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Pinski AN, Gan T, Lin SC, Droit L, Diamond M, Barouch DH, Wang D. Isolation of a recombinant simian adenovirus encoding the human adenovirus G52 hexon suggests a simian origin for human adenovirus G52. J Virol 2024; 98:e0004324. [PMID: 38497664 PMCID: PMC11019922 DOI: 10.1128/jvi.00043-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 02/25/2024] [Indexed: 03/19/2024] Open
Abstract
Human adenoviruses (HAdVs) are causative agents of morbidity and mortality throughout the world. These double-stranded DNA viruses are phylogenetically classified into seven different species (A-G). HAdV-G52, originally isolated in 2008 from a patient presenting with gastroenteritis, is the sole human-derived member of species G. Phylogenetic analysis previously suggested that HAdV-G52 may have a simian origin, indicating a potential zoonotic spillover into humans. However, evidence of HAdV-G52 in either human or simian populations has not been reported since. Here, we describe the isolation and in vitro characterization of rhesus (rh)AdV-69, a novel simian AdV with clear evidence of recombination with HAdV-G52, from the stool of a rhesus macaque. Specifically, the rhAdV-69 hexon capsid protein is 100% identical to that of HAdV-G52, whereas the remainder of the genome is most similar to rhAdV-55, sharing 95.36% nucleic acid identity. A second recombination event with an unknown adenovirus (AdV) is evident at the short fiber gene. From the same sample, we also isolated a second, highly related recombinant AdV (rhAdV-68) that harbors a distinct hexon gene but nearly identical backbone compared to rhAdV-69. In vitro, rhAdV-68 and rhAdV-69 demonstrate comparable growth kinetics and tropisms in human cell lines, nonhuman cell lines, and human enteroids. Furthermore, we show that coinfection of highly related AdVs is not unique to this sample since we also isolated coinfecting rhAdVs from two additional rhesus macaque stool samples. Our data collectively contribute to elucidating the origins of HAdV-G52 and provide insights into the frequency of coinfections and subsequent recombination in AdV evolution.IMPORTANCEUnderstanding the host origins of adenoviruses (AdVs) is critical for public health as transmission of viruses from animals to humans can lead to emergent viruses. Recombination between animal and human AdVs can also produce emergent viruses. HAdV-G52 is the only human-derived member of the HAdV G species. It has been suggested that HAdV-G52 has a simian origin. Here, we isolated from a rhesus macaque, a novel rhAdV, rhAdV-69, that encodes a hexon protein that is 100% identical to that of HAdV-G52. This observation suggests that HAdV-G52 may indeed have a simian origin. We also isolated a highly related rhAdV, differing only in the hexon gene, from the same rhesus macaque stool sample as rhAdV-69, illustrating the potential for co-infection of closely related AdVs and recombination at the hexon gene. Furthermore, our study highlights the critical role of whole-genome sequencing in understanding AdV evolution and monitoring the emergence of pathogenic AdVs.
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Affiliation(s)
- Amanda N. Pinski
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Tianyu Gan
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Shih-Ching Lin
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Lindsay Droit
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Diamond
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - David Wang
- Department of Molecular Microbiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, USA
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Chiu KHY, Wong SC, Tam AR, Sridhar S, Yip CCY, Chan KH, Chew NFS, Man KKY, Chan WM, Ip JD, Chu AWH, Lo JYC, Hung IFN, Yuen KY, To KKW, Cheng VCC. The first case of monkeypox in Hong Kong presenting as infectious mononucleosis-like syndrome. Emerg Microbes Infect 2023; 12:2146910. [PMID: 36357955 PMCID: PMC9718374 DOI: 10.1080/22221751.2022.2146910] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kelvin Hei-Yeung Chiu
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of China
| | - Shuk-Ching Wong
- Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong Special Administrative Region, China
| | - Anthony Raymond Tam
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Siddharth Sridhar
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Hung Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Nicholas Foo-Siong Chew
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kenyon Ka-Yun Man
- Department of Radiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of China
| | - Wan-Mui Chan
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Jonathan Daniel Ip
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Allen Wing-Ho Chu
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Janice Yee-Chi Lo
- Centre for Health Protection, Department of Health, Hong Kong Special Administrative Region, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong Province, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China.,Co-correspondence: Vincent Chi-Chung Cheng, Department of Microbiology, Queen Mary Hospital, Hong Kong, China. (+852-22552378, +852-28724555, E-mail: ) and Kelvin Kai-Wang To, Department of Microbiology, The University of Hong Kong, Hong Kong, China (+852-22552413, +852-28551241, E-mail: )
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, People’s Republic of China,Co-correspondence: Vincent Chi-Chung Cheng, Department of Microbiology, Queen Mary Hospital, Hong Kong, China. (+852-22552378, +852-28724555, E-mail: ) and Kelvin Kai-Wang To, Department of Microbiology, The University of Hong Kong, Hong Kong, China (+852-22552413, +852-28551241, E-mail: )
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Badawi AE, Kasem MA, Moemen D, El Sayed Zaki M. Molecular, Epidemiological and Clinical Assessment of Adenoviral Keratoconjunctivitis in Egypt: Institutional Study. Ocul Immunol Inflamm 2023; 31:1640-1646. [PMID: 35816022 DOI: 10.1080/09273948.2022.2092004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
PURPOSE To evaluate the frequency of Human adenovirus (HAdV) and its serotypes in keratoconjunctivitis patients who attended the outpatient clinics of Mansoura Ophthalmic Center, Egypt. METHODS Conjunctival secretions and corneal scrapings were collected from patients complaining of clinically diagnosed viral keratoconjunctivitis. The molecular method for HAdV detection was performed by polymerase chain reaction (PCR) followed by restriction enzymes (REA) determination of serotypes for hexone gene. RESULTS HAdV infection was detected in 38% of samples. There were 4 serotypes of Human adenovirus species D (HAdV-D) isolated (4, 8, 37, 3), where HAdV-D8 was the most dominant. Contact with infected patient, follicular conjunctivitis and subepithelial corneal infiltrates are useful features for clinical diagnosis of adenoviral conjunctivitis. CONCLUSION HAdV was significant etiological factor of acute follicular conjunctivitis. Accurate diagnosis of adenoviral conjunctivitis is essential for appropriate management, reducing permanent visual impairment and to limit the transmission of the virus within the community.
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Affiliation(s)
- Amani E Badawi
- Mansoura Ophthalmic Center, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Manal Ali Kasem
- Mansoura Ophthalmic Center, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Dalia Moemen
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Maysaa El Sayed Zaki
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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Mah J, Huang CH, Sahoo MK, Pinsky BA. Evaluation of a Semiautomated System for the Quantitation of Human Adenovirus DNA from Clinical Samples. Microbiol Spectr 2023; 11:e0501022. [PMID: 36847504 PMCID: PMC10100871 DOI: 10.1128/spectrum.05010-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/03/2023] [Indexed: 03/01/2023] Open
Abstract
Human adenoviruses (HAdVs) cause severe disease in immunocompromised patients. Quantitation of HAdV DNA in peripheral blood is used to assess the risk of disseminated disease and to monitor response to therapy. The lower limit of detection, precision, and linearity of the semiautomated AltoStar adenovirus quantitative PCR (qPCR) was evaluated using reference HAdV-E4 in EDTA plasma and respiratory virus matrix. Qualitative and quantitative agreement was determined using 122 clinical EDTA plasma specimens previously tested using a laboratory-developed HAdV qPCR. The 95% lower limit of detection (LLOD) was 33 IU/mL (95% confidence interval [CI], 10 to 56) for EDTA plasma and 188 IU/mL (95% CI, 145 to 304) for respiratory swab matrix. In both matrices, the AltoStar HAdV qPCR was linear from 7.0 to 2.0 log10 IU/mL. For the clinical specimens, overall agreement was 96.7% (95% CI, 91.8 to 99.1), positive percent agreement was 95.5% (95% CI, 87.6 to 98.5), and negative percent agreement was 98.2% (95% CI, 88.5 to 99.7). Passing-Bablok analysis of specimens quantifiable by both methods revealed a regression line of Y = 1.11 · X + 0.00; there was positive proportional bias (95% CI of the slope, 1.05 to 1.22) but no systematic bias (95% CI of the Y-intercept, -0.43 to 0.23) compared to the reference. The AltoStar platform provides accurate quantitation of HAdV DNA and provides a semiautomated option for the clinical monitoring of HAdV following transplantation. IMPORTANCE Accurate quantification of human adenovirus DNA in the peripheral blood plays a critical role in the management of adenovirus infections in transplant recipients. Many laboratories utilize in-house laboratory-based PCR assays for the quantification of human adenovirus, as there are few commercial options available. Here, we describe the analytical and clinical performance of the semiautomated AltoStar adenovirus quantitative PCR (Altona Diagnostics). This platform provides sensitive, precise, and accurate quantification of adenovirus DNA that is well suited for virological testing following transplantation. Prior to implementing a new quantitative test in the clinical laboratory, a rigorous evaluation is required to determine assay performance characteristics and to correlate results to current in-house methods of quantitation.
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Affiliation(s)
- Jordan Mah
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Chun Hong Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Malaya K. Sahoo
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin A. Pinsky
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
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Air dispersal of respiratory viruses other than severe acute respiratory coronavirus virus 2 (SARS-CoV-2) and the implication on hospital infection control. Infect Control Hosp Epidemiol 2022; 44:768-773. [PMID: 35811422 PMCID: PMC9304945 DOI: 10.1017/ice.2022.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: Air dispersal of respiratory viruses other than SARS-CoV-2 has not been systematically reported. The incidence and factors associated with air dispersal of respiratory viruses are largely unknown. Methods: We performed air sampling by collecting 72,000 L of air over 6 hours for pediatric and adolescent patients infected with parainfluenza virus 3 (PIF3), respiratory syncytial virus (RSV), rhinovirus, and adenovirus. The patients were singly or 2-patient cohort isolated in airborne infection isolation rooms (AIIRs) from December 3, 2021, to January 26, 2022. The viral load in nasopharyngeal aspirates (NPA) and air samples were measured. Factors associated with air dispersal were investigated and analyzed. Results: Of 20 singly isolated patients with median age of 30 months (range, 3 months–15 years), 7 (35%) had air dispersal of the viruses compatible with their NPA results. These included 4 (40%) of 10 PIF3-infected patients, 2 (66%) of 3 RSV-infected patients, and 1 (50%) of 2 adenovirus-infected patients. The mean viral load in their room air sample was 1.58×103 copies/mL. Compared with 13 patients (65%) without air dispersal, these 7 patients had a significantly higher mean viral load in their NPA specimens (6.15×107 copies/mL vs 1.61×105 copies/mL; P < .001). Another 14 patients were placed in cohorts as 7 pairs infected with the same virus (PIF3, 2 pairs; RSV, 3 pairs; rhinovirus, 1 pair; and adenovirus, 1 pair) in double-bed AIIRs, all of which had air dispersal. The mean room air viral load in 2-patient cohorts was significantly higher than in rooms of singly isolated patients (1.02×104 copies/mL vs 1.58×103 copies/mL; P = .020). Conclusion: Air dispersal of common respiratory viruses may have infection prevention and public health implications.
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Ouyang W, Fu S, Zhao X, Su S, Zhang J, Luo D, Liu L, Ding W, Cao D, Liu L, He Z, Lu B. Recombinant human endostatin combined with radiotherapy promotes cardiomyocyte apoptosis in rats via TGFβ1/Smads/CTGF signaling pathway. BMC Cardiovasc Disord 2022; 22:97. [PMID: 35279096 PMCID: PMC8917752 DOI: 10.1186/s12872-022-02499-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
Purpose The aim of the present study was to investigate the efficacy of recombinant human endostatin (ES) (rh-ES) combined with radiation on rat cardiomyocyte apoptosis and the regulatory mechanism of transforming growth factor beta1 (TGF-β1)/Sma and Mad-related protein 3 (Smad3)/connective tissue growth factor (CTGF) signaling. Method The primary cardiomyocytes were isolated from neonatal Sprague–Dawley rats for culture in vitro and divided into blank control group (without treatment), 10 Gy radiation + siTGF-β1 siRNA (gene silencing) group, ES + siTGF-β1 siRNA group, and 10 Gy radiation + ES + siTGF-β1 siRNA group. Methyl thiazolyl tetrazolium assay was used to calculate the half-maximal inhibitory concentration (IC50) of rh-ES on cardiomyocytes. Adenoviral vector was constructed for virus packaging to silence TGF-β1 expression in cardiomyocytes. Quantitative real-time polymerase chain reaction and Western blot were carried out to analyze TGF-β1, Smad2, Smad3 and CTGF expression at both gene and protein levels. Flow cytometry and electron microscope were used to examine cell apoptosis. Results ES had a dose-dependent inhibitory effect on the proliferation of primary rat cardiomyocytes. ES combined with radiotherapy significantly inhibited cardiomyocyte proliferation and promoted cell apoptosis (P < 0.01). The gene and protein expression of TGF-β1, Smad2, Smad3 and CTGF were significantly up-regulated in primary cardiomyocytes transfected with TGF-β1 gene (P < 0.05). Conclusion The combination therapy with rh-ES and radiation can promote cardiomyocyte apoptosis and aggravate myocardial cell damage via TGF-β1/Smad3/CTGF signaling pathway. Supplementary information The online version contains supplementary material available at 10.1186/s12872-022-02499-8.
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Idris OO, Kolawole OM. Seroprevalence and molecular characterization of human respiratory syncytial virus and human adenovirus among children in Ado-Ekiti, Nigeria. J Med Virol 2021; 94:2548-2557. [PMID: 34816447 DOI: 10.1002/jmv.27473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022]
Abstract
In children, the respiratory syncytial virus and adenovirus majorly cause acute respiratory infections. The study evaluated the seroprevalence and conducted the molecular characterization of human respiratory syncytial virus (HRSV) and human adenovirus (HAdV) among children. Venous blood, nasopharyngeal, and oropharyngeal swabs were collected from children presenting with acute respiratory infections in a tertiary health facility in Ado-Ekiti, Nigeria. A serological investigation was carried out on the sera samples for the detection of anti-HRSV immunoglobulin M (IgM), anti-HRSV IgG, anti-HAdV IgM, and anti-HAdV IgG using ELISA (enzyme-linked immunosorbent assay) kits. The amplification and sequencing of HRSV and HAdV were carried out using specific primer pairs that targeted the glycoprotein (G) gene of HRSV and the hexon gene of HAdV, respectively. The seroprevalence of HRSV IgG and IgM was 73% and 7.5%, respectively, while the seroprevalence of HAdV IgG and IgM was 98.5% and 8.5%, respectively. The age of enrolled children, presence of fever, and cough were associated (p < 0.05) with the infection. HRSV subtype B (HRSV-B) (13.3%), and species of HAdV (Mastadenovirus B and C) (11.7%) were detected among the studied population. There was no viral coinfection with both HRSV and HAdV. In infancy and early childhood, HRSV-B, HAdV species B and C are common etiologic agents of respiratory infections as reported in this study. Further studies on molecular characterization of respiratory tract viruses including circulating respiratory syncytial virus and adenovirus are hereby advocated.
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Affiliation(s)
- Olayinka O Idris
- Department of Microbiology, Faculty of Life Sciences, Infectious Diseases and Environmental Health Research Group, University of Ilorin, Ilorin, Nigeria.,Department of Biological Sciences, College of Sciences, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Olatunji M Kolawole
- Department of Microbiology, Faculty of Life Sciences, Infectious Diseases and Environmental Health Research Group, University of Ilorin, Ilorin, Nigeria
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Yip CCY, Sridhar S, Lau JHN, Cheng AKW, Leung KH, Chen JHK, Chan KH, Cheng VCC, Yuen KY. Comparative performance of two commercial sample-to-result systems for hepatitis C virus quantitation and genotyping. Expert Rev Mol Diagn 2020; 20:1253-1258. [PMID: 32893699 DOI: 10.1080/14737159.2020.1820327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVES Accurate assays for hepatitis C virus (HCV) quantitation and genotyping are important for the management of HCV infection. In this study, we evaluated the performance of cobas HCV and cobas HCV GT assays (Roche) for HCV quantitation and genotyping on the cobas 4800 System. METHODS We compared the performance of the cobas HCV assays with another commercial system (Abbott m2000) using a panel of well-characterized patient samples and proficiency testing samples. RESULTS The limit-of-detection of the cobas HCV assay in our center was higher (15 IU/mL) than the manufacturer claim (9.2 IU/mL). The assay showed high analytical specificity, accuracy, precision, and linearity. Performance was congruent with the RealTime HCV assay (Abbott). For genotyping, the cobas HCV GT assay only showed moderate agreement with the RealTime HCV Genotype II assay (kappa = 0.550). The cobas assay outperformed the RealTime assay for typing HCV genotypes 1b and 6 (p = 0.033). CONCLUSION Our results confirm that the cobas 4800 System is a reliable platform for HCV quantitation and genotyping. The cobas HCV GT assay is a good choice for genotype 1b/6 endemic areas in east Asia, clearly outperforming the RealTime HCV Genotype II assay.
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Affiliation(s)
- Cyril C Y Yip
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong Special Administrative Region, China
| | - John H N Lau
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Andrew K W Cheng
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China
| | - Jonathan H K Chen
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China
| | - Vincent C C Cheng
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- Department of Microbiology, Queen Mary Hospital , Hong Kong Special Administrative Region, China.,Department of Microbiology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong , Hong Kong Special Administrative Region, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong , Hong Kong Special Administrative Region, China
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Yip CCY, Sridhar S, Cheng AKW, Leung KH, Choi GKY, Chen JHK, Poon RWS, Chan KH, Wu AKL, Chan HSY, Chau SKY, Chung TWH, To KKW, Tsang OTY, Hung IFN, Cheng VCC, Yuen KY, Chan JFW. Evaluation of the commercially available LightMix® Modular E-gene kit using clinical and proficiency testing specimens for SARS-CoV-2 detection. J Clin Virol 2020; 129:104476. [PMID: 32516739 PMCID: PMC7255195 DOI: 10.1016/j.jcv.2020.104476] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND Rapid and sensitive diagnostic assays for SARS-CoV-2 detection are required for prompt patient management and infection control. The analytical and clinical performances of LightMix® Modular SARS and Wuhan CoV E-gene kit, a widely used commercial assay for SARS-CoV-2 detection, have not been well studied. OBJECTIVE To evaluate the performance characteristics of the LightMix® E-gene kit in comparison with well-validated in-house developed COVID-19 RT-PCR assays. STUDY DESIGN Serial dilutions of SARS-CoV-2 culture isolate extracts were used for analytical sensitivity evaluation. A total of 289 clinical specimens from 186 patients with suspected COVID-19 and 8 proficiency testing (PT) samples were used to evaluate the diagnostic performance of the LightMix® E-gene kit against in-house developed COVID-19-RdRp/Hel and COVID-19-N RT-PCR assays. RESULTS The LightMix® E-gene kit had a limit of detection of 1.8 × 10-1 TCID50/mL, which was one log10 lower than those of the two in-house RT-PCR assays. The LightMix® E-gene kit (149/289 [51.6%]) had similar sensitivity as the in-house assays (144/289 [49.8%] for RdRp/Hel and 146/289 [50.5%] for N). All three assays gave correct results for all the PT samples. Cycle threshold (Cp) values of the LightMix® E-gene kit and in-house assays showed excellent correlation. Reproducibility of the Cp values was satisfactory with intra- and inter-assay coefficient of variation values <5%. Importantly, the LightMix® E-gene kit, when used as a stand-alone assay, was equally sensitive as testing algorithms using multiple COVID-19 RT-PCR assays. CONCLUSIONS The LightMix® E-gene kit is a rapid and sensitive assay for SARS-CoV-2 detection. It has fewer verification requirements compared to laboratory-developed tests.
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Siddharth Sridhar
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Andrew Kim-Wai Cheng
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Kit-Hang Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Garnet Kwan-Yue Choi
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Jonathan Hon-Kwan Chen
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Rosana Wing-Shan Poon
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Alan Ka-Lun Wu
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Hong Kong Special Administrative Region, China
| | - Helen Shuk-Ying Chan
- Department of Medicine, Queen Elizabeth Hospital, Hong Kong Special Administrative Region, China
| | - Sandy Ka-Yee Chau
- Department of Pathology, United Christian Hospital, Hong Kong Special Administrative Region, China
| | - Tom Wai-Hin Chung
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Owen Tak-Yin Tsang
- Department of Medicine and Geriatrics, Princess Margaret Hospital, Hong Kong Special Administrative Region, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
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10
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Yip CCY, Ho CC, Chan JFW, To KKW, Chan HSY, Wong SCY, Leung KH, Fung AYF, Ng ACK, Zou Z, Tam AR, Chung TWH, Chan KH, Hung IFN, Cheng VCC, Tsang OTY, Tsui SKW, Yuen KY. Development of a Novel, Genome Subtraction-Derived, SARS-CoV-2-Specific COVID-19-nsp2 Real-Time RT-PCR Assay and Its Evaluation Using Clinical Specimens. Int J Mol Sci 2020; 21:E2574. [PMID: 32276333 PMCID: PMC7177594 DOI: 10.3390/ijms21072574] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 01/02/2023] Open
Abstract
The pandemic novel coronavirus infection, Coronavirus Disease 2019 (COVID-19), has affected at least 190 countries or territories, with 465,915 confirmed cases and 21,031 deaths. In a containment-based strategy, rapid, sensitive and specific testing is important in epidemiological control and clinical management. Using 96 SARS-CoV-2 and 104 non-SARS-CoV-2 coronavirus genomes and our in-house program, GolayMetaMiner, four specific regions longer than 50 nucleotides in the SARS-CoV-2 genome were identified. Primers were designed to target the longest and previously untargeted nsp2 region and optimized as a probe-free real-time reverse transcription-polymerase chain reaction (RT-PCR) assay. The new COVID-19-nsp2 assay had a limit of detection (LOD) of 1.8 TCID50/mL and did not amplify other human-pathogenic coronaviruses and respiratory viruses. Assay reproducibility in terms of cycle threshold (Cp) values was satisfactory, with the total imprecision (% CV) values well below 5%. Evaluation of the new assay using 59 clinical specimens from 14 confirmed cases showed 100% concordance with our previously developed COVID-19-RdRp/Hel reference assay. A rapid, sensitive, SARS-CoV-2-specific real-time RT-PCR assay, COVID-19-nsp2, was developed.
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Affiliation(s)
- Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, HKSAR, Hong Kong, China; (C.C.-Y.Y.); (T.W.-H.C.); (V.C.-C.C.)
| | - Chi-Chun Ho
- Genomics and Bioinformatics Programme, The Chinese University of Hong Kong, HKSAR, Hong Kong, China;
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HKSAR, Hong Kong, China; (J.F.-W.C.); (K.K.-W.T.); (K.-H.C.)
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HKSAR, Hong Kong, China; (J.F.-W.C.); (K.K.-W.T.); (K.-H.C.)
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China
| | | | | | - Kit-Hang Leung
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
| | - Agnes Yim-Fong Fung
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
| | - Anthony Chin-Ki Ng
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
| | - Zijiao Zou
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
| | | | - Tom Wai-Hin Chung
- Department of Microbiology, Queen Mary Hospital, HKSAR, Hong Kong, China; (C.C.-Y.Y.); (T.W.-H.C.); (V.C.-C.C.)
| | - Kwok-Hung Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HKSAR, Hong Kong, China; (J.F.-W.C.); (K.K.-W.T.); (K.-H.C.)
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China;
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, HKSAR, Hong Kong, China; (C.C.-Y.Y.); (T.W.-H.C.); (V.C.-C.C.)
| | - Owen Tak-Yin Tsang
- Department of Medicine and Geriatrics, Princess Margaret Hospital, HKSAR, Hong Kong, China;
| | - Stephen Kwok Wing Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, HKSAR, Hong Kong, China;
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, HKSAR, Hong Kong, China; (J.F.-W.C.); (K.K.-W.T.); (K.-H.C.)
- Department of Microbiology, The University of Hong Kong, HKSAR, Hong Kong, China; (K.-H.L.); (A.Y.-F.F.); (A.C.-K.N.); (Z.Z.)
- Department of Clinical Microbiology and Infection, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, HKSAR, Hong Kong, China
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11
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 DOI: 10.1002/jmv.v92.410.1002/jmv.25674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 05/24/2023]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019-nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray-based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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12
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Zhang N, Wang L, Deng X, Liang R, Su M, He C, Hu L, Su Y, Ren J, Yu F, Du L, Jiang S. Recent advances in the detection of respiratory virus infection in humans. J Med Virol 2020; 92:408-417. [PMID: 31944312 PMCID: PMC7166954 DOI: 10.1002/jmv.25674] [Citation(s) in RCA: 250] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 01/12/2020] [Indexed: 12/20/2022]
Abstract
Respiratory tract viral infection caused by viruses or bacteria is one of the most common diseases in human worldwide, while those caused by emerging viruses, such as the novel coronavirus, 2019‐nCoV that caused the pneumonia outbreak in Wuhan, China most recently, have posed great threats to global public health. Identification of the causative viral pathogens of respiratory tract viral infections is important to select an appropriate treatment, save people's lives, stop the epidemics, and avoid unnecessary use of antibiotics. Conventional diagnostic tests, such as the assays for rapid detection of antiviral antibodies or viral antigens, are widely used in many clinical laboratories. With the development of modern technologies, new diagnostic strategies, including multiplex nucleic acid amplification and microarray‐based assays, are emerging. This review summarizes currently available and novel emerging diagnostic methods for the detection of common respiratory viruses, such as influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus, and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. It is anticipated that such data will assist researchers and clinicians to develop appropriate diagnostic strategies for timely and effective detection of respiratory virus infections. Respiratory tract viral infection including 2019‐nCoV poses great threats worldwide. Currently available and novel emerging diagnostic methods are summarized for several common respiratory viruses, including influenza virus, human respiratory syncytial virus, coronavirus, human adenovirus and human rhinovirus. Multiplex assays for simultaneous detection of multiple respiratory viruses are also described. This review is aimed to assist researchers and clinicians to develop timely and effective diagnostic strategies to detect respiratory virus infections.
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Affiliation(s)
- Naru Zhang
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou, China
| | - Lili Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Ruiying Liang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Meng Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Chen He
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanfang Hu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Yudan Su
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Jing Ren
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Fei Yu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Life and Science, Hebei Agricultural University, Baoding, China
| | - Lanying Du
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York
| | - Shibo Jiang
- Lindsley F. Kimball Research Institute, New York Blood Center, New York, New York.,Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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