1
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Wilson R, Kovacs D, Crosby M, Ho A. Global Epidemiology and Seasonality of Human Seasonal Coronaviruses: A Systematic Review. Open Forum Infect Dis 2024; 11:ofae418. [PMID: 39113828 PMCID: PMC11304597 DOI: 10.1093/ofid/ofae418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024] Open
Abstract
Background We characterized the global epidemiology and seasonality of human coronaviruses (HCoVs) OC43, NL63, 229E, and HKU1. Methods In this systematic review, we searched MEDLINE, EMBASE, Web of Science, SCOPUS, CINAHL, and backward citations for studies published until 1 September 2023. We included studies with ≥12 months of consecutive data and tested for ≥1 HCoV species. Case reports, review articles, animal studies, studies focusing on SARS-CoV-1, SARS-CoV-2, and/or Middle East respiratory syndrome, and those including <100 cases were excluded. Study quality and risk of bias were assessed using Joanna Briggs Institute Critical Appraisal Checklist tools. We reported the prevalence of all HCoVs and individual species. Seasonality was reported for studies that included ≥100 HCoVs annually. This study is registered with PROSPERO, CRD42022330902. Results A total of 201 studies (1 819 320 samples) from 68 countries were included. A high proportion were from China (19.4%; n = 39), whereas the Southern Hemisphere was underrepresented. Most were case series (77.1%, n = 155) with samples from secondary care (74.1%, n = 149). Seventeen (8.5%) studies included asymptomatic controls, whereas 76 (37.8%) reported results for all 4 HCoV species. Overall, OC43 was the most prevalent HCoV. Median test positivity of OC43 and NL63 was higher in children, and 229E and HKU1 in adults. Among 18 studies that described seasonality (17 from the Northern Hemisphere), circulation of all HCoVs mostly peaked during cold months. Conclusions In our comprehensive review, few studies reported the prevalence of individual HCoVs or seasonality. Further research on the burden and circulation of HCoVs is needed, particularly from Africa, South Asia, and Central/South America.
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Affiliation(s)
- Rory Wilson
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Dory Kovacs
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Mairi Crosby
- College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, UK
| | - Antonia Ho
- Medical Research Council-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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2
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Alamri KA, Farrag MA, Aziz IM, Dudin GA, Mohammed AA, Almajhdi FN. Prevalence of Human Coronaviruses in Children and Phylogenetic Analysis of HCoV-OC43 during 2016-2022 in Riyadh, Saudi Arabia. Viruses 2022; 14:v14122592. [PMID: 36560596 PMCID: PMC9784458 DOI: 10.3390/v14122592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/17/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022] Open
Abstract
With the emergence of SARS-CoV-2, routine surveillance combined with sequence and phylogenetic analysis of coronaviruses is urgently required. In the current study, the four common human coronaviruses (HCoVs), OC43, NL63, HKU1, and 229E, were screened in 361 clinical samples collected from hospitalized children with respiratory symptoms during four winter seasons. RT-PCR-based detection and typing revealed different prevalence rates of HCoVs across the four seasons. Interestingly, none of the four HCoVs were detected in the samples (n = 100) collected during the winter season of the COVID-19 pandemic. HCoV-OC43 (4.15%) was the most frequently detected, followed by 229E (1.1%). Partial sequences of S and N genes of OC43 from the winter seasons of 2015/2016 and 2021/2022 were used for sequence and phylogenetic analysis. Multiple sequence alignment of the two Saudi OC43s strains with international strains revealed the presence of sequence deletions and several mutations, of which some changed their corresponding amino acids. Glycosylation profiles revealed a number of O-and N-glycosylation sites in both genes. Based on phylogenetic analysis, four genotypes were observed with Riyadh strains grouped into the genotype C. Further long-term surveillance with a large number of clinical samples and sequences is necessary to resolve the circulation patterns and evolutionary kinetics of OC43 in Saudi Arabia.
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Affiliation(s)
- Khalid A. Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed A. Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ibrahim M. Aziz
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Gani Asa Dudin
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Arif Ahmed Mohammed
- Center of Excellence in Biotechnology Research, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fahad N. Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence:
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Valadan R, Golchin S, Alizadeh-Navaei R, Haghshenas M, Zargari M, Mousavi T, Ghamati M. Differential gene expression analysis of common target genes for the detection of SARS-CoV-2 using real time-PCR. AMB Express 2022; 12:112. [PMID: 36053466 PMCID: PMC9438354 DOI: 10.1186/s13568-022-01454-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 08/19/2022] [Indexed: 11/10/2022] Open
Abstract
COVID-19 currently is the main cause of the severe acute respiratory disease and fatal outcomes in human beings worldwide. Several genes are used as targets for the detection of SARS-CoV-2, including the RDRP, N, and E genes. The present study aimed to determine the RDRP, N, and E genes expressions of SARS-CoV- 2 in clinical samples. For this purpose, 100 SARS-CoV-2 positive samples were collected from diagnostic laboratories of Mazandaran province, Iran. After RNA extraction, the real-time reverse transcription PCR (real-time RT-PCR) assay was performed for differential gene expressions' analysis of N, E, and RDRP. The threshold cycle (Ct) values for N, RDRP, and E targets of 100 clinical samples for identifying SARS-CoV-2 were then evaluated using quantitative real-time PCR (qRT-PCR). This result suggests N gene as a potential target for the detection of the SARS-CoV-2, since it was observed to be highly expressed in the nasopharyngeal or oropharynges of COVID-19 patients (P < 0.0001). Herein, we showed that SARS-CoV- 2 genes were differentially expressed in the host cells. Therefore, to reduce obtaining false negative results and to increase the sensitivity of the available diagnostic tests, the target genes should be carefully selected based on the most expressed genes in the cells.
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Affiliation(s)
- Reza Valadan
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Immunology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Soheila Golchin
- Gastrointestinal Cancer Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Center, Non-communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammadreza Haghshenas
- Department of Microbiology, Molecular and Cell-Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mehryar Zargari
- Department of Clinical Biochemistry and Genetics, Molecular and cell biology research center, Faculty of Medicine, Mazandaran University of medical sciences, Sari, Iran
| | - Tahoora Mousavi
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran. .,Molecular and Cell Biology Research Center, Hemoglobinopathy Research Institute, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mohammad Ghamati
- Medical student, Mazandaran University of Medical Sciences, Sari, Iran
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Cimolai N. Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses. Health Secur 2020; 19:195-208. [PMID: 33186086 DOI: 10.1089/hs.2020.0067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold. They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications. These viruses are usually seasonal (with winter dominance) and affect nearly all age groups. The seasonal and annual variation in virus prevalence has implications for understanding the concept of acquired immunity and its persistence or diminution. Coronaviruses generally have outbreak potential in susceptible populations of any age, particularly in patients with comorbidities, who tend to have increased clinical disease. These 4 coronaviruses are often found in the context of what appears to be coinfection with other pathogens, but especially other viruses. If coronaviruses are not specifically tested for, the sole detection of a viral copathogen would suggest the pathogen is the causative agent, when a coronavirus may be culpable, or both. The detection of these viruses in circumstances where respiratory viruses are generally sought in clinical samples is, therefore, justified. These pathogens can be chronically shed from the respiratory tract, which is more likely to occur among immunocompromised and complicated patients. These viruses share the potential for genetic drift. The genome is among the largest of RNA viruses, and the capability of these viruses to further change is likely underestimated. Given the potential disease among humans, it is justified to search for effective antiviral chemotherapy for these viruses and to consider uses in niche situations should effective therapy be defined. Whereas SARS-CoV-2 may follow the epidemiological pattern of SARS-CoV and extinguish slowly over time, there is yet concern that SARS-CoV-2 may establish itself as an endemic human respiratory coronavirus similar to OC43, 2299E, NL63, and HKU1. Until sufficient data are acquired to better understand the potential of SARS-CoV-2, continued work on antiviral therapy and vaccination is imperative.
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Affiliation(s)
- Nevio Cimolai
- Nevio Cimolai, MD, FRCPC, is a Professor, Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia; he is also Medical Staff, Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia; both in Vancouver, Canada
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Ogimi C, Greninger AL, Waghmare AA, Kuypers JM, Shean RC, Xie H, Leisenring WM, Stevens-Ayers TL, Jerome KR, Englund JA, Boeckh M. Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution. J Infect Dis 2017; 216:203-209. [PMID: 28838146 PMCID: PMC5853311 DOI: 10.1093/infdis/jix264] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022] Open
Abstract
Background Recent data suggest that human coronavirus (HCoV) pneumonia is associated with significant mortality in hematopoietic cell transplant (HCT) recipients. Investigation of risk factors for prolonged shedding and intrahost genome evolution may provide critical information for development of novel therapeutics. Methods We retrospectively reviewed HCT recipients with HCoV detected in nasal samples by polymerase chain reaction (PCR). HCoV strains were identified using strain-specific PCR. Shedding duration was defined as time between first positive and first negative sample. Logistic regression analyses were performed to evaluate factors for prolonged shedding (≥21 days). Metagenomic next-generation sequencing (mNGS) was conducted when ≥4 samples with cycle threshold values of <28 were available. Results Seventeen of 44 patients had prolonged shedding. Among 31 available samples, 35% were OC43, 32% were NL63, 19% were HKU1, and 13% were 229E; median shedding duration was similar between strains (P = .79). Bivariable logistic regression analyses suggested that high viral load, receipt of high-dose steroids, and myeloablative conditioning were associated with prolonged shedding. mNGS among 5 subjects showed single-nucleotide polymorphisms from OC43 and NL63 starting 1 month following onset of shedding. Conclusions High viral load, high-dose steroids, and myeloablative conditioning were associated with prolonged shedding of HCoV in HCT recipients. Genome changes were consistent with the expected molecular clock of HCoV.
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Affiliation(s)
- Chikara Ogimi
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Pediatrics, University of Washington.,Pediatric Infectious Diseases Division, Seattle Children's Hospital
| | - Alexander L Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Laboratory Medicine, University of Washington
| | - Alpana A Waghmare
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Pediatrics, University of Washington.,Pediatric Infectious Diseases Division, Seattle Children's Hospital
| | - Jane M Kuypers
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Laboratory Medicine, University of Washington
| | - Ryan C Shean
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Laboratory Medicine, University of Washington
| | - Hu Xie
- Clinical Research Division, Fred Hutchinson Cancer Research Center
| | - Wendy M Leisenring
- Clinical Research Division, Fred Hutchinson Cancer Research Center.,Biostatistics
| | | | - Keith R Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Department of Laboratory Medicine, University of Washington
| | - Janet A Englund
- Department of Pediatrics, University of Washington.,Pediatric Infectious Diseases Division, Seattle Children's Hospital
| | - Michael Boeckh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center.,Clinical Research Division, Fred Hutchinson Cancer Research Center.,Medicine, University of Washington, Seattle, Washington
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Identification and evolutionary dynamics of two novel human coronavirus OC43 genotypes associated with acute respiratory infections: phylogenetic, spatiotemporal and transmission network analyses. Emerg Microbes Infect 2017; 6:e3. [PMID: 28050020 PMCID: PMC5285497 DOI: 10.1038/emi.2016.132] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 02/05/2023]
Abstract
Human coronavirus OC43 (HCoV-OC43) is commonly associated with respiratory tract infections in humans, with five genetically distinct genotypes (A to E) described so far. In this study, we obtained the full-length genomes of HCoV-OC43 strains from two previously unrecognized lineages identified among patients presenting with severe upper respiratory tract symptoms in a cross-sectional molecular surveillance study in Kuala Lumpur, Malaysia, between 2012 and 2013. Phylogenetic, recombination and comparative genomic analyses revealed two distinct clusters diverging from a genotype D-like common ancestor through recombination with a putative genotype A-like lineage in the non-structural protein (nsp) 10 gene. Signature amino acid substitutions and a glycine residue insertion at the N-terminal domain of the S1 subunit of the spike gene, among others, exhibited further distinction in a recombination pattern, to which these clusters were classified as genotypes F and G. The phylogeographic mapping of the global spike gene indicated that the genetically similar HCoV-OC43 genotypes F and G strains were potentially circulating in China, Japan, Thailand and Europe as early as the late 2000s. The transmission network construction based on the TN93 pairwise genetic distance revealed the emergence and persistence of multiple sub-epidemic clusters of the highly prevalent genotype D and its descendant genotypes F and G, which contributed to the spread of HCoV-OC43 in the region. Finally, a more consistent nomenclature system for non-recombinant and recombinant HCoV-OC43 lineages is proposed, taking into account genetic recombination as an important feature in HCoV evolution and classification.
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7
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Safe and Sensitive Antiviral Screening Platform Based on Recombinant Human Coronavirus OC43 Expressing the Luciferase Reporter Gene. Antimicrob Agents Chemother 2016; 60:5492-503. [PMID: 27381385 DOI: 10.1128/aac.00814-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 06/27/2016] [Indexed: 12/14/2022] Open
Abstract
Human coronaviruses (HCoVs) cause 15 to 30% of mild upper respiratory tract infections. However, no specific antiviral drugs are available to prevent or treat HCoV infections to date. Here, we developed four infectious recombinant HCoVs-OC43 (rHCoVs-OC43) which express the Renilla luciferase (Rluc) reporter gene. Among these four rHCoVs-OC43, rOC43-ns2DelRluc (generated by replacing ns2 with the Rluc gene) showed robust luciferase activity with only a slight impact on its growth characteristics. Additionally, this recombinant virus remained stable for at least 10 passages in BHK-21 cells. rOC43-ns2DelRluc was comparable to its parental wild-type virus (HCoV-OC43-WT) with respect to the quantity of the antiviral activity of chloroquine and ribavirin. We showed that chloroquine strongly inhibited HCoV-OC43 replication in vitro, with a 50% inhibitory concentration (IC50) of 0.33 μM. However, ribavirin showed inhibition of HCoV-OC43 replication only at high concentrations which may not be applicable to humans in clinical treatment, with an IC50 of 10 μM. Furthermore, using a luciferase-based small interfering RNA (siRNA) screening assay, we identified double-stranded-RNA-activated protein kinase (PKR) and DEAD box RNA helicases (DDX3X) that exhibited antiviral activities, which were further verified by the use of HCoV-OC43-WT. Therefore, rOC43-ns2DelRluc represents a promising safe and sensitive platform for high-throughput antiviral screening and quantitative analysis of viral replication.
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8
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Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, Hanafi NS, Kamarulzaman A, Tee KK. Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia. Virol J 2016; 13:33. [PMID: 26916286 PMCID: PMC4766700 DOI: 10.1186/s12985-016-0488-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/11/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Despite the worldwide circulation of human coronavirus OC43 (HCoV-OC43) and HKU1 (HCoV-HKU1), data on their molecular epidemiology and evolutionary dynamics in the tropical Southeast Asia region is lacking. METHODS The study aimed to investigate the genetic diversity, temporal distribution, population history and clinical symptoms of betacoronavirus infections in Kuala Lumpur, Malaysia between 2012 and 2013. A total of 2,060 adults presented with acute respiratory symptoms were screened for the presence of betacoronaviruses using multiplex PCR. The spike glycoprotein, nucleocapsid and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. RESULTS A total of 48/2060 (2.4 %) specimens were tested positive for HCoV-OC43 (1.3 %) and HCoV-HKU1 (1.1 %). Both HCoV-OC43 and HCoV-HKU1 were co-circulating throughout the year, with the lowest detection rates reported in the October-January period. Phylogenetic analysis of the spike gene showed that the majority of HCoV-OC43 isolates were grouped into two previously undefined genotypes, provisionally assigned as novel lineage 1 and novel lineage 2. Sign of natural recombination was observed in these potentially novel lineages. Location mapping showed that the novel lineage 1 is currently circulating in Malaysia, Thailand, Japan and China, while novel lineage 2 can be found in Malaysia and China. Molecular dating showed the origin of HCoV-OC43 around late 1950s, before it diverged into genotypes A (1960s), B (1990s), and other genotypes (2000s). Phylogenetic analysis revealed that 27.3 % of the HCoV-HKU1 strains belong to genotype A while 72.7 % belongs to genotype B. The tree root of HCoV-HKU1 was similar to that of HCoV-OC43, with the tMRCA of genotypes A and B estimated around the 1990s and 2000s, respectively. Correlation of HCoV-OC43 and HCoV-HKU1 with the severity of respiratory symptoms was not observed. CONCLUSIONS The present study reported the molecular complexity and evolutionary dynamics of human betacoronaviruses among adults with acute respiratory symptoms in a tropical country. Two novel HCoV-OC43 genetic lineages were identified, warranting further investigation on their genotypic and phenotypic characteristics.
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Affiliation(s)
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yutaka Takebe
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan.
- School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan.
| | - Jack Bee Chook
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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Yip CCY, Lam CSF, Luk HKH, Wong EYM, Lee RA, So LY, Chan KH, Cheng VCC, Yuen KY, Woo PCY, Lau SKP. A six-year descriptive epidemiological study of human coronavirus infections in hospitalized patients in Hong Kong. Virol Sin 2016; 31:41-8. [PMID: 26920709 PMCID: PMC7090542 DOI: 10.1007/s12250-016-3714-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/11/2016] [Indexed: 11/25/2022] Open
Abstract
We conducted a six-year epidemiological study on human coronaviruses (HCoVs) circulating in Hong Kong, using 8275 nasopharyngeal samples from patients with acute respiratory tract infections. HCoVs were detected in 77 (0.93%) of the samples by a pan-HCoV RT-PCR assay. The most frequently detected HCoV species was HCoV-OC43 (0.58%), followed by HCoV-229E (0.15%), HCoV-HKU1 (0.13%) and HCoV-NL63 (0.07%). HCoVs were detected throughout the study period (September 2008–August 2014), with the highest detection rate from September 2010 to August 2011 (22/1500, 1.47%). Different seasonal patterns of each HCoV species in Hong Kong were noted. HCoV-OC43 was predominant in the fall and winter, whereas HCoV-HKU1 showed peak activity in winter, with a few cases occurred in spring and summer. HCoV-229E mainly occurred in winter and spring, while HCoV-NL63 was predominant in summer and autumn. HCoVs most commonly infect the elderly and young children, with median age of 79.5 years (range, 22 days to 95 years). Intriguingly, the detection rate of HCoV-OC43 in the age group of > 80 years (26/2380, 1.09%) was significantly higher than that in the age group of 0–10 years (12/2529, 0.47%) (P < 0.05). These data provides new insight into the epidemiology of coronaviruses.![]()
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Affiliation(s)
- Cyril C Y Yip
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Carol S F Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Hayes K H Luk
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Emily Y M Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Rodney A Lee
- Department of Microbiology, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | - Lok-Yee So
- Department of Paediatrics and Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong SAR, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Vincent C C Cheng
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China.
| | - Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China. .,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China. .,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China.
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Kin N, Miszczak F, Lin W, Ar Gouilh M, Vabret A. Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes. Viruses 2015; 7:2358-77. [PMID: 26008694 PMCID: PMC4452910 DOI: 10.3390/v7052358] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/23/2015] [Accepted: 05/04/2015] [Indexed: 01/19/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.
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Affiliation(s)
- Nathalie Kin
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-0-2-31-27-25-54
| | - Fabien Miszczak
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Department of Virology, University Hospital of Caen, F-14033 Caen, France
| | - Wei Lin
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
| | - Meriadeg Ar Gouilh
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France
| | - Astrid Vabret
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Department of Virology, University Hospital of Caen, F-14033 Caen, France
| | - Epicorem Consortium
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
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