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Tang Y, Zhao K, Yin HM, Yang LP, Wu YC, Li FY, Yang Z, Lu HX, Wang B, Yang Y, Zhang YZ, Yang XL. Identification and Genomic Characterization of Two Novel Hepatoviruses in Shrews from Yunnan Province, China. Viruses 2024; 16:969. [PMID: 38932262 PMCID: PMC11209087 DOI: 10.3390/v16060969] [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: 05/13/2024] [Revised: 06/11/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Hepatitis A virus (HAV), a member of the genus Hepatovirus (Picornaviridae HepV), remains a significant viral pathogen, frequently causing enterically transmitted hepatitis worldwide. In this study, we conducted an epidemiological survey of HepVs carried by small terrestrial mammals in the wild in Yunnan Province, China. Utilizing HepV-specific broad-spectrum RT-PCR, next-generation sequencing (NGS), and QNome nanopore sequencing (QNS) techniques, we identified and characterized two novel HepVs provisionally named EpMa-HAV and EpLe-HAV, discovered in the long-tailed mountain shrew (Episoriculus macrurus) and long-tailed brown-toothed shrew (Episoriculus leucops), respectively. Our sequence and phylogenetic analyses of EpMa-HAV and EpLe-HAV indicated that they belong to the species Hepatovirus I (HepV-I) clade II, also known as the Chinese shrew HepV clade. Notably, the codon usage bias pattern of novel shrew HepVs is consistent with that of previously identified Chinese shrew HepV. Furthermore, our structural analysis demonstrated that shrew HepVs differ from other mammalian HepVs in RNA secondary structure and exhibit variances in key protein sites. Overall, the discovery of two novel HepVs in shrews expands the host range of HepV and underscores the existence of genetically diverse animal homologs of human HAV within the genus HepV.
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Affiliation(s)
- Yi Tang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (Y.T.); (H.-M.Y.); (Z.Y.)
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
| | - Kai Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Hong-Min Yin
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (Y.T.); (H.-M.Y.); (Z.Y.)
| | - Li-Ping Yang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
| | - Yue-Chun Wu
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Feng-Yi Li
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Ze Yang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (Y.T.); (H.-M.Y.); (Z.Y.)
| | - Hui-Xuan Lu
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA;
| | - Yin Yang
- Department of Medical, The Second People’s Hospital of Dali Prefecture, Dali 67100, China;
| | - Yun-Zhi Zhang
- Yunnan Key Laboratory of Screening and Research on Anti-Pathogenic Plant Resources from Western Yunnan, Key Laboratory for Cross-Border Control and Quarantine of Zoonoses in Universities of Yunnan Province, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (Y.T.); (H.-M.Y.); (Z.Y.)
| | - Xing-Lou Yang
- Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; (K.Z.); (L.-P.Y.); (Y.-C.W.); (F.-Y.L.); (H.-X.L.)
- University of Chinese Academy of Sciences, Beijing 101408, China
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Hanke K, Rykalina V, Koppe U, Gunsenheimer-Bartmeyer B, Heuer D, Meixenberger K. Developing a next level integrated genomic surveillance: Advances in the molecular epidemiology of HIV in Germany. Int J Med Microbiol 2024; 314:151606. [PMID: 38278002 DOI: 10.1016/j.ijmm.2024.151606] [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: 10/31/2023] [Revised: 01/12/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Advances in the molecular epidemiological studies of the Human Immunodeficiency Virus (HIV) at the Robert Koch Institute (RKI) by laboratory and bioinformatic automation should allow the processing of larger numbers of samples and more comprehensive and faster data analysis in order to provide a higher resolution of the current HIV infection situation in near real-time and a better understanding of the dynamic of the German HIV epidemic. The early detection of the emergence and transmission of new HIV variants is important for the adaption of diagnostics and treatment guidelines. Likewise, the molecular epidemiological detection and characterization of spatially limited HIV outbreaks or rapidly growing sub-epidemics is of great importance in order to interrupt the transmission pathways by regionally adapting prevention strategies. These aims are becoming even more important in the context of the SARS-CoV2 pandemic and the Ukrainian refugee movement, which both have effects on the German HIV epidemic that should be monitored to identify starting points for targeted public health measures in a timely manner. To this end, a next level integrated genomic surveillance of HIV is to be established.
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Affiliation(s)
- Kirsten Hanke
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany.
| | - Vera Rykalina
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Uwe Koppe
- Unit 34: HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Seestraße 10, 13353 Berlin, Germany
| | | | - Dagmar Heuer
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
| | - Karolin Meixenberger
- Unit 18: Sexually transmitted bacterial Pathogens (STI) and HIV, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
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Guo L, Li B, Han P, Dong N, Zhu Y, Li F, Si H, Shi Z, Wang B, Yang X, Zhang Y. Identification of a Novel Hepacivirus in Southeast Asian Shrew ( Crocidura fuliginosa) from Yunnan Province, China. Pathogens 2023; 12:1400. [PMID: 38133285 PMCID: PMC10745850 DOI: 10.3390/pathogens12121400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/18/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023] Open
Abstract
The genus Hepacivirus contains single-stranded positive-sense RNA viruses belonging to the family Flaviviridae, which comprises 14 species. These 14 hepaciviruses have been found in different mammals, such as primates, dogs, bats, and rodents. To date, Hepacivirus has not been reported in the shrew genus of Crocidura. To study the prevalence and genetic evolution of Hepacivirus in small mammals in Yunnan Province, China, molecular detection of Hepacivirus in small mammals from Yunnan Province during 2016 and 2017 was performed using reverse-transcription polymerase chain reaction (RT-PCR). Our results showed that the overall infection rate of Hepacivirus in small mammals was 0.12% (2/1602), and the host animal was the Southeast Asian shrew (Crocidura fuliginosa) (12.5%, 2/16). Quantitative real-time PCR showed that Hepacivirus had the highest viral RNA copy number in the liver. Phylogenetic analysis revealed that the hepaciviruses obtained in this study does not belong to any designated species of hepaciviruses and forms an independent clade. To conclude, a novel hepacivirus was identified for the first time in C. fuliginosa specimens from Yunnan Province, China. This study expands the host range and viral diversity of hepaciviruses.
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Affiliation(s)
- Ling Guo
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
- Chongqing Jiangbei District Center for Disease Control and Prevention, Chongqing 400020, China
| | - Bei Li
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Peiyu Han
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
| | - Na Dong
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
| | - Yan Zhu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Fuli Li
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
| | - Haorui Si
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Zhengli Shi
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (B.L.); (Y.Z.); (H.S.); (Z.S.)
| | - Bo Wang
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650023, China
| | - Yunzhi Zhang
- Yunnan Province Key Laboratory of Anti-Pathogenic Plant Resources Screening, Yunnan Province Key University Laboratory of Zoonoses Cross-Border Prevention and Quarantine, Institute of Preventive Medicine, School of Public Health, Dali University, Dali 671000, China; (L.G.); (P.H.); (N.D.); (F.L.)
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Di Stefano M, Ismail MH, Leitner T, Faleo G, Alwazzeh MJ, Mbisa JL, Fiore JR, Santantonio TA. A novel candidate hepatitis C virus genotype 4 subtype identified by next generation sequencing full-genome characterization in a patient from Saudi Arabia. Front Microbiol 2023; 14:1285367. [PMID: 38029191 PMCID: PMC10653324 DOI: 10.3389/fmicb.2023.1285367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/03/2023] [Indexed: 12/01/2023] Open
Abstract
Background and aim Hepatitis C virus (HCV) infection is a major global public health concern, being a leading cause of chronic liver diseases such as chronic hepatitis, cirrhosis, and hepatocellular carcinoma. The virus is classified into 8 genotypes and 93 subtypes, each displaying distinct geographic distributions. Genotype 4 is the most predominant in the Middle East and Eastern Mediterranean and is associated with high rates of hepatitis C infection worldwide. This study used next-generation sequencing to fully characterize the HCV genome and identify a novel subtype within genotype 4 isolated from a 64-year-old Saudi man diagnosed with hepatitis C. Methods We analyzed the complete genome of the 141-HCV isolate using whole-genome sequencing. Results Our phylogenetic reconstructions, based on the entire genome of HCV-4 strains, revealed that the 141-HCV isolate formed a distinct group within the genotype 4 classification, providing valuable new insights into the variability of HCV. Conclusion This discovery of a previously unclassified HCV subtype within genotype 4 sheds light on the ongoing evolution and diversity of the virus. Such knowledge has significant implications for diagnostic and therapeutic approaches, as different subtypes may exhibit varying drug sensitivities and resistance profiles.
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Affiliation(s)
- Mariantonietta Di Stefano
- Section of Infectious Diseases, Department of Clinical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Mona H. Ismail
- Division of Gastroenterology, King Fahd Hospital of the University, Al-Khobar, Saudi Arabia
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Thomas Leitner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Giuseppina Faleo
- Section of Infectious Diseases, Department of Clinical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Marwan Jabr Alwazzeh
- College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
- Infectious Disease Division, King Fahd Hospital of the University, Al-Khobar, Saudi Arabia
| | - Jean Lutamyo Mbisa
- Antiviral Unit, Blood Safety, Hepatitis, Sexually Transmitted Infections, and HIV (BSHSH) Service, UK Health Security Agency, London, United Kingdom
| | - Josè Ramon Fiore
- Section of Infectious Diseases, Department of Clinical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Teresa Antonia Santantonio
- Section of Infectious Diseases, Department of Clinical and Surgical Sciences, University of Foggia, Foggia, Italy
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Eshetu A, Hauser A, Schmidt D, Bartmeyer B, Bremer V, Obermeier M, Ehret R, Volkwein A, Bock CT, Bannert N. Comparison of two immunoassays for concurrent detection of HCV antigen and antibodies among HIV/HCV co-infected patients in dried serum/plasma spots. J Virol Methods 2020; 279:113839. [PMID: 32087189 DOI: 10.1016/j.jviromet.2020.113839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/28/2020] [Accepted: 02/18/2020] [Indexed: 01/08/2023]
Abstract
Hepatitis C virus (HCV) antigen/antibody (Ag/Ab) assays offer the benefit of reducing the window period compared to assays that detect only HCV-Ab. In this study the performance of the Murex Ag/Ab (Murex, Abbott) and Monolisa Ag/Ab Ultra (Monolisa, Bio-Rad) ELISAs was compared for the use of filter dried serum/plasma spots (DS/PS) with a focus on the sensitivity and the percentage of correct positive test results. Correct positive ELISA results were assumed for samples that subsequently tested positive for HCV RNA by RT-qPCR, or RNA negative samples that tested positive in a Western blot (confirmed ELISA results). Sensitivity was evaluated from DS/PS eluates using HCV seroconversion panels [plasma samples of subtypes-(St) 1a, 2b)] and longitudinal HCV antibody positive serum panels (St 1b, 2b, 3a, and 4d). The proportion of correct positive test results was evaluated using 1102 newly diagnosed HIV positive clinical dried serum spots (DSS) eluates for screening of potential HCV co-infection. For the plasma HCV seroconversion samples, which were used as a reference for DSS eluates, the Murex became reactive earlier for antigen positive bleeds. However, for the HCV antibody positive eluates and dilutions thereof, the Monolisa demonstrated a superior sensitivity. Of the clinical DSS 22.8 % (28/123) of samples reactive in the Murex were negative in a subsequent RT-qPCR and Western blot, while only 1.9 % (2/105) of the samples reactive in the Monolisa were negative in these confirmatory assays. Our results indicate that the Monolisa provides fewer false positive results for HCV detection in DSS, whereas for undiluted plasma or serum samples, the Murex can serve as an additional diagnostic tool to narrow the window period.
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Affiliation(s)
- Amare Eshetu
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany
| | - Andrea Hauser
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany; Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel Schmidt
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Barbara Bartmeyer
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | - Viviane Bremer
- Division of HIV/AIDS, STI and Blood-borne Infections, Robert Koch Institute, Berlin, Germany
| | | | - Robert Ehret
- Medizinisches Infektiologiezentrum Berlin, Berlin, Germany
| | | | - Claus-Thomas Bock
- Division for Viral Gastroenteritis and Hepatitis Pathogens and Enteroviruses, Robert Koch Institute, Berlin, Germany
| | - Norbert Bannert
- Division of HIV and Other Retroviruses, Robert Koch Institute, Berlin, Germany; Institute of Virology, Charité Universitätsmedizin Berlin, Berlin, Germany.
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Establishment of an anti-hepatitis C virus IgG avidity test for dried serum/plasma spots. J Immunol Methods 2020; 479:112744. [PMID: 31958450 DOI: 10.1016/j.jim.2020.112744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/18/2019] [Accepted: 01/14/2020] [Indexed: 11/22/2022]
Abstract
Monitoring recency of infection helps to identify current transmission in vulnerable populations for effective disease control. We have established an in-house avidity based hepatitis C virus (HCV) recency assay based on the Monolisa Anti-HCV PLUS Version 3 ELISA kit for use of dried serum/plasma spots (DS/PS) in order to distinguish recent and long-term infections. A first panel of DS/PS (n = 218; genotype 1 n = 170 and non-genotype 1 n = 48) consisting of primary and at least one follow up sample was used to analyze the temporal changes of the Avidity Index (AI) over time. Sub-panels of longitudinal DS/PS (n = 66) and acute cases (<26 weeks; n = 34) were taken to calculate the Mean Duration of Recent Infection (MDRI) and the False Long-term Rate (FLTR), respectively. A second panel of DS/PS >104 weeks (n = 132) and a third panel of DS/PS prepared from resolved infections (≥180 days since last positive; n = 32) were used to calculate the False Recent Rate (FRR). For all genotypes, the optimal AI cut-off was determined to be 40% resulting in an MDRI of 364 days (95% CI: 223-485). FLTR was 5.9% (95% CI: 0.7-19.7), 8.3% (95% CI: 1-27), and 0% (-) and FRR was 13.6% (95% CI: 8.3-20.7), 11.7% (95% CI: 6.6-19), and 30.6% (95% CI: 9.1-61.4) for all genotypes, genotype 1, and non-genotype 1 infections, respectively. For resolved infections, the FRR was 53.1% (95% CI: 35.8-70.4). Thus, this assay performs particularly well for genotype 1 reaching a high rate of correct discriminations between infections acquired less than a year before diagnosis and those acquired earlier by applying an AI cut-off of 40%. Due to a rapid decline in avidity post resolution of an HCV infection this assay is not recommended to be used in HCV RNA negative patients.
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