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Yu J, Wen Z, Hu W, Chen M, Zhang Y, Liu S, Wang G, Wang Z, Wang D, Zhai SL, Wei WK, Li T, Liao M. Influenza D virus infection in China, 2022-2023. Emerg Microbes Infect 2024; 13:2343907. [PMID: 38738553 PMCID: PMC11097708 DOI: 10.1080/22221751.2024.2343907] [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: 12/14/2023] [Accepted: 04/11/2024] [Indexed: 05/14/2024]
Abstract
Influenza D virus (IDV) plays an important role in the bovine respiratory disease (BRD) complex. Its potential for the zoonotic transmission is of particular concern. In China, IDV has previously been identified in agricultural animals by molecular surveys with no live virus isolates reported. In this study, live IDVs were successfully isolated from cattle in China, which prompted us to further investigate the national prevalence, antigenic property, and infection biology of the virus. IDV RNA was detected in 11.1% (51/460) of cattle throughout the country in 2022-2023. Moreover, we conducted the first IDV serosurveillance in China, revealing a high seroprevalence (91.4%, 393/430) of IDV in cattle during the 2022-2023 winter season. Notably, all the 16 provinces from which cattle originated possessed seropositive animals, and 3 of them displayed the 100% IDV-seropositivity rate. In contrast, a very low seroprevalence of IDV was observed in pigs (3%, 3/100) and goats (1%, 1/100) during the same period of investigation. Furthermore, besides D/Yama2019 lineage-like IDVs, we discovered the D/660 lineage-like IDV in Chinese cattle, which has not been detected to date in Asia. Finally, the Chinese IDVs replicated robustly in diverse cell lines but less efficiently in the swine cell line. Considering the nationwide distribution, high seroprevalence, and appreciably genetic diversity, further studies are required to fully evaluate the risk of Chinese IDVs for both animal and human health in China, which can be evidently facilitated by IDV isolates reported in this study.
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Affiliation(s)
- Jieshi Yu
- State Key Laboratory of Swine and Poultry Breeding Industry, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, People’s Republic of China
| | - Zhenyu Wen
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Wanke Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People’s Republic of China
| | - Mingwang Chen
- Zhongshan Animal Disease Control Center, Zhongshan, People’s Republic of China
| | - Yuanlong Zhang
- Guangdong Animal Disease Control Center, Guangzhou, People’s Republic of China
| | - Shasha Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Gang Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, People’s Republic of China
| | - Zhao Wang
- School of Laboratory Animal & Shandong Laboratory Animal Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Dan Wang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, USA
| | - Shao-lun Zhai
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, People’s Republic of China
| | - Wen-kang Wei
- State Key Laboratory of Swine and Poultry Breeding Industry, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, People’s Republic of China
| | - Tianyu Li
- Zhongshan Animal Disease Control Center, Zhongshan, People’s Republic of China
- College of Animal Science and Technology, Guangxi University, Nanning, People’s Republic of China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, People’s Republic of China
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, People’s Republic of China
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, People’s Republic of China
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Limaye S, Shelke A, Kale MM, Kulkarni-Kale U, Kuchipudi SV. IDV Typer: An Automated Tool for Lineage Typing of Influenza D Viruses Based on Return Time Distribution. Viruses 2024; 16:373. [PMID: 38543738 PMCID: PMC10976072 DOI: 10.3390/v16030373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/24/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Influenza D virus (IDV) is the most recent addition to the Orthomyxoviridae family and cattle serve as the primary reservoir. IDV has been implicated in Bovine Respiratory Disease Complex (BRDC), and there is serological evidence of human infection of IDV. Evolutionary changes in the IDV genome have resulted in the expansion of genetic diversity and the emergence of multiple lineages that might expand the host tropism and potentially increase the pathogenicity to animals and humans. Therefore, there is an urgent need for automated, accurate and rapid typing tools for IDV lineage typing. Currently, IDV lineage typing is carried out using BLAST-based searches and alignment-based molecular phylogeny of the hemagglutinin-esterase fusion (HEF) gene sequences, and lineage is assigned to query sequences based on sequence similarity (BLAST search) and proximity to the reference lineages in the tree topology, respectively. To minimize human intervention and lineage typing time, we developed IDV Typer server, implementing alignment-free method based on return time distribution (RTD) of k-mers. Lineages are assigned using HEF gene sequences. The server performs with 100% sensitivity and specificity. The IDV Typer server is the first application of an RTD-based alignment-free method for typing animal viruses.
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Affiliation(s)
- Sanket Limaye
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (A.S.)
| | - Anant Shelke
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (A.S.)
| | - Mohan M. Kale
- Department of Statistics, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India;
| | - Urmila Kulkarni-Kale
- Bioinformatics Centre, Savitribai Phule Pune University (Formerly University of Pune), Pune 411007, India; (S.L.); (A.S.)
| | - Suresh V. Kuchipudi
- Department of Infectious Diseases and Microbiology, University of Pittsburgh School of Public Health, Pittsburgh, PA 15261, USA
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Gaudino M, Chiapponi C, Moreno A, Zohari S, O’Donovan T, Quinless E, Sausy A, Oliva J, Salem E, Fusade-Boyer M, Meyer G, Hübschen JM, Saegerman C, Ducatez MF, Snoeck CJ. Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009-22). Virus Evol 2022; 8:veac081. [PMID: 36533151 PMCID: PMC9752663 DOI: 10.1093/ve/veac081] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/25/2022] [Accepted: 08/31/2022] [Indexed: 07/30/2023] Open
Abstract
Influenza D virus (IDV) is an emerging influenza virus that was isolated for the first time in 2011 in the USA from swine with respiratory illness. Since then, IDV has been detected worldwide in different animal species, and it was also reported in humans. Molecular epidemiological studies revealed the circulation of two major clades, named D/OK and D/660. Additional divergent clades have been described but have been limited to specific geographic areas (i.e. Japan and California). In Europe, IDV was detected for the first time in France in 2012 and subsequently also in Italy, Luxembourg, Ireland, the UK, Switzerland, and Denmark. To understand the time of introduction and the evolutionary dynamics of IDV on the continent, molecular screening of bovine and swine clinical samples was carried out in different European countries, and phylogenetic analyses were performed on all available and newly generated sequences. Until recently, D/OK was the only clade detected in this area. Starting from 2019, an increase in D/660 clade detections was observed, accompanied by an increase in the overall viral genetic diversity and genetic reassortments. The time to the most recent common ancestor (tMRCA) of all existing IDV sequences was estimated as 1995-16 years before its discovery, indicating that the virus could have started its global spread in this time frame. Despite the D/OK and D/660 clades having a similar mean tMRCA (2007), the mean tMRCA for European D/OK sequences was estimated as January 2013 compared to July 2014 for European D/660 sequences. This indicated that the two clades were likely introduced on the European continent at different time points, as confirmed by virological screening findings. The mean nucleotide substitution rate of the hemagglutinin-esterase-fusion (HEF) glycoprotein segment was estimated as 1.403 × 10-3 substitutions/site/year, which is significantly higher than the one of the HEF of human influenza C virus (P < 0.0001). IDV genetic drift, the introduction of new clades on the continent, and multiple reassortment patterns shape the increasing viral diversity observed in the last years. Its elevated substitution rate, diffusion in various animal species, and the growing evidence pointing towards zoonotic potential justify continuous surveillance of this emerging influenza virus.
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Affiliation(s)
- Maria Gaudino
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Chiara Chiapponi
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna ‘Bruno Ubertini’, Brescia 25124, Italy
| | - Ana Moreno
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna ‘Bruno Ubertini’, Brescia 25124, Italy
| | - Siamak Zohari
- Department of microbiology, National Veterinary Institute, Uppsala SE-751 89, Sweden
| | - Tom O’Donovan
- Central Veterinary Research Laboratory, Celbridge, Co. Kildare W23 X3PH, Ireland
| | - Emma Quinless
- Central Veterinary Research Laboratory, Celbridge, Co. Kildare W23 X3PH, Ireland
| | - Aurélie Sausy
- Clinical and Applied Virology Group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Justine Oliva
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Elias Salem
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | | | - Gilles Meyer
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Judith M Hübschen
- Clinical and Applied Virology Group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
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Yu J, Li T, Wen Z, Wu S, Wang Z, Zheng J, Chen M, Chen F, Wei WK, Zhai SL, Liao M. Identification of D/Yama2019 Lineage-Like Influenza D Virus in Chinese Cattle. Front Vet Sci 2022; 9:939456. [PMID: 35909676 PMCID: PMC9330358 DOI: 10.3389/fvets.2022.939456] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Outbreaks of influenza D virus (IDV) continue to be reported in many countries. On the basis of the hemagglutinin-esterase fusion (HEF) gene, five IDV genetic lineages have been identified: D/OK, D/660, D/Yama2016, D/Yama2019 and D/CA2019 lineages. Previously reported IDV strains in China all form a sub-clade (D/China sub-lineage) within D/OK lineage. From October 2021 to February 2022, nasal swab samples (n = 250) were collected from apparently healthy cattle in slaughterhouses around the city of Guangzhou, China, and screened for IDV by RT-PCR. Ten samples were positive for IDV. An IDV strain with nearly complete genome sequences was identified and designated as D/bovine/CHN/JY3001/2021. Importantly, sequence alignments and phylogenetic analyses revealed that this IDV strain is genetically close to the strains (>98% homology) in the D/Yama2019 lineage that has been found only in Japan, but distant from the previously reported Chinese IDV strains (~95% similarity). These results demonstrate the emergence of D/Yama2019 lineage IDV in Chinese cattle herds, highlighting a need for future surveillance of D/Yama2019-like viruses toward better understanding both epidemiology and diversity of IDV in China.
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Affiliation(s)
- Jieshi Yu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tianyu Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Zhongshan Animal Disease Control Center, Zhongshan, China
| | - Zhenyu Wen
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou, China
| | - Siyu Wu
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Zhilin Wang
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jiaying Zheng
- Zhongshan Animal Disease Control Center, Zhongshan, China
| | - Mingwang Chen
- Zhongshan Animal Disease Control Center, Zhongshan, China
| | - Faming Chen
- Zhongshan Animal Disease Control Center, Zhongshan, China
| | - Wen-Kang Wei
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Wen-Kang Wei
| | - Shao-Lun Zhai
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, China
- Shao-Lun Zhai
| | - Ming Liao
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Key Laboratory of Zoonosis of Ministry of Agriculture and Rural Affairs, Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, South China Agricultural University, Guangzhou, China
- Maoming Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Maoming, China
- Ming Liao
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Robinson E, Schulein C, Jacobson BT, Jones K, Sago J, Huber V, Jutila M, Bimczok D, Rynda-Apple A. Pathophysiology of Influenza D Virus Infection in Specific-Pathogen-Free Lambs with or without Prior Mycoplasma ovipneumoniae Exposure. Viruses 2022; 14:1422. [PMID: 35891403 PMCID: PMC9321583 DOI: 10.3390/v14071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Polymicrobial pneumonias occur frequently in cattle, swine, and sheep, resulting in major economic losses. Individual pathogens comprising these complex infections may be mild on their own but can instead exhibit synergism or increase host susceptibility. Two examples of such pathogens, Mycoplasma ovipneumoniae (M. ovipneumoniae) and influenza D viruses (IDVs), naturally infect domestic sheep. In sheep, the role of M. ovipneumoniae in chronic nonprogressive pneumonia is well-established, but the pathogenesis of IDV infection has not previously been studied. We utilized a specific-pathogen-free sheep flock to study the clinical response to IDV infection in naïve vs. M. ovipneumoniae-exposed lambs. Lambs were inoculated intranasally with M. ovipneumoniae or mock infection, followed after four weeks by infection with IDV. Pathogen shedding was tracked, and immunological responses were evaluated by measuring acute phase response and IDV-neutralizing antibody titers. While lamb health statuses remained subclinical, M. ovipneumoniae-exposed lambs had significantly elevated body temperatures during IDV infection compared to M. ovipneumoniae-naïve, IDV-infected lambs. Moreover, we found a positive correlation between prior M. ovipneumoniae burden, early-infection IDV shedding, and IDV-neutralizing antibody response. Our findings suggest that IDV infection may not induce clinical symptoms in domestic sheep, but previous M. ovipneumoniae exposure may promote mild IDV-associated inflammation.
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Affiliation(s)
- Ema Robinson
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
| | - Clyde Schulein
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
| | - B. Tegner Jacobson
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
| | - Kerri Jones
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
| | - Jonathon Sago
- Montana State Veterinary Diagnostic Laboratory, 1911 West Lincoln Street, Bozeman, MT 59718, USA;
| | - Victor Huber
- Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, SD 57069, USA;
| | - Mark Jutila
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
| | - Diane Bimczok
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
| | - Agnieszka Rynda-Apple
- Department of Microbiology and Cell Biology, Montana State University, 2155 Analysis Drive, Bozeman, MT 59718, USA; (E.R.); (C.S.); (B.T.J.); (K.J.); (M.J.); (D.B.)
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Characterization of Influenza D Virus in Danish Calves. Viruses 2022; 14:v14020423. [PMID: 35216016 PMCID: PMC8880214 DOI: 10.3390/v14020423] [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: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/17/2022] Open
Abstract
Influenza D virus (IDV) was first described in 2011 and has been found to mainly circulate among cattle and swine populations worldwide. Nasal swab samples were collected from 100 Danish calf herds (83 dairy and 17 veal herds) from 2018-2020. Influenza D virus was detected in 12 of the herds. Samples with the lowest cycle quantification value were selected for full genome sequencing. A hemagglutinin-esterase fusion (HEF) gene sequence from a Danish IDV collected in 2015 was also included in this study. Phylogenetic analysis showed that viruses from seven of the IDV-positive herds belonged to the D/OK lineage and clustered together in the HEF tree with the IDV collected in 2015. Viruses from the four other herds belonged to the D/660 lineage, where three of the viruses clustered closely together, while the fourth virus was more phylogenetically distant in all gene segments. The high level of genetic similarity between viruses from two different herds involved in calf trading suggests that transmission occurred through the movement of calves. This study is, to our knowledge, the first to describe the characterization of IDV in calves in Denmark.
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