike glycoprotein (S), the membrane glycoprotein (M), the envelope protein (E), and the nucleocapsid protein (N). All these proteins have key roles in the process of coronavirus assembly and budding. In this review, we gathered the current knowledge about betacoronavirus structural proteins involved in viral particle assembly, membrane curvature and scission, and then egress in order to suggest and question a coherent model for SARS-CoV-2 particle production and release.
Betacoronavirus
Coronavirus
Coronaviridae
Pandemic
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Since the emergence of severe acute respiratory syndrome coronavirus (SARS - CoV) and Middle East respiratory syndrome coronavirus (MERS - CoV), it has become increasingly clear that bats are important reservoirs of coronaviruses. This investigation, with the apparition of the n ew coronavirus SARS - CoV - 2 in Wuhan (China, December 2019), has shown 96.2% sequence similarity with the bat coronavirus. Through this review, we report the characterization of a SARS - CoV - 2. The virus belongs to the Betacoronavirus genera and shares less th an 80% of identity with the SARS - CoV. This similarity was helpful to develop RT - PCR and other tools involved in SARS - CoV - 2 RNA detection. We also report the importance of the different molecular tools and, the possible use of serology tests in the diagnosi s of COVID - 19. We discussed the strengths and weaknesses of each of these methods.
Coronavirus
Betacoronavirus
Coronaviridae
Bovine coronavirus
2019-20 coronavirus outbreak
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