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Xu S, Man Y, Yu Z, Xu X, Ji J, Kan Y, Bi Y, Xie Q, Yao L. Molecular analysis of Gyrovirus galga1 variants identified from the sera of dogs and cats in China. Vet Q 2024; 44:1-8. [PMID: 38595267 PMCID: PMC11008310 DOI: 10.1080/01652176.2024.2338381] [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: 12/11/2023] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
Gyrovirus galga1 (GyVg1), a member of the Anelloviridae family and Gyrovirus genus, has been detected in chicken and human tissue samples. In this study, the DNA of GyVg1-related gyroviruses in the sera of six dogs and three cats from Central and Eastern China was identified using PCR. Alignment analysis between the nine obtained and reference GyVg1 strains revealed that the genome identity ranged from 99.20% (DOG03 and DOG04 strains) to 96.17% (DOG01 and DOG06 strains). Six recombination events were predicted in multiple strains, including DOG01, DOG05, DOG06, CAT01, CAT02, and CAT03. The predicted major and minor parents of DOG05 came from Brazil. The DOG06 strain is potentially recombined from strains originating from humans and cats, whereas DOG01 is potentially recombined from G17 (ferret-originated) and Ave3 (chicken-originated), indicating that transmissions across species and regions may occur. Sixteen representative amino acid mutation sites were identified: nine in VP1 (12 R/H, 114S/N, 123I/M, 167 L/P, 231 P/S, 237 P/L, 243 R/W, 335 T/A, and 444S/N), four in VP2 (81 A/P, 103 R/H, 223 R/G, and 228 A/T), and three in VP3 (38 M/I, 61 A/T, and 65 V/A). These mutations were only harbored in strains identified in dogs and cats in this study. Whether this is related to host tropism needs further investigation. In this study, GyVg1 was identified in the sera of dogs and cats, and the molecular characteristics prompted the attention of public health.
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Affiliation(s)
- Shuqi Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Yuanzhuo Man
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Zhengli Yu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Yunchao Kan
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou, PR China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou, PR China
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, PR China
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Su M, Wang Y, Yan J, Xu X, Zheng H, Cheng J, Du X, Liu Y, Ying J, Zhao Y, Wang Z, Duan X, Yang Y, Cheng C, Ye Z, Sun J, Sun D, Song H. Isolation and characterization of a novel S1-gene insertion porcine epidemic diarrhea virus with low pathogenicity in newborn piglets. Virulence 2024; 15:2397512. [PMID: 39282989 PMCID: PMC11407387 DOI: 10.1080/21505594.2024.2397512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) causes diarrhea and vomiting in piglets, leading to a mortality rate of 100%. Due to the high frequency of mutation, it is important to monitor the evolution of PEDV and develop potential vaccine candidates. In this study, two PEDV strains (ZJ2022 and ZQ2022) were identified by PCR. These strains were subsequently isolated, and their genome sequences, growth characteristics, and pathogenicity were compared. Phylogenetic and recombination analyses revealed that both strains belonged to GIIa-subgroup, and ZQ2022 was identified as a recombinant strain derived from ZJ2022. Further sequence analysis showed that the ZJ2022 strain had a modified top region of the S1 protein due to a three amino acid insertion (T380_Y380insGGE) in the S1 gene. According to the virus growth curve, ZJ2022 exhibited better cellular adaptation than ZQ2022, with higher viral titers from 8 hpi to 24 hpi. Additionally, ZQ2022 exhibited a high level of pathogenicity, causing severe diarrhea in piglets at 36 hpi and a 100% mortality rate by 96 hpi. In contrast, ZJ2022 showed lower pathogenicity, inducing severe diarrhea in piglets at 60 hpi, with a mortality rate of 60% at 96 hpi and 100% at 120 hpi. In summary, our findings provided evidence of the undergoing mutations in Chinese PEDV strains. Furthermore, the S gene insertion strain ZJ2022 exhibited strong cellular adaptability and low pathogenicity, making it a potential candidate strain for vaccine development.
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Affiliation(s)
- Mingjun Su
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
- Ningbo Creator Animal Pharmaceutical Co. Ltd, Ningbo, Zhejiang Province, PR China
| | - Yutao Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Junfang Yan
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Xiangwen Xu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Huihua Zheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Jiongze Cheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Xiaoxu Du
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Yijia Liu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Jiale Ying
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Yulin Zhao
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Ziqi Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Xing Duan
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Yang Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Changyong Cheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Zhihui Ye
- Ningbo Creator Animal Pharmaceutical Co. Ltd, Ningbo, Zhejiang Province, PR China
| | - Jing Sun
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
| | - Dongbo Sun
- Laboratory for the Prevention and Control of Swine Infectious Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, PR China
| | - Houhui Song
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, Zhejiang Province, China
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3
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Jayappa K, Rajkhowa TK, Gaikwad SS. Canine parvovirus in North-East India: a phylogenetic and evolutionary analysis. Vet Q 2024; 44:1-13. [PMID: 39350725 PMCID: PMC11445921 DOI: 10.1080/01652176.2024.2408742] [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: 10/17/2023] [Revised: 08/09/2024] [Accepted: 09/05/2024] [Indexed: 10/04/2024] Open
Abstract
Canine parvovirus type 2 (CPV-2) infection in dogs is considered as one of the most common cause of morbidity and mortality in young dogs and continues to occur with high incidence worldwide. Despite a single-stranded DNA virus, CPV-2 possesses a high mutation rate which has led to the development of new variants from time to time. These variants are classically classified based on the amino acid markers present in the VP2 gene. In this study, we examined 20 different cases of CPV-2 infection from seven different states of the North East region (NER) of India. The near-complete genome sequences of all these isolates were subjected to phylodynamic and phylogeographic analysis to evaluate the genetic diversity and geographical spread of CPV-2 variants. Analysis of the deduced amino acid sequences revealed residues characteristic of the 'Asian CPV-2c lineage' in all the 20 sequences confirming it as the dominant strain circulating in NER, India. The phylogenetic analysis based on the whole genome showed that all 20 sequences formed a monophyletic clade together with other Asian CPV-2c sequences. Furthermore, phylogeographic analysis based on the VP2 gene showed the likely introduction of Asian CPV-2c strain to India from China. This study marks the first comprehensive report elucidating the molecular epidemiology of CPV-2 in India.
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Affiliation(s)
- Kiran Jayappa
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
| | - Tridib Kumar Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences & Animal Husbandry, Central Agricultural University (I), Selesih, Aizawl, Mizoram, India
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Zhang Z, Man Y, Xu X, Wang Y, Ji J, Yao L, Bi Y, Xie Q. Genetic heterogeneity and potential recombination across hosts of Gyrovirus galga1 in central and eastern China during 2021 to 2024. Poult Sci 2024; 103:104149. [PMID: 39154608 PMCID: PMC11381743 DOI: 10.1016/j.psj.2024.104149] [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: 05/27/2024] [Revised: 07/16/2024] [Accepted: 07/27/2024] [Indexed: 08/20/2024] Open
Abstract
Gyrovirus galga1 (GyVg1), formerly known as AGV2, was initially identified in chickens in southern Brazil. The prevalence of GyVg1 from 2021 to 2024 in 28 out of the 63 poultry farms located in Jiangsu, Anhui, Henan, Hunan, Shandong, and Hubei provinces in eastern and central China was detected via PCR. The complete genomes of the 28 strains were sequenced and exhibited a full length of 2,376 bp. Similarity analysis of these strains did not suggest definite correlation with evolutionary branching and geographical distribution. Compared with the reference GyVg1 strains, HN2202 shared the highest similarity of 99.71% with HLJ1511 (chicken-originated) from northeastern China in 2015 to 2016. Recombination analysis revealed that AH2102 was a potential recombinant of peafowl-originated HN2019-PF1 and chicken-originated HLJ1506-2, whereas HN2304 was a recombinant of peafowl-originated HN2019-PF1 and the Hungarian ferret strain G13. Mutation site analysis of the capsid protein revealed that highly mutated regions occurred between sites 288 to 316 and 383 to 419. These results indicate that GyVg1 may have undergone an interspecies transmission, which involved complex mutations and recombination. This study may provide a reference for subsequent investigations targeting the molecular epidemiology and viral evolution of GyVg1.
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Affiliation(s)
- Zhibin Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, China
| | - Yuanzhuo Man
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, China
| | - Xin Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, China
| | - Yan Wang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, China
| | - Jun Ji
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, China.
| | - Lunguang Yao
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Henan Provincial Engineering, and Technology Center of Health Products for Livestock and Poultry, Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Nanyang Normal University, Nanyang, 473061, China
| | - Yingzuo Bi
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingmei Xie
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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Şevik M, Zerek A, Erdem İ, Yaman M. Evidence of circulating recombinants between deformed wing virus and Varroa destructor virus-1 in honey bee colonies in Türkiye. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-11. [PMID: 39465573 DOI: 10.1017/s000748532400052x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Deformed wing virus (DWV), which is an important honey bee virus transmitted by Varroa destructor (V. destructor), causes colony losses in honey bee colonies. This study aimed to investigate the prevalence and genetic diversity of DWV in honey bees in Türkiye and to determine the role of V. destructor in the transmission of the genetic variants of DWV. Honey bee samples were collected from 62 apiaries, by simple random sampling, during March 2022 and April 2023. The presence of V. destructor in collected bee samples was examined using a stereo microscope. Real-time RT-PCR was used for the detection of DWV-A and DWV-B (Varroa destructor virus-1 (VDV-1)) viruses. Genetic characterisation of the positive samples was conducted by sequencing polyprotein genomic region. Considering the V. destructor infestation rate of 3% as relevant, out of the 62 apiaries examined, 17 (27.4%) were positive. However, DWV-A and VDV-1 specific RNA was not detected in V. destructor samples. VDV-1 specific RNA was detected in 6.5% (4/62) of the apiaries, whereas DWV-A was not detected in the sampled apiaries. Phylogenetic analysis showed that isolates detected in this study were located in a separate cluster from previously characterised DWV-A and VDV-1 isolates. According to RDP4 and GARD analyses, DWV-VDV-1 recombination breakpoints were detected in field isolates. To the best our knowledge, this is the first report of the presence of VDV-1-DWV recombinants in Türkiye. Further studies are needed to determine the impact of VDV-1-DWV recombinants and their virological and antigenic properties.
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Affiliation(s)
- Murat Şevik
- Department of Virology, Veterinary Faculty, Necmettin Erbakan University, Ereğli, 42310 Konya, Turkey
| | - Aykut Zerek
- Department of Parasitology, Veterinary Faculty, Hatay Mustafa Kemal University, Antakya, 31060 Hatay, Turkey
| | - İpek Erdem
- Department of Parasitology, Veterinary Faculty, Hatay Mustafa Kemal University, Antakya, 31060 Hatay, Turkey
| | - Mehmet Yaman
- Department of Parasitology, Veterinary Faculty, Hatay Mustafa Kemal University, Antakya, 31060 Hatay, Turkey
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Wang X, Zhu L, Huo C, He D, Tian H, Fan X, Lyu Y, Li Y. Genetic characterization of immune adaptor molecule MyD88 in Culex pipiens complex (Diptera: Culicidae) mosquitoes from China. JOURNAL OF MEDICAL ENTOMOLOGY 2024:tjae128. [PMID: 39436778 DOI: 10.1093/jme/tjae128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/18/2024] [Accepted: 09/21/2024] [Indexed: 10/25/2024]
Abstract
Mosquitoes of the Culex (Cx.) pipiens complex are vectors of severe diseases including West Nile fever by West Nile virus, Japanese encephalitis by Japanese encephalitis virus, and Lymphatic filariasis by filarial nematode Wuchereria bancrofti. As a major portion of mosquito immune system, the Toll pathway implicates in response against infections of mosquito-borne pathogens and biocontrol agents. The genetic diversity of immune-related molecules is expected to be a feasible and effective introduction to expand our knowledge of the mosquito-microbe interplay. However, a comprehensive description is currently lacking regarding the genetic characteristic of the Toll pathway molecules in Cx. pipiens complex mosquitoes. In the present study, genetic changes in Cx. pipiens complex MyD88 (Myeloid differentiation primary response protein 88) were analyzed as a precedent for the Toll pathway molecules in this taxon. MyD88 is a critical adaptor of the pathway transducing signals from TIR-containing receptors to downstream death domain-containing molecules. Our results revealed that adaptive selection has influenced the genetic changes of the molecule, giving rise to acceleration of diversity at a number of amino acid sites. The adaptively selected sites lie in the death domain, intermediate domain, and C-terminal extension. The characteristics of the genetic changes shed insights into the prominent molecular-level structural basis and the involvement strategy of the adaptor in the arms race against exogenous challenges. This finding would be beneficial for further exploration and deeper understanding of the mosquitoes' vectorial capacity and facilitating the effectiveness and sustainability of the biocontrol agents.
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Affiliation(s)
- Xueting Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Lilan Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Caifei Huo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Dan He
- College of Animal Science, Guizhou University, Guiyang, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, People's Republic of China
| | - Haifeng Tian
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, People's Republic of China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
| | - Yongqing Lyu
- The First Hospital of Kunming, Kunming, People's Republic of China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, People's Republic of China
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Wei X, Wang L, Li M, Qi J, Kang L, Hu G, Gong C, Wang C, Wang Y, Huang F, Gao GF. Novel imported clades accelerated the RSV surge in Beijing, China, 2023-2024. J Infect 2024; 89:106321. [PMID: 39426631 DOI: 10.1016/j.jinf.2024.106321] [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: 08/01/2024] [Revised: 10/10/2024] [Accepted: 10/13/2024] [Indexed: 10/21/2024]
Abstract
OBJECTIVES Despite the optimization of the zero-COVID policy in late 2022, there was a subsequent increase noted in the number of respiratory syncytial virus (RSV) cases in Northern China. In this study, we investigated and characterized the dynamics of this surge at the genomic level in Beijing, China. METHODS Patients with acute respiratory tract infections (ARTIs) were enrolled from 35 sentinel hospitals in Beijing, China. Epidemiological investigations, G gene amplification, and whole-genome sequencing were performed, followed by epidemiological analysis, imported clade detection, and mutation identification. We also combined global data to illustrate the biological and epidemiological characteristics of the emerging clades. RESULTS A total of 60,423 patients with ARTIs were recruited between January 2015 and January 2024. The RSV peak observed in the winter of 2023 was the highest in the past 9 years. Two novel imported clades, A.D.5.2 and B.D.E.1, were detected for the first time in China. This surge was mainly driven by B.D.E.1, which exhibited a significantly higher proportion of older individuals both in Beijing and globally. Seven non-synonymous mutations in B.D.E.1 were found in Beijing. B.D.E.1 had more sites suffering from positive selection than its parent. CONCLUSIONS The novel imported clade B.D.E.1 accelerated an unprecedented RSV surge in Beijing, presenting noteworthy epidemiological and biological characteristics. Continuous RSV genome monitoring has important implications for RSV outbreak identification, genetic diversity tracking, vaccine development, and strategy implementation.
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Affiliation(s)
- Xiaofeng Wei
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; School of Public Health, Capital Medical University, Beijing 100069, China
| | - Liang Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Maozhong Li
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; Beijing Research Center for Respiratory Infectious Diseases, Beijing 100013, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
| | - Lu Kang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; Beijing Research Center for Respiratory Infectious Diseases, Beijing 100013, China
| | - Geng Hu
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; Beijing Research Center for Respiratory Infectious Diseases, Beijing 100013, China
| | - Cheng Gong
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; Beijing Research Center for Respiratory Infectious Diseases, Beijing 100013, China
| | - Chengcheng Wang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; School of Public Health, Capital Medical University, Beijing 100069, China
| | - Yiting Wang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; Beijing Research Center for Respiratory Infectious Diseases, Beijing 100013, China
| | - Fang Huang
- Beijing Center for Disease Prevention and Control, Beijing Academy for Preventive Medicine, Beijing Institute of Tuberculosis Control Research and Prevention, Beijing 100013, China; School of Public Health, Capital Medical University, Beijing 100069, China; Beijing Research Center for Respiratory Infectious Diseases, Beijing 100013, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China.
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Zhao YY, Ma X, Chen XM, Song YP, Zheng LL, Ma SJ, Chen HY. Molecular detection and genetic characteristics of porcine reproductive and respiratory syndrome virus in central China. Microb Pathog 2024; 197:107024. [PMID: 39426634 DOI: 10.1016/j.micpath.2024.107024] [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: 01/15/2024] [Revised: 09/27/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
Abstract
Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically devastating viral diseases in the global pork industry. To further clarify the epidemic characteristics of the virus, 365 clinical samples were collected from diseased pigs suffering from abortion and respiratory disease from 2018 to 2023 on 63 pig farms in Henan and Shanxi provinces, and screened for the presence of PRRSV using reverse transcription-polymerase chain reaction (RT-PCR). A total of 62 clinical samples (62/365, 16.99 %) were positive for PRRSV, and subsequently, full-length ORF5 gene sequences of 29 PRRSV strains and the complete genome sequence of one PRRSV HeN-HC isolate were obtained and analyzed. Phylogenetic analysis based on the ORF5 gene showed that 22 of the 29 PRRSV2 strains belonged to sublineage 1.8 (NADC30-like), 5 belonged to sublineage 8.5 (HP-PRRSV), and 2 belonged to sublineage 5.1 (VR-2332-like), indicating that both HP-PRRSV and NADC30-like strains were mainly circulating in Henan and Shanxi provinces. Compared to VR-2332 strain, different types of amino acid mutations were found in the GP5 protein of these 29 strains, and the amino acid deletions were displayed in the Nsp2 protein of the HeN-HC isolate, leading to the variation of protein structures. It is noteworthy that recombination events were identified in the HeN-Ping and HeN-B strains. In addition, a total of 60, 094 pig serum samples from Henan province were collected, and the positive rate of specific antibodies against PRRSV was 86.37 % from 2019 to 2022, and 86.66 %, 84.85 %, 87.54 % and 86.30 % in 2019, 2020, 2021 and 2022, respectively. Overall, this study provides valuable insights into the molecular epidemiology and evolution of PRRSV circulating in central China.
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Affiliation(s)
- You-Yi Zhao
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Xiao Ma
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Xi-Meng Chen
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Ya-Peng Song
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Lan-Lan Zheng
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China; International Joint Research Center of National Animal Immunology, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China
| | - Shi-Jie Ma
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China; International Joint Research Center of National Animal Immunology, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China.
| | - Hong-Ying Chen
- Ministry of Education Key Laboratory for Animal Pathogens and Biosafety, College of Veterinary Medicine, Henan Agricultural University, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China; International Joint Research Center of National Animal Immunology, Zhengdong New District Longzi Lake 15#, Zhengzhou, 450046, People's Republic of China.
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9
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Chu XN, Shah PT, Ma ZH, Wang Y, Xing L. Genotyping and phylogeographic dynamics of coxsackievirus A16. Heliyon 2024; 10:e38248. [PMID: 39381092 PMCID: PMC11456955 DOI: 10.1016/j.heliyon.2024.e38248] [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: 04/04/2024] [Revised: 09/20/2024] [Accepted: 09/20/2024] [Indexed: 09/25/2024] Open
Abstract
Coxsackievirus A16 (CV-A16) is one of the major pathogens of Hand, Foot and Mouth disease. Here, we analyzed 287 full-length genome sequences of CV-A16 found worldwide from 1994 to 2019 to see the genomic evolution characteristics. Full-length genome-based phylogenetic tree divided the viruses into five different genotypes, G-a to G-e. The CV-A16 strains circulating in China dominate G-a and G-c, but can also be found in other genotypes including G-b and G-e. Phylogeographic analysis showed a high diversity of CV-A16 distribution. In addition, recombination was shown to drive the genomic evolution of CV-A16 during past decades. However, the structural proteins still remain relative conserved while there is extensive genomic recombination. This study updates the phylogenetic and phylogeographic information of CV-A16 and provides insights into the genetic characteristics of CV-A16.
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Affiliation(s)
- Xia-Nan Chu
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, Shanxi province, China
| | - Pir Tariq Shah
- Faculty of Medicine, School of Biomedical Engineering, Dalian University of Technology, No.2 Linggong Road, Dalian, 116024, Liaoning province, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, 264000, Shandong province, China
| | - Zi-Hui Ma
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, Shanxi province, China
| | - Yan Wang
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, Shanxi province, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, Shanxi province, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, 92 Wucheng Road, Taiyuan, 030006, China
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10
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Tessmann A, Sumienski J, Sita A, Mallmann L, Birlem GE, da Silva Nunes NJ, Lupion CG, Eckert JS, Demoliner M, Gularte JS, de Almeida PR, Spilki FR, Weber MN. Domestic cat hepadnavirus genotype B is present in Southern Brazil. Virus Genes 2024:10.1007/s11262-024-02115-1. [PMID: 39397195 DOI: 10.1007/s11262-024-02115-1] [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: 04/12/2024] [Accepted: 10/02/2024] [Indexed: 10/15/2024]
Abstract
Domestic cat hepadnavirus (DCH) (Orthohepadnavirus felisdomestici) is an emerging virus related to the hepatitis B virus (HBV) already reported in many countries. The molecular prevalence of DCH varies widely in the regions investigated so far. In the present work, we reported the presence of DCH in Brazil. Sixty cat serum samples tested by DCH presence using PCR and 1.67% (1/60) were positive, similar to the low positive molecular rates reported in United States and Japan. The DCH full-length genome was classified in genotype B, which is uncommon since this genotype was only reported once in Japan. The DCH-positive sample was obtained in a stray cat female apparently healthy, presenting ALT, AST, and ALKP normal values, and negative for FIV and FeLV. Due the low positivity rate detected, some factors as alteration in hepatic enzymes and FIV/FeLV infection could not be evaluated. Other works are necessary to statistically validate these observations in Brazil.
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Affiliation(s)
- Alaíse Tessmann
- Hospital Veterinário, Universidade Feevale, Campo Bom, RS, Brazil
| | | | - Alexandre Sita
- Hospital Veterinário, Universidade Feevale, Campo Bom, RS, Brazil
| | - Larissa Mallmann
- Hospital Veterinário, Universidade Feevale, Campo Bom, RS, Brazil
| | | | | | | | | | - Meriane Demoliner
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Juliana Schons Gularte
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, RS, Brazil
- Laboratório de Imunologia e Biologia Molecular, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil
| | - Paula Rodrigues de Almeida
- Hospital Veterinário, Universidade Feevale, Campo Bom, RS, Brazil
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Fernando Rosado Spilki
- Hospital Veterinário, Universidade Feevale, Campo Bom, RS, Brazil
- Laboratório de Microbiologia Molecular, Universidade Feevale, Novo Hamburgo, RS, Brazil
| | - Matheus Nunes Weber
- Laboratório de Imunologia e Biologia Molecular, Faculdade de Veterinária, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, Brazil.
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11
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Li F, Zhu Y, Li Q, Guan X, Zhang H, Li C, Zhang M, Li L, Fu Y, Duan Y, Huang L, Xie Z, Chen X. Genomic characteristics of human respiratory syncytial virus from children in China during 2017-2020. Arch Virol 2024; 169:219. [PMID: 39387930 DOI: 10.1007/s00705-024-06138-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 08/10/2024] [Indexed: 10/12/2024]
Abstract
Acute lower respiratory tract infections (ALRTIs) are a leading cause of mortality in young children worldwide due to human respiratory syncytial virus (RSV). The aim of this study was to monitor genetic variations in RSV and provide genomic data support for RSV prevention and control. A total of 105 complete RSV genome sequences were determined during 2017-2020. Phylogenetic analysis showed that all of the RSVA sequences were of genotype ON1, and all of the RSVB sequences were of genotype BA9. Notably, a phylogenetic tree based on the whole genome had more branches than a tree based on the G gene. In comparison to the RSV prototype sequences, 71.43% (50/70) of the ON1 sequences had five amino acid substitutions (T113I, V131N, N178G, H258Q, and H266L) that occurred simultaneously, and 68.57% (24/35) of the BA9 genotype sequences had 12 amino acid substitutions, four of which (A131T, T137I, T288I, and T310I) occurred simultaneously. In the F gene, there were 19 amino acid substitutions, which were mainly located in the antigenic sites Ø, II, V, and VII. Other amino acid substitutions were found in the NS1, NS2, P, SH, and L proteins. No significant evidence of recombination was found in any of the sequences. These findings provide important data that will be useful for prevention, control, and vaccine development against RSV.
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Affiliation(s)
- Fei Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Qiuping Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaolei Guan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Hailin Zhang
- The 2nd Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Changchong Li
- The 2nd Affiliated Hospital, Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325027, China
| | - Meng Zhang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Lei Li
- Yinchuan Maternal and Child Health Care Hospital, Yinchuan, 750001, China
| | - Yiliang Fu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Yali Duan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Luci Huang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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12
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Bouzidi HS, Sen S, Piorkowski G, Pezzi L, Ayhan N, Fontaine A, Canivez T, Geulen M, Amaral R, Grard G, Durand GA, de Lamballerie X, Touret F, Klitting R. Genomic surveillance reveals a dengue 2 virus epidemic lineage with a marked decrease in sensitivity to Mosnodenvir. Nat Commun 2024; 15:8667. [PMID: 39384752 PMCID: PMC11464713 DOI: 10.1038/s41467-024-52819-z] [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: 04/10/2024] [Accepted: 09/23/2024] [Indexed: 10/11/2024] Open
Abstract
Dengue fever is the most important arbovirosis for public health, with more than 5 million cases worldwide in 2023. Mosnodenvir is the first anti-dengue compound with very high preclinical pan-serotype activity, currently undergoing phase 2 clinical evaluation. Here, by analyzing dengue virus (DENV) genomes from the 2023-2024 epidemic in the French Caribbean Islands, we show that they all exhibit mutation NS4B:V91A, previously associated with a marked decrease in sensitivity to mosnodenvir in vitro. Using antiviral activity tests on four clinical and reverse-genetic strains, we confirm a marked decrease in mosnodenvir sensitivity for DENV-2 ( > 1000 fold). Finally, combining phylogenetic analysis and experimental testing for resistance, we find that virus lineages with low sensitivity to mosnodenvir due to the V91A mutation likely emerged multiple times over the last 30 years in DENV-2 and DENV-3. These results call for increased genomic surveillance, in particular to track lineages with resistance mutations. These efforts should allow to better assess the activity profile of DENV treatments in development against circulating strains.
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Affiliation(s)
- Hawa Sophia Bouzidi
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Selin Sen
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Laura Pezzi
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Nazli Ayhan
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Albin Fontaine
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Institut de Recherche Biomédicale des Armées (IRBA), Unité de virologie, Marseille, France
| | - Thomas Canivez
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Manon Geulen
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Rayane Amaral
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
| | - Gilda Grard
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Guillaume André Durand
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France.
| | - Raphaëlle Klitting
- Unité des Virus Émergents (Aix-Marseille Université, Università di Corsica, IRD 190, Inserm 1207, IRBA), Marseille, France.
- Centre National de Référence des Arbovirus, Inserm-IRBA, Marseille, France.
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Deiana M, Malagò S, Mori A, Accordini S, Matucci A, Passarelli Mantovani R, Gianesini N, Huits R, Piubelli C, Gobbi FG, Capobianchi MR, Castilletti C. Full Genome Characterization of the First Oropouche Virus Isolate Imported in Europe from Cuba. Viruses 2024; 16:1586. [PMID: 39459919 PMCID: PMC11512199 DOI: 10.3390/v16101586] [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: 09/06/2024] [Revised: 10/03/2024] [Accepted: 10/07/2024] [Indexed: 10/28/2024] Open
Abstract
On 27 May 2024, the Cuban Ministry of Health reported the first outbreak of Oropouche fever on the island. The etiologic agent, Oropouche virus (OROV), is a poorly understood arbovirus that has been known since the 1960s and represents a public health burden in Latin America. We report the whole-genome characterization of the first European OROV isolate from a returning traveler from Cuba with Oropouche fever-like symptoms. The isolate was obtained from the patient's serum; whole-genome sequencing was performed by next-generation sequencing, followed by phylogenetic analysis and genetic variability studies. The analysis showed that the most closely related sequence was from the French Guiana 2020 outbreak. Interestingly, our isolate is a reassortant virus, included in a highly supported monophyletic clade containing recent OROV cases (Brazil 2015-Colombia 2021), separated from the other four previously known genotypes. More deeply, it was found to be included in a distinct branch containing the sequences of the Brazil 2022-2024 outbreak. The reassortment event involved the S and L segments, which have high similarity with sequences belonging to a new cluster (here defined as OROV_SCDC_2024), while the M segment shows high similarity with older sequences. These results likely describe the viral strain responsible for the current outbreak in Cuba, which may also reflect the ongoing outbreak in Latin America. Further studies are needed to understand how OROV evolves towards traits that facilitate its spread and adaptation outside its original basin, and to track its spread and evolution in the European continent.
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Affiliation(s)
- Michela Deiana
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Simone Malagò
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
- PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Antonio Mori
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Silvia Accordini
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Andrea Matucci
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Rebeca Passarelli Mantovani
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Natasha Gianesini
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Ralph Huits
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Chiara Piubelli
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Federico Giovanni Gobbi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
- Department of Clinical and Experimental Sciences, University of Brescia, 25121 Brescia, Italy
| | - Maria Rosaria Capobianchi
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
| | - Concetta Castilletti
- Department of Infectious-Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar di Valpolicella, 37024 Verona, Italy; (M.D.); (S.M.); (A.M.); (S.A.); (A.M.); (R.P.M.); (N.G.); (R.H.); (F.G.G.); (M.R.C.); (C.C.)
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14
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Magdy M, Werner O, Patiño J, Ros RM. Landscape Heterogeneity Drives Genetic Diversity in the Highly Dispersive Moss Funaria hygrometrica Hedw. PLANTS (BASEL, SWITZERLAND) 2024; 13:2785. [PMID: 39409657 PMCID: PMC11478527 DOI: 10.3390/plants13192785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 09/23/2024] [Accepted: 10/01/2024] [Indexed: 10/20/2024]
Abstract
Funaria hygrometrica, a cosmopolitan moss species known for its remarkable dispersal capacity, was selected as the focal organism to investigate the relationship between landscape features and genetic diversity. Our study encompassed samples collected from two distinct regions: the Spanish Sierra Nevada Mountains (SN), characterized by a diverse landscape with an altitudinal difference of nearly 3500 m within a short distance, and the Murcia Region (MU) in Southeast Spain, characterized by a uniform landscape akin to the lowlands of Sierra Nevada. Genotyping analysis targeted three genetic regions: the nuclear ribosomal internal transcribed spacer (nrITS), the chloroplast rps3-rpl16 region, and the mitochondrial rpl5-rpl16 spacer. Through this analysis, we aimed to assess genetic variability and population structure across these environmentally contrasting regions. The Sierra Nevada populations exhibited significantly higher haplotype diversity (Hd = 0.78 in the highlands and 0.67 overall) and nucleotide diversity (π% = 0.51 for ITS1) compared to the Murcia populations (Hd = 0.35, π% = 0.14). Further investigation unveiled that samples from the lowlands of Sierra Nevada showed a closer genetic affinity to Murcia than to the highlands of Sierra Nevada. Furthermore, the genetic differentiation between highland and lowland populations was significant (ΦST = 0.55), with partial Mantel tests and ResistanceGA analysis revealing a strong correlation between ITS1-based genetic diversity and landscape features, including altitude and bioclimatic variables. Our study elucidated potential explanations for the observed genetic structuring within F. hygrometrica samples' populations. These included factors such as a high selfing rate within restricted habitats, a limited average dispersal distance of spores, hybrid depression affecting partially incompatible genetic lineages, and recent migration facilitated via human activities into formerly unoccupied areas of the dry zones of Southeast Spain.
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Affiliation(s)
- Mahmoud Magdy
- Department of Plant Biology, Faculty of Biology, Murcia University, 30100 Murcia, Spain;
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, Murcia University, 30100 Murcia, Spain;
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology, (IPNA-CSIC), 38206 Tenerife, Spain;
| | - Rosa María Ros
- Department of Plant Biology, Faculty of Biology, Murcia University, 30100 Murcia, Spain;
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15
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Chang H, Gao X, Wu Y, Wang F, Lai M, Zheng J, Qiu Y, He Y, Liang X, Yuan K, Lin L, Zhao H, Zhang G, Li Q, Sun Y. Genomic and pathogenicity analysis of two novel highly pathogenic recombinant NADC30-like PRRSV strains in China, in 2023. Microbiol Spectr 2024; 12:e0036824. [PMID: 39162500 PMCID: PMC11448138 DOI: 10.1128/spectrum.00368-24] [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: 02/11/2024] [Accepted: 05/29/2024] [Indexed: 08/21/2024] Open
Abstract
Porcine reproductive and respiratory syndrome viruses (PRRSVs) exhibit high mutability and recombination, posing challenges to their immunization and control. This study isolated two new PRRSV strains, GD-7 and GX-3, from samples collected in Guangdong and Guangxi in 2023. Whole-genome sequencing, along with phylogenetic and recombination analyses, confirmed that GD-7 and GX-3 are natural novel recombinant strains of NADC30 PRRSV. Moreover, we established a pathogenicity model for piglets and sows based on the two isolates. The results of piglet pathogenicity revealed that both GD-7 and GX-3 caused clinical symptoms such as fever, loss of appetite, depression, and slow weight gain. Moreover, we observed that the mortality rate of GD-7-inoculated group piglets was 33.3%, which was similar to that of piglets infected with other highly pathogenic PRRSV strains and exceeded the mortality rate of most NADC30-like PRRSV. In pregnant sow models, the survival rate of sows in the GD-7 group was 75%, in contrast to the GX-3 group, where no sow mortality was observed, and both strains resulted in abortion, mummified fetuses, and stillbirths. These results highlight the elevated pathogenicity of these recombinant strains in sows, with GD-7 mainly causing sows to abort, and GX-3 mainly causing sows to give birth to mummified fetuses. This study introduces two distinct clinical recombinant PRRSV strains that differ from the prevalent strains in China. This research furthers our understanding of the epidemiology of PRRSV and underscores the significance of ongoing monitoring and research in the face of evolving virus strains. Moreover, these discoveries act as early warnings, underscoring the necessity for active control and immunization against PRRSV.IMPORTANCESince the discovery of NADC30-like PRRSV in China in 2013, it has gradually become the dominant strain of PRRSV in China. NADC30-like PRRSV exhibits high recombination characteristics, constantly recombining with different strains, leading to the emergence of numerous novel strains. Of particular importance is the observation that NADC30-like PRRSV with different recombination patterns exhibits varying pathogenicity, which has a significant impact on the pig farming industry. This emphasizes the necessity of monitoring and responding to evolving PRRSV strains to develop effective immunization and control strategies. In this paper, we conducted pathogenicity studies on the isolated NADC30-like PRRSV and analyzed the differences in the genomes and pathogenicity of the different strains by recording clinical symptoms, temperature changes, detoxification tests, and changes in viremia and histopathology in infected pigs. This was done to provide a theoretical basis for the epidemiological situation and epidemic prevention and control of PRRSV.
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Affiliation(s)
- Hao Chang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Xiaopeng Gao
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Yu Wu
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
| | - Fang Wang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Minting Lai
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jiaying Zheng
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
| | - Yingwu Qiu
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
| | - Yiping He
- Guangzhou Yue Xiu animal husbandry food technology limited, Guangzhou, China
| | - Xiangjie Liang
- Guangzhou Yue Xiu animal husbandry food technology limited, Guangzhou, China
| | - Kun Yuan
- Guangzhou Yue Xiu animal husbandry food technology limited, Guangzhou, China
| | - Limiao Lin
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
| | - Haishen Zhao
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
| | - Guihong Zhang
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qunhui Li
- Wen’s Group Academy, Wen’s Foodstuffs Group Co., Ltd., Xinxing, Guangdong, China
| | - Yankuo Sun
- Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, China
- National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
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16
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Zhu Y, Sun Y, Li C, Lu G, Jin R, Xu B, Shang Y, Ai J, Wang R, Duan Y, Chen X, Xie Z. Genetic characteristics of human parainfluenza viruses 1-4 associated with acute lower respiratory tract infection in Chinese children, during 2015-2021. Microbiol Spectr 2024; 12:e0343223. [PMID: 39264196 PMCID: PMC11448424 DOI: 10.1128/spectrum.03432-23] [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: 09/21/2023] [Accepted: 08/09/2024] [Indexed: 09/13/2024] Open
Abstract
Human parainfluenza viruses (HPIVs) are a significant cause of acute lower respiratory tract infections (ALRTIs) among young children and elderly individuals worldwide. The four types of HPIVs (HPIV1-4) can cause recurrent infections and pose a significant economic burden on health care systems globally. However, owing to the limited availability of complete genome sequences, the genetic evolution of these viruses and the development of vaccines and antiviral treatments are hampered. To address this issue, this study utilized next-generation sequencing to obtain 156 complete genome sequences of HPIV1-4, which were isolated from hospitalized children with ALRTIs in six regions of China between 2015 and 2021. This study revealed multiple clades, lineages, or sublineages of HPIVs circulating in mainland China, with a novel clade D of HPIV1 identified as geographically restricted to China. Moreover, this study identified the endemic dominant genotype of HPIV3, lineage C3, which has widely spread and continuously circulated in China. Bioinformatic analysis of the genome sequences revealed that the proteins of HPIV3 possessed the most variable sites, with the P protein showing more diversity than the other proteins among all types of HPIVs. The HN proteins of HPIV1-3 are all under negative/purifying selection, and two amino acid substitutions in the HN proteins correspond to known mAb neutralizing sites in the two HPIV3 strains. These findings provide crucial insights into the genetic diversity and evolutionary dynamics of HPIVs circulating among children in China and may facilitate research on the molecular diagnosis, vaccine development, and surveillance of HPIVs.IMPORTANCEPhylogenetic analysis revealed the prevalence of multiple clades, lineages, or sublineages of human parainfluenza viruses (HPIVs) circulating in mainland China. Notably, a unique evolutionary branch of HPIV1 containing only Chinese strains was identified and designated clade D. Furthermore, in 2023, HPIV3 strains from Pakistan and Russia formed a new lineage within clade C, named C6. The first HPIV4b sequence obtained in this study from China belongs to lineage C2. Evolutionary rate assessments revealed that both the HN and whole-genome sequences of HPIV3 presented the lowest evolutionary rates compared with those of the other HPIV types, with rates of 6.98E-04 substitutions/site/year (95% HPD: 5.87E-04 to 8.25E-03) and 5.85E-04 substitutions/site/year (95% HPD: 5.12E-04 to 6.62E-04), respectively. Recombination analysis revealed a potential recombination event in the F gene of an HPIV1 strain in this study. Additionally, all the newly obtained HPIV1-3 strains exhibited negative selection pressure, and two mutations were identified in the HN protein of two HPIV3 strains at monoclonal antibody-binding sites.
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MESH Headings
- Humans
- China/epidemiology
- Respiratory Tract Infections/virology
- Respiratory Tract Infections/epidemiology
- Phylogeny
- Child, Preschool
- Genome, Viral/genetics
- Child
- Male
- Genotype
- Female
- Infant
- Parainfluenza Virus 1, Human/genetics
- Parainfluenza Virus 1, Human/isolation & purification
- Parainfluenza Virus 1, Human/classification
- Parainfluenza Virus 4, Human/genetics
- Parainfluenza Virus 4, Human/classification
- Parainfluenza Virus 4, Human/isolation & purification
- Parainfluenza Virus 3, Human/genetics
- Parainfluenza Virus 3, Human/classification
- Parainfluenza Virus 3, Human/isolation & purification
- High-Throughput Nucleotide Sequencing
- Whole Genome Sequencing
- Genetic Variation
- Respirovirus Infections/virology
- Respirovirus Infections/epidemiology
- Respirovirus/genetics
- Respirovirus/classification
- Respirovirus/isolation & purification
- Parainfluenza Virus 2, Human/genetics
- Parainfluenza Virus 2, Human/classification
- Parainfluenza Virus 2, Human/isolation & purification
- East Asian People
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Affiliation(s)
- Yun Zhu
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Yun Sun
- The Division of General Pediatrics, Yinchuan Women and Children Healthcare Hospital, Yinchuan, China
| | - Changchong Li
- Department of Pediatric of Pulmonology, The 2nd Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Gen Lu
- The Respiratory Department, Guangzhou Women and Children’s Medical Center, Guangzhou, China
| | - Rong Jin
- The Respiratory Department, Guizhou Maternal and Child Health Care Hospital, Guiyang Children’s Hospital, Guiyang, China
| | - Baoping Xu
- Department of Respiratory Diseases I, Beijing Children’s Hospital, Capital Medical University, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
| | - Yunxiao Shang
- The Division of Pediatric Respiratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Junhong Ai
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Ran Wang
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Yali Duan
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangpeng Chen
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengde Xie
- Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Children’s Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children’s Health, Beijing, China
- Research Unit of Critical infection in Children, Chinese Academy of Medical Sciences, Beijing, China
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17
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Tau RL, Marandino AE, Panzera Y, Alamos F, Vissani MA, Romera SA, Pérez R, Maidana SS. The complete genome of equid herpesvirus-1 (EHV-1) field isolates from Argentina reveals an interspecific recombinant strain. Virus Genes 2024; 60:559-562. [PMID: 39028407 DOI: 10.1007/s11262-024-02093-4] [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: 02/08/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
The Equid alphaherpesvirus type 1 (EHV-1) infection can have devastating economic consequences in the horse industry due to large-scale outbreaks of abortions, perinatal foal mortality, and myeloencephalopathy. The present study analyzed the genome of two isolates obtained from aborted fetuses in Argentina, E/745/99 and E/1297/07. The E745/99 genome shares 98.2% sequence identity with Ab4, a reference EHV-1 strain. The E/1297/07 genome shares 99.8% identity with NY03, a recombinant strain containing part of ORF64 and part of the intergenic region from Equid alphaherpesvirus-4 (EHV-4). The E/1297/07 genome has the same breakpoints as other United States and Japanese recombinants, including NY03. The recombinant regions have varying numbers of tandem repeat sequences and different minor parental sequences (EHV-4), suggesting distinct origins of the recombinant events. These are the first complete genomes of EHV-1 from Argentina and South America available in the Databases.
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Affiliation(s)
- Rocio Lucia Tau
- Institute of Virology and Technological Innovations, Dr Nicolas Repetto and De losReseros, IVIT (INTA-CONICET), 1686, Hurlingham, Buenos Aires, Argentina
| | - Ana Eugenia Marandino
- Evolutionary Genetics Section, Faculty of Sciences, Institute of Biology, University of the Republic, Montevideo, Uruguay
| | - Yanina Panzera
- Evolutionary Genetics Section, Faculty of Sciences, Institute of Biology, University of the Republic, Montevideo, Uruguay
| | - Florencia Alamos
- Institute of Virology and Technological Innovations, Dr Nicolas Repetto and De losReseros, IVIT (INTA-CONICET), 1686, Hurlingham, Buenos Aires, Argentina
- Faculty of Agricultural and Veterinary Sciences, Veterinary Research Institute, University of the Salvador, Buenos Aires, Argentina
| | - Maria Aldana Vissani
- Institute of Virology and Technological Innovations, Dr Nicolas Repetto and De losReseros, IVIT (INTA-CONICET), 1686, Hurlingham, Buenos Aires, Argentina
- Faculty of Agricultural and Veterinary Sciences, Veterinary Research Institute, University of the Salvador, Buenos Aires, Argentina
| | - Sonia Alejandra Romera
- Institute of Virology and Technological Innovations, Dr Nicolas Repetto and De losReseros, IVIT (INTA-CONICET), 1686, Hurlingham, Buenos Aires, Argentina
- Faculty of Agricultural and Veterinary Sciences, Veterinary Research Institute, University of the Salvador, Buenos Aires, Argentina
| | - Ruben Pérez
- Evolutionary Genetics Section, Faculty of Sciences, Institute of Biology, University of the Republic, Montevideo, Uruguay
| | - Silvina Soledad Maidana
- Institute of Virology and Technological Innovations, Dr Nicolas Repetto and De losReseros, IVIT (INTA-CONICET), 1686, Hurlingham, Buenos Aires, Argentina.
- Faculty of Agricultural and Veterinary Sciences, Veterinary Research Institute, University of the Salvador, Buenos Aires, Argentina.
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18
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Zhao J, Wan W, Yu K, Lemey P, Pettersson JHO, Bi Y, Lu M, Li X, Chen Z, Zheng M, Yan G, Dai J, Li Y, Haerheng A, He N, Tu C, Suchard MA, Holmes EC, He WT, Su S. Farmed fur animals harbour viruses with zoonotic spillover potential. Nature 2024; 634:228-233. [PMID: 39232170 DOI: 10.1038/s41586-024-07901-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 08/01/2024] [Indexed: 09/06/2024]
Abstract
Animals such as raccoon dogs, mink and muskrats are farmed for fur and are sometimes used as food or medicinal products1,2, yet they are also potential reservoirs of emerging pathogens3. Here we performed single-sample metatranscriptomic sequencing of internal tissues from 461 individual fur animals that were found dead due to disease. We characterized 125 virus species, including 36 that were novel and 39 at potentially high risk of cross-species transmission, including zoonotic spillover. Notably, we identified seven species of coronaviruses, expanding their known host range, and documented the cross-species transmission of a novel canine respiratory coronavirus to raccoon dogs and of bat HKU5-like coronaviruses to mink, present at a high abundance in lung tissues. Three subtypes of influenza A virus-H1N2, H5N6 and H6N2-were detected in the lungs of guinea pig, mink and muskrat, respectively. Multiple known zoonotic viruses, such as Japanese encephalitis virus and mammalian orthoreovirus4,5, were detected in guinea pigs. Raccoon dogs and mink carried the highest number of potentially high-risk viruses, while viruses from the Coronaviridae, Paramyxoviridae and Sedoreoviridae families commonly infected multiple hosts. These data also reveal potential virus transmission between farmed animals and wild animals, and from humans to farmed animals, indicating that fur farming represents an important transmission hub for viral zoonoses.
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Affiliation(s)
- Jin Zhao
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Wenbo Wan
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Kang Yu
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - John H-O Pettersson
- Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
- Clinical Microbiology and Hospital Hygiene, Uppsala University Hospital, Uppsala, Sweden
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Yuhai Bi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Meng Lu
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Xinxin Li
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Zhuohang Chen
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Mengdi Zheng
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
| | - Ge Yan
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - JianJun Dai
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yuxing Li
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Ayidana Haerheng
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Na He
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China
| | - Wan-Ting He
- State Key Laboratory of Natural Medicines, School of Pharmacy, China Pharmaceutical University, Nanjing, China.
| | - Shuo Su
- Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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19
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Wang X, Liu W, Hu M, He Y, Wang B, Li K, Zhang R, Zhang H, Wang T, Wang Y, Chen L, Hu X, Ren H, Song H. Coinfection of human adenovirus and recombinant human astrovirus in a case of acute gastroenteritis: A report from China. J Med Virol 2024; 96:e29940. [PMID: 39327785 DOI: 10.1002/jmv.29940] [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: 06/12/2024] [Revised: 09/03/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
Diarrhea is one of the major public health issues worldwide. Although the infections of individual enteric virus have been extensively studied, elucidation of the coinfection involving multiple viruses is still limited. In this study, we identified the coinfection of human adenovirus (HAdV) and human astrovirus (HAstV) in a child with acute gastroenteritis, analyzed their genotypes and molecular evolution characteristics. The sample was collected and identified using RT-PCR and subjected to whole-genome sequencing on the NovaSeq (Illumina) platform. Obtained sequences were assembled into the complete genome of HAdV and the ORF1 of HAstV. We conducted phylogenetic analysis using IQ-TREE software and conducted recombination analysis with the Recombination Detection Program. The sequenced HAdV was confirmed to be genotype 41, and was genetically close to some European strains. Phylogenetic analysis revealed that the HAstV was genetically close to both HAstV-2 and HAstV-4 and was different from the genotype prevalent in Shenzhen before. The recombination analysis confirmed that the sequenced HAstV strain is a recombinant of HAstV-2 and HAstV-4. Our analysis has shown that the strains in this coinfection are both uncommon variants in this geographical region, instead of dominant subtypes that have prevailed for years. This study presents a coinfection of HAdV and HAstV and conducts an evolutionary analysis on involved viruses, which reveals the genetic diversity of epidemic strains in Southern China and offers valuable insights into vaccine and medical research.
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MESH Headings
- Humans
- Coinfection/virology
- Coinfection/epidemiology
- Gastroenteritis/virology
- Phylogeny
- Mamastrovirus/genetics
- Mamastrovirus/isolation & purification
- Mamastrovirus/classification
- China/epidemiology
- Astroviridae Infections/virology
- Astroviridae Infections/epidemiology
- Adenoviruses, Human/genetics
- Adenoviruses, Human/classification
- Adenoviruses, Human/isolation & purification
- Genotype
- Adenovirus Infections, Human/virology
- Adenovirus Infections, Human/epidemiology
- Recombination, Genetic
- Genome, Viral/genetics
- Whole Genome Sequencing
- Male
- Sequence Analysis, DNA
- Child, Preschool
- Evolution, Molecular
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Affiliation(s)
- Xin Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Wanqiu Liu
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- School of Public Health, University of South China, Hengyang, China
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Mingda Hu
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Yaqing He
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Boqian Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Kexin Li
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- China Medical University, Shenyang, China
| | - Rui Zhang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- China Medical University, Shenyang, China
| | - Hailong Zhang
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Tianyi Wang
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Yuxin Wang
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
- China Medical University, Shenyang, China
| | - Long Chen
- Institute of Pathogen Biology, Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaofeng Hu
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
| | - Hongguang Ren
- Laboratory of Advanced Biotechnology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, China
| | - Hongbin Song
- Chinese PLA Center for Disease Control and Prevention, Beijing, China
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20
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Volodina S, Titov I, Zhivoderov S, Yurkov S, Malogolovkin A. Comparative analysis of two novel complete genomes of myxoma virus vaccine strains. Virus Genes 2024; 60:528-536. [PMID: 38990486 DOI: 10.1007/s11262-024-02090-7] [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: 02/22/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
Myxoma virus (MYXV) is a double-stranded DNA-containing virus of the family Poxviridae, genus Leporipoxvirus. MYXV is an important model virus for evolutionary and immunological research and a promising oncolytic. In this study, we sequenced and analyzed two complete genomes of MYXV virus vaccine strains B-82 and Rabbivac-B, which are widely used for vaccine production in Russia. Here, we first show that MYXV vaccine strains B-82 and Rabbivac-B share a common origin with the American recombinant MYXV MAV vaccine strain. In addition, our data suggest that the MYXV B-82 and Rabbivac-B strains contain a number of genes at the 5' and 3' ends that are identical to the virulent MYXV Lausanne strain. Several unique genetic signatures were identified in the M013L, M017L, M023, and M121R genes, helping to achieve high genetic resolution between vaccine strains. Overall, these findings highlight the evolutionary flexibility of certain genes in the MYXV genome and provide insights into the molecular epidemiology of the virus and subsequent vaccine development.
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Affiliation(s)
- Sofya Volodina
- Molecular Virology Laboratory, First Moscow State Medical University (Sechenov University), Trubetskaya 8, 119048, Moscow, Russia
| | - Ilya Titov
- Federal Research Center for Virology and Microbiology, Bakoulova Street, B.1, 601125, Volginskiy, Russia
| | - Sergey Zhivoderov
- Federal Research Center for Virology and Microbiology, Bakoulova Street, B.1, 601125, Volginskiy, Russia
| | - Sergey Yurkov
- Federal Research Center for Virology and Microbiology, Bakoulova Street, B.1, 601125, Volginskiy, Russia
| | - Alexander Malogolovkin
- Molecular Virology Laboratory, First Moscow State Medical University (Sechenov University), Trubetskaya 8, 119048, Moscow, Russia.
- Gene Therapy Department, Science Center for Translational Medicine, Sirius University of Science and Technology, Olimpiyskiy Ave, B.1, 354340, Sirius, Russia.
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21
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Diksha D, Sidharthan VK, Baranwal VK. Identification of a novel monopartite begomovirus associated with leaf curl disease of Citharexylum spinosum in India. Virus Genes 2024; 60:568-571. [PMID: 38935183 DOI: 10.1007/s11262-024-02087-2] [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: 01/14/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
The present study reports the complete genome of a novel monopartite begomovirus, named tentatively as "Citharexylum leaf curl virus" (CitLCuV), associated with leaf curl disease of Citharexylum spinosum in India. CitLCuV genome (2767 nucleotide) contained the typical genome organization of Old World begomoviruses and shared the maximum nucleotide sequence identity of 89.7% with a papaya leaf crumple virus (PaLCrV) isolate. In addition, two small non-canonical open reading frames (C5 and C6) were determined in the complementary strand of CitLCuV genome. Phylogenetic analysis revealed the relatedness of CitLCuV to PaLCrV and rose leaf curl virus. Recombination analysis detected a possible recombination event in CitLCuV genome. Based on begomovirus species demarcation criteria, CitLCuV can be regarded as a novel begomoviral species.
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Affiliation(s)
- Damini Diksha
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - V K Baranwal
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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22
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Peacock DE, Iannella A, Sinclair RG, Kovaliski J. Surveillance of Wildlife Viruses: Insights from South Australia's Monitoring of Rabbit Haemorrhagic Disease Virus (RHDV GI.1 and GI.2). Viruses 2024; 16:1553. [PMID: 39459889 PMCID: PMC11512407 DOI: 10.3390/v16101553] [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: 09/06/2024] [Revised: 09/29/2024] [Accepted: 09/29/2024] [Indexed: 10/28/2024] Open
Abstract
Surveillance of wildlife virus impacts can be passive or active. Both approaches have their strengths and weaknesses, especially regarding cost and knowledge that can be gained. Monitoring of rabbit haemorrhagic disease virus (GI.1 and GI.2) in South Australia has utilised both strategies and their methods and gained insights are discussed. Active strategies to monitor the continuing impact of rabbit haemorrhagic disease virus 2 (GI.2) on susceptible lagomorphs in countries such as the USA, Mexico, South Africa, Spain, France and Portugal are encouraged to gain critical insights into the evolution, spread and impact of this virus. Furthermore, there are lessons here for the international monitoring of diseases in wildlife, particularly where there is a risk of them becoming zoonotic.
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Affiliation(s)
- David E. Peacock
- Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Amy Iannella
- Foundation for Rabbit Free Australia, P.O. Box 145, Collinswood, Adelaide, SA 5081, Australia
| | - Ron G. Sinclair
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - John Kovaliski
- Independent Researcher, 6/43B Bridge Street Kensington, Kensington, SA 5068, Australia
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23
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Ludwig S, Amorim L, Barcelos AC, Guimarães PR, Vargas SM. Inferring the origin of new D-loop haplotypes of loggerhead sea turtles (Testudinata: Cheloniidae) from the Southwest Atlantic lineage. Mitochondrial DNA A DNA Mapp Seq Anal 2024:1-8. [PMID: 39329372 DOI: 10.1080/24701394.2024.2409067] [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: 08/03/2023] [Accepted: 09/19/2024] [Indexed: 09/28/2024]
Abstract
The populations of the loggerhead turtles, Caretta caretta, present four main D-loop mitochondrial haplogroups that are distributed across the Indo-Pacific, Mediterranean, and Atlantic oceans. The Southwestern Atlantic (SWA) is one of the Regional Management Units (RMUs) of loggerheads, characterized by unique haplotypes, high nest density, and distinct life history traits. Detecting new D-loop haplogroups is important, particularly endemic ones, as they can enhance our understanding of their life history within the RMUs and contribute to the resolution of mixed stock analysis. In this study, we conducted a series of phylogenetic delimitation and network analyses to identify, validate, and infer the origin of four new D-loop haplotypes detected in the loggerhead populations from the SWA. Our findings demonstrate that these new D-loop haplotypes are valid and unique to the SWA lineage, potentially aiding in the delimitation of individuals' origins and the inference of their lineage.
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Affiliation(s)
- Sandra Ludwig
- Laboratório de Genética e Evolução Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Lais Amorim
- Laboratório de Genética e Evolução Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Ana C Barcelos
- Laboratório de Genética e Evolução Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Paula R Guimarães
- Laboratório de Genética e Evolução Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
| | - Sarah M Vargas
- Laboratório de Genética e Evolução Molecular, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo, Vitória, ES, Brazil
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24
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Lohavicharn P, Kasantikul T, Piewbang C, Techangamsuwan S. Feline bocaviruses found in Thailand have undergone genetic recombination for their evolutions. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 125:105675. [PMID: 39342978 DOI: 10.1016/j.meegid.2024.105675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/10/2024] [Accepted: 09/26/2024] [Indexed: 10/01/2024]
Abstract
Feline bocaviruses (FBoVs) have been discovered for a decade and are often detected in feces, possibly associated with diarrhea in cats. Studies on FBoV evolution remain limited and have mainly focused on prevalence and genetic characterization. Although genetic recombination serves as a potential mechanism in bocavirus evolution, research on this process for FBoVs has been scarce. In this study, we characterized 19 complete coding sequences of FBoVs obtained from Thai cats, revealing that FBoV-1, -2, and -3 were endemic in Thailand. Genetic characterizations showed that most Thai FBoVs were closely related to previously detected strains in Thailand and China. Recombination analyses indicated intragenic, intraspecies recombination in all FBoV species, with recombination breakpoints commonly found in the NP1 and VP1/2 genes, highlighting these genes may be hotspots for FBoV recombination. However, no interspecies recombination was detected. Selective pressure analysis of various FBoV genes revealed that these viruses underwent purifying selection. Although the VP1/2 gene of all FBoV species was under the strongest negative selection pressure, positive selection sites were only found in FBoV-1 and FBoV-3. This study is the first to identify natural recombination in FBoV-2 and FBoV-3 and provides evidence that genetic recombination is a potential driver of FBoV evolutions. Additionally, this study offers up-to-date information on the genetic characteristics, evolutionary dynamics, and selective pressure status of FBoVs, which should be continuously monitored.
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Affiliation(s)
- Pattiya Lohavicharn
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Chutchai Piewbang
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Somporn Techangamsuwan
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand.
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25
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Adero J, Wokorach G, Stomeo F, Yao N, Machuka E, Njuguna J, Byarugaba DK, Kreuze J, Yencho GC, Otema MA, Yada B, Kitavi M. Next Generation Sequencing and Genetic Analyses Reveal Factors Driving Evolution of Sweetpotato Viruses in Uganda. Pathogens 2024; 13:833. [PMID: 39452705 PMCID: PMC11510311 DOI: 10.3390/pathogens13100833] [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: 06/21/2024] [Revised: 07/30/2024] [Accepted: 08/07/2024] [Indexed: 10/26/2024] Open
Abstract
Sweetpotato (Ipomoea batatas L.) is an essential food crop globally, especially for farmers facing resource limitations. Like other crops, sweetpotato cultivation faces significant production challenges due to viral infections. This study aimed to identify and characterize viruses affecting sweetpotato crops in Uganda, mostly those associated with sweetpotato virus disease (SPVD). Infected leaf samples were collected from farmers' fields in multiple districts spanning three regions in Uganda. MiSeq, a next-generation sequencing platform, was used to generate reads from the viral nucleic acid. The results revealed nine viruses infecting sweetpotato crops in Uganda, with most plants infected by multiple viral species. Sweet potato pakakuy and sweet potato symptomless virus_1 are reported in Uganda for the first time. Phylogenetic analyses demonstrated that some viruses have evolved to form new phylogroups, likely due to high mutations and recombination, particularly in the coat protein, P1 protein, cylindrical inclusion, and helper component proteinase regions of the potyvirus. The sweet potato virus C carried more codons under positive diversifying selection than the closely related sweet potato feathery mottle virus, particularly in the P1 gene. This study provides valuable insights into the viral species infecting sweetpotato crops, infection severity, and the evolution of sweet potato viruses in Uganda.
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Affiliation(s)
- Joanne Adero
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala P.O. Box 7084, Uganda; (M.A.O.); (B.Y.)
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Godfrey Wokorach
- Department of Biology, Faculty of Science, Muni University, Arua P.O. Box 725, Uganda;
| | - Francesca Stomeo
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Nasser Yao
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Eunice Machuka
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Joyce Njuguna
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709, Kenya; (F.S.); (N.Y.); (E.M.); (J.N.)
| | - Denis K. Byarugaba
- College of Veterinary Medicine Animal Resources and Biosecurity, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Jan Kreuze
- International Potato Centre, CIP Headquarters Lima, Avenida La Molina 1895, La Molina Apartado Postal 1558, Lima 15024, Peru;
| | - G. Craig Yencho
- Department of Horticultural Science, North Carolina State University, 214 Kilgore Hall, P.O. Box 7609, Raleigh, NC 27695, USA;
| | - Milton A. Otema
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala P.O. Box 7084, Uganda; (M.A.O.); (B.Y.)
| | - Benard Yada
- National Crops Resources Research Institute, National Agricultural Research Organization, Kampala P.O. Box 7084, Uganda; (M.A.O.); (B.Y.)
| | - Mercy Kitavi
- International Potato Centre, SSA Regional Office, Nairobi P.O. Box 25171, Kenya
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26
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Domanska-Blicharz K, Lisowska A, Opolska J, Ruszkowski JJ, Gogulski M, Pomorska-Mól M. Whole genome characteristics of hedgehog coronaviruses from Poland and analysis of the evolution of the Spike protein for its interspecies transmission potential. BMC Vet Res 2024; 20:424. [PMID: 39304831 PMCID: PMC11415979 DOI: 10.1186/s12917-024-04277-4] [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: 05/21/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND The hedgehogs have been recently identified as possible reservoir of Middle East respiratory syndrome coronavirus like (MERS-CoV-like). These viruses were classified as a distinct Betacoronavirus erinacei (BCoV-Eri) species within the MerBCoV-Eriirus subgenus. As coronaviruses are known for their ability to jump between different hosts, including humans, this can pose a particular threat to people in direct contact with hedgehogs, such as those working at animal asylums. Our previous studies have shown the presence of BCoV-Eri strains in animals collected in the wildlife rehabilitation centre. This study aimed to investigate the presence of CoV in subsequent hedgehogs collected from the urban area of Poland and their molecular characteristics. RESULTS Monitoring for the presence of coronavirus infection in hedgehogs revealed five positive individuals. The presence of BCoV-Eri was found in a total of 20% of animals tested. Our analyses revealed no correlation between CoVs positivity and animal health conditions but a higher probability of such infection in juveniles and females. The whole genome of two Polish Hedgehog coronavirus 1 strains were sequenced and compared with available counterparts from European and Asian countries. Phylogenetic analysis showed that both CoV strains formed common cluster with other similar MerBCoV-Eriirus, but they were also found to be genetically variable and most changes in the S protein were identified. Our analysis revealed that some S protein sites of the Hedgehog coronavirus 1 strains evolved under positive selection pressure and of five such sites, three are in the S1 region while the other two in the S2 region of the Spike. CONCLUSIONS BCoV-Eri is to some extent prevalent in wildlife asylums in Poland. Given that the S protein of BCoVs-Eri is highly variable and that some sites of this protein evolve under positive selection pressure, these strains could potentially acquire a favourable feature for cross-species transmission. Consequently, the threat to humans working in such asylums is particularly high. Adequate biosecurity safeguards, but also human awareness of such risks, are therefore essential.
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Affiliation(s)
- Katarzyna Domanska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland.
| | - Anna Lisowska
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland
| | - Justyna Opolska
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantów 57, Puławy, 24-100, Poland
| | - Jakub J Ruszkowski
- Department of Animal Anatomy, University of Life Sciences in Poznań, ul. Wojska Polskiego 71C, Poznań, 60-625, Poland
- University Centre for Veterinary Medicine, University of Life Sciences in Poznań, Szydłowska 43, Poznań, 60-656, Poland
| | - Maciej Gogulski
- Department of Animal Anatomy, University of Life Sciences in Poznań, ul. Wojska Polskiego 71C, Poznań, 60-625, Poland
- University Centre for Veterinary Medicine, University of Life Sciences in Poznań, Szydłowska 43, Poznań, 60-656, Poland
| | - Małgorzata Pomorska-Mól
- Department of Preclinical Sciences and Infectious Diseases, University of Life Sciences in Poznań, ul. Wołyńska 35, Poznań, 60-637, Poland
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Wei KJ, Jiang AM, Jiang S, Huang YJ, Jiang SY, Su XL, Tettey CK, Wang XQ, Tang W, Cheng DJ. New isolate of sweet potato virus 2 from Ipomoea nil: molecular characterization, codon usage bias, and phylogenetic analysis based on complete genome. Virol J 2024; 21:222. [PMID: 39300471 DOI: 10.1186/s12985-024-02500-0] [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: 07/02/2024] [Accepted: 09/11/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Viral diseases of sweet potatoes are causing severe crop losses worldwide. More than 30 viruses have been identified to infect sweet potatoes among which the sweet potato latent virus (SPLV), sweet potato mild speckling virus (SPMSV), sweet potato virus G (SPVG) and sweet potato virus 2 (SPV2) have been recognized as distinct species of the genus Potyvirus in the family Potyviridae. The sweet potato virus 2 (SPV2) is a primary pathogen affecting sweet potato crops. METHODS In this study, we detected an SPV2 isolate (named SPV2-LN) in Ipomoea nil in China. The complete genomic sequence of SPV2-LN was obtained using sequencing of small RNAs, RT-PCR, and RACE amplification. The codon usage, phylogeny, recombination analysis and selective pressure analysis were assessed on the SPV2-LN genome. RESULTS The complete genome of SPV2-LN consisted of 10,606 nt (GenBank No. OR842902), encoding 3425 amino acids. There were 28 codons in the SPV2-LN genome with a relative synonymous codon usage (RSCU) value greater than 1, of which 21 end in A/U. Among the 12 proteins of SPV2, P3 and P3N-PIPO exhibited the highest variability in their amino acid sequences, while P1 was the most conserved, with an amino acid sequence identity of 87-95.3%. The phylogenetic analysis showed that 21 SPV2 isolates were clustered into four groups, and SPV2-LN was clustered together with isolate yu-17-47 (MK778808) in group IV. Recombination analysis indicated no major recombination sites in SPV2-LN. Selective pressure analysis showed dN/dS of the 12 proteins of SPV2 were less than 1, indicating that all were undergoing negative selection, except for P1N-PISPO. CONCLUSION This study identified a sweet potato virus, SPV2-LN, in Ipomoea nil. Sequence identities and genome analysis showed high similarity between our isolate and a Chinese isolate, yu-17-47, isolated from sweet potato. These results will provide a theoretical basis for understanding the genetic evolution and viral spread of SPV2.
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Affiliation(s)
- Kun-Jiang Wei
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China
| | - Ai-Ming Jiang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China
| | - Shuo Jiang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China
| | - Yang-Jian Huang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China
| | - Song-Yu Jiang
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China
| | - Xiao-Ling Su
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China
| | - Carlos Kwesi Tettey
- Department of Molecular Biology and Biotechnology, University of Cape Coast, PMB UCC, Cape Coast, Ghana
| | - Xiao-Qiang Wang
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.
| | - Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area, Xuzhou, 221131, China.
| | - De-Jie Cheng
- Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, Agricultural College, Guangxi University, Nanning, 520004, China.
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Sun YD, Yokomi R. The Discovery of a Citrus Yellow Vein Clearing Virus Hacienda Heights Isolate Diversifies the Geological Origins of the Virus in California, United States. Viruses 2024; 16:1479. [PMID: 39339955 PMCID: PMC11437496 DOI: 10.3390/v16091479] [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: 08/16/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
The citrus yellow vein clearing virus (CYVCV) is an emerging threat to the U.S. citrus industry. Reports from China shows it cause significant reductions in fruit yield and growth, particularly in lemon trees. In 2022, CYVCV was detected in a wide range of citrus cultivars in localized urban properties in Tulare, California. In 2024, a CYVCV-infected lemon tree was detected in Hacienda Heights in Los Angeles County, California, geographically separated from the Tulare foci. Through long-read sequencing technology, the whole-genome sequence of a CYVCV isolate from Hacienda Heights (designated as CYVCV-CA-HH1, Accession number PP840891.1) was obtained. Sequence alignments and neighbornet analysis strongly suggested that the CYVCV-CA-HH1 isolate has a different origin than the Tulare CYVCV (CYVCV CA-TL) isolates. The CYVCV CA-TL isolates were grouped with those from South Asia (India and Pakistan) and the Middle East (Türkiye), while the CYVCV-CA-HH1 isolate was grouped with isolates from East Asia (China and South Korea). Maximum likelihood phylogenetic analysis further supports this finding, showing that the CYVCV-CA-HH1 isolate shares the most recent common ancestor with a South Korean lineage, which derives from Chinese isolates. Together, our data suggest a diverse geological origin of CYVCV isolates in California.
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Affiliation(s)
- Yong-Duo Sun
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
| | - Raymond Yokomi
- United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648, USA
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29
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Pyke AT, Wilson DJ, Michie A, Mackenzie JS, Imrie A, Cameron J, Doggett SL, Haniotis J, Herrero LJ, Caly L, Lynch SE, Mee PT, Madzokere ET, Ramirez AL, Paramitha D, Hobson-Peters J, Smith DW, Weir R, Sullivan M, Druce J, Melville L, Robson J, Gibb R, van den Hurk AF, Duchene S. Independent repeated mutations within the alphaviruses Ross River virus and Barmah Forest virus indicates convergent evolution and past positive selection in ancestral populations despite ongoing purifying selection. Virus Evol 2024; 10:veae080. [PMID: 39411152 PMCID: PMC11477980 DOI: 10.1093/ve/veae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/25/2024] [Accepted: 09/12/2024] [Indexed: 10/19/2024] Open
Abstract
Ross River virus (RRV) and Barmah Forest virus (BFV) are arthritogenic arthropod-borne viruses (arboviruses) that exhibit generalist host associations and share distributions in Australia and Papua New Guinea (PNG). Using stochastic mapping and discrete-trait phylogenetic analyses, we profiled the independent evolution of RRV and BFV signature mutations. Analysis of 186 RRV and 88 BFV genomes demonstrated their viral evolution trajectories have involved repeated selection of mutations, particularly in the nonstructural protein 1 (nsP1) and envelope 3 (E3) genes suggesting convergent evolution. Convergent mutations in the nsP1 genes of RRV (residues 248 and 441) and BFV (residues 297 and 447) may be involved with catalytic enzyme mechanisms and host membrane interactions during viral RNA replication and capping. Convergent E3 mutations (RRV site 59 and BFV site 57) may be associated with enzymatic furin activity and cleavage of E3 from protein precursors assisting viral maturation and infectivity. Given their requirement to replicate in disparate insect and vertebrate hosts, convergent evolution in RRV and BFV may represent a dynamic link between their requirement to selectively 'fine-tune' intracellular host interactions and viral replicative enzymatic processes. Despite evidence of evolutionary convergence, selection pressure analyses did not reveal any RRV or BFV amino acid sites under strong positive selection and only weak positive selection for nonstructural protein sites. These findings may indicate that their alphavirus ancestors were subject to positive selection events which predisposed ongoing pervasive convergent evolution, and this largely supports continued purifying selection in RRV and BFV populations during their replication in mosquito and vertebrate hosts.
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Affiliation(s)
- Alyssa T Pyke
- Public Health Virology Laboratory, Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O. Box 594, Archerfield, Coopers Plains, Queensland, Australia
| | - Daniel J Wilson
- Big Data Institute, Oxford Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford OX3 7LF, United Kingdom
- Department for Continuing Education, University of Oxford, 1 Wellington Square, Oxford OX1 2JA, United Kingdom
| | - Alice Michie
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - John S Mackenzie
- Faculty of Health Sciences, Curtin University, G.P.O. Box U1987, Bentley, Western Australia 6845, Australia
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Jane Cameron
- Public Health Virology Laboratory, Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O. Box 594, Archerfield, Coopers Plains, Queensland, Australia
| | - Stephen L Doggett
- NSW Health Pathology, Westmead Hospital, 166-174 Hawkesbury Road Westmead, Sydney, New South Wales 2145, Australia
| | - John Haniotis
- NSW Health Pathology, Westmead Hospital, 166-174 Hawkesbury Road Westmead, Sydney, New South Wales 2145, Australia
| | - Lara J Herrero
- Gold Coast Campus, Institute for Glycomics, Griffith University, 1 Parklands Drive, Southport, Queensland 4215, Australia
| | - Leon Caly
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia
| | - Eugene T Madzokere
- Gold Coast Campus, Institute for Glycomics, Griffith University, 1 Parklands Drive, Southport, Queensland 4215, Australia
| | - Ana L Ramirez
- College of Public Health, Medical and Veterinary Sciences, James Cook University, P.O. Box 6811, Cairns, Queensland 4870, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, P.O. Box 6811, Cairns, Queensland 4870, Australia
- The Jackson Laboratory, 10 Discovery Drive Connecticut, Farmington, CT 06032, United States of America
| | - Devina Paramitha
- School of Chemistry and Molecular Biosciences, The University of Queensland, Bdg 68 Cooper Road, St. Lucia, Queensland 4072, Australia
| | - Jody Hobson-Peters
- School of Chemistry and Molecular Biosciences, The University of Queensland, Bdg 68 Cooper Road, St. Lucia, Queensland 4072, Australia
| | - David W Smith
- NSW Health Pathology, Westmead Hospital, 166-174 Hawkesbury Road Westmead, Sydney, New South Wales 2145, Australia
- School of Medicine, University of Western Australia, 35 Stirling Highway, Perth, Western Australia 6009, Australia
| | - Richard Weir
- Department of Primary Industries and Fisheries, Berrimah Veterinary Laboratory, P.O. Box 3000, Darwin, Northern Territory 0801, Australia
| | - Mitchell Sullivan
- Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O Box 594 Archerfield, Coopers Plains, Queensland 4108, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
| | - Lorna Melville
- Department of Primary Industries and Fisheries, Berrimah Veterinary Laboratory, P.O. Box 3000, Darwin, Northern Territory 0801, Australia
| | - Jennifer Robson
- Department of Microbiology and Molecular Pathology, Sullivan Nicolaides Pathology, P.O. Box 2014 Fortitude Valley, Brisbane, Queensland 4006, Australia
| | - Robert Gibb
- Serology, Pathology Queensland Central Laboratory, Royal Brisbane and Women’s Hospital, 40 Butterfield Street Herston, Brisbane, Queensland 4029, Australia
| | - Andrew F van den Hurk
- Public Health Virology Laboratory, Public and Environmental Health Reference Laboratories, Department of Health, Queensland Government, P.O. Box 594, Archerfield, Coopers Plains, Queensland, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth Street, Melbourne, Victoria 3000, Australia
- Evolutionary Dynamics of Infectious Diseases, Department of Computational Biology, Institut Pasteur, 28 Rue du Dr Roux, Paris 75015, France
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Kang SF, Chen Y, Chen J. Wolbachia of phylogenetic supergroup K identified in oribatid mite Nothrus anauniensis (Acari: Oribatida: Nothridae). EXPERIMENTAL & APPLIED ACAROLOGY 2024:10.1007/s10493-024-00961-0. [PMID: 39266798 DOI: 10.1007/s10493-024-00961-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 08/23/2024] [Indexed: 09/14/2024]
Abstract
Heritable endosymbionts widely occur in arthropod and nematode hosts. Among these endosymbionts, Wolbachia has been extensively detected in many arthropods, such as insects and crustaceans. Maternal inheritance is the most basic and dominant mode of transmission of Wolbachia, and it might regulate the reproductive system of the host in four ways: feminization, parthenogenesis, male killing, and cytoplasmic incompatibility. There is a relatively high percentage (10%) of thelytokous species in Oribatida, a suborder under the subclass Acari of arthropods, but the study of the endosymbionts in oribatid mites is almost negligible. In this paper, we detected endosymbiotic bacteria in two parthenogenetic oribatid species, Nothrus anauniensis Canestrini and Fanzago, 1877, which has never been tested for endosymbionts, and Oppiella nova, in which Wolbachia and Cardinium have been reported before. The results showed that Wolbachia was first found in N. anauniensis with an infection rate of 100% across three populations. Phylogenetic analysis showed that Wolbachia in N. anauniensis belonged to the supergroup K, marking the second supergroup of Wolbachia found in oribatid mites. Unlike previous studies, our study did not detect Wolbachia in O. nova, leading to the exclusion of Wolbachia's role in mediating thelytoky in this species.
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Affiliation(s)
- Shuo-Fang Kang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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31
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Wei S, Liu L, Chen G, Yang H, Qiu X, Luo L, Gong G, Zhang M. Bayesian phylogeographic inference of wheat yellow mosaic virus in China and Japan suggests that the virus migration history coincided with historical events. Virology 2024; 600:110242. [PMID: 39288612 DOI: 10.1016/j.virol.2024.110242] [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: 06/24/2024] [Revised: 09/04/2024] [Accepted: 09/10/2024] [Indexed: 09/19/2024]
Abstract
Wheat yellow mosaic virus (WYMV) is one of the most serious viral pathogens causing reductions in wheat yield in East Asia. We investigated the phylodynamics of WYMV by analysing the CP, VPg and P1 genes to understand the origin and dispersal of the virus. A Bayesian phylogenetic analysis revealed that the most recent common WYMV ancestor occurred in approximately 1742 (95% credibility interval, 1439-1916) CE (Common Era), and the evolutionary rates of the VPg, CP and P1 genes were 6.669 × 10-4 (95% credibility interval: 4.575 × 10-4-8.927 × 10-4), 2.468 × 10-4 (95% credibility interval: 1.667 × 10-4-3.338 × 10-4) and 5.765 × 10-5 (95% credibility interval: 3.285 × 10-6-1.252 × 10-4), respectively. Our phylogeographic analysis indicated that the WYMV population may have originated in Henan Province, China, first spreading to Japan in the mid-19th century and stopping after the Japanese surrender in World War II. The second wave spread to Japan from Shandong Province, China, in approximately 1977, a few years after the establishment of diplomatic relations between China and Japan. Before the founding of the People's Republic of China, Henan Province was the emigration centre of WYMV in East Asia, and after the late 20th century, Jiangsu and Shandong Provinces were also the virus emigration centres in East Asia. In addition, there were two migration pathways from Japan to Jiangsu and Shandong Provinces, China, in approximately 1918 and approximately 1999 respectively. Our results suggest that the wide spread of WYMV in East Asia is strongly related to human factors.
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Affiliation(s)
- Shiqing Wei
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linwen Liu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoliang Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hui Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoyan Qiu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liya Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoshu Gong
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Zhang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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32
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Li X, Trovão NS. The evolutionary and transmission dynamics of HIV-1 CRF08_BC. PLoS One 2024; 19:e0310027. [PMID: 39241052 PMCID: PMC11379155 DOI: 10.1371/journal.pone.0310027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 08/22/2024] [Indexed: 09/08/2024] Open
Abstract
HIV-1 CRF08_BC is a significant subtype in China, though its origin and spread remain incompletely understood. Previous studies using partial genomic data have provided insights but lack comprehensive analysis. Here, we investigate the early evolutionary and spatiotemporal dynamics of HIV-1 CRF08_BC in China and Myanmar using near-complete genome sequences. We analyzed 28 near-complete HIV-1 CRF08_BC genomes from China and Myanmar (1997-2013). Phylogenetic, molecular clock, and Bayesian discrete trait analyses were performed to infer the virus's origin, spread, and associated risk groups. Based on Bayesian time-scaled inference with the best-fitting combination of models determined by marginal likelihood estimation (MLE), we inferred the time to the most recent common ancestor (TMRCA) and evolutionary rate of HIV-1 CRF08_BC to be at 3 October 1991 (95% HPD: 22 February1989-27 November 1993) and 2.30 × 10-3 substitutions per site per year (95% HPD: 1.96 × 10-3-2.63 × 10-3), respectively. Our analysis suggests that HIV-1 CRF08_BC originated in Yunnan Province, China, among injecting drug users, and subsequently spread to other regions. This study provides valuable insights into the early dynamics of HIV-1 CRF08_BC through combined genomic and epidemiological data, which may inform effective prevention and mitigation efforts. However, the limited genomic data influenced the extent of our findings, and challenges in collecting accurate risk group information during surveillance were evident.
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Affiliation(s)
- Xingguang Li
- Ningbo No.2 Hospital, Ningbo, China
- Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, China
| | - Nídia S Trovão
- National Institutes of Health, Fogarty International Center, Bethesda, Maryland, United States of America
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33
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Sang S, Chen P, Li C, Zhang A, Wang Y, Liu Q. The classification, origin, and evolutionary dynamics of severe fever with thrombocytopenia syndrome virus circulating in East Asia. Virus Evol 2024; 10:veae072. [PMID: 39310090 PMCID: PMC11416872 DOI: 10.1093/ve/veae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/01/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
The classification of severe fever with thrombocytopenia syndrome virus (SFTSV) lacked consistency due to limited virus sequences used across previous studies, and the origin and transmission dynamics of the SFTSV remains not fully understood. In this study, we analyzed the diversity and phylodynamics of SFTSV using the most comprehensive and largest dataset publicly available for a better understanding of SFTSV classification and transmission. A total of 1267 L segments, 1289 M segments, and 1438 S segments collected from China, South Korea, and Japan were included in this study. Maximum likelihood trees were reconstructed to classify the lineages. Discrete phylogeographic analysis was conducted to infer the phylodynamics of SFTSV. We found that the L, M, and S segments were highly conserved, with mean pairwise nucleotide distances of 2.80, 3.36, and 3.35% and could be separated into 16, 13, and 15 lineages, respectively. The evolutionary rate for L, M, and the S segment was 0.61 × 10-4 (95% HPD: 0.48-0.73 × 10-4), 1.31 × 10-4 (95% HPD: 0.77-1.77 × 10-4) and 1.27 × 10-4 (95% HPD: 0.65-1.85 × 10-4) subs/site/year. The SFTSV most likely originated from South Korea around the year of 1617.6 (95% HPD: 1513.1-1724.3), 1700.4 (95% HPD: 1493.7-1814.0), and 1790.1 (95% HPD: 1605.4-1887.2) for L, M, and S segments, respectively. Hubei Province in China played a critical role in the geographical expansion of the SFTSV. The effective population size of SFTSV peaked around 2010 to 2013. We also identified several codons under positive selection in the RdRp, Gn-Gc, and NS genes. By leveraging the largest dataset of SFTSV, our analysis could provide new insights into the evolution and dispersal of SFTSV, which may be beneficial for the control and prevention of severe fever with thrombocytopenia syndrome.
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Affiliation(s)
- Shaowei Sang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
- Clinical Research Center of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Peng Chen
- Department of Healthcare-associated Infection Management, School and Hospital of Stomatology, Shandong University, No. 44-1 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Chuanxi Li
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Anran Zhang
- Clinical Epidemiology Unit, Qilu Hospital of Shandong University, No. 107 Wenhua Road, Lixia District, Jinan 250012, People’s Republic of China
| | - Yiguan Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, No. 300 Fenglin Road, Xuhui District, Shanghai 200032, People’s Republic of China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Vector Surveillance and Management, No. 55 Changbai Road, Changping District, Beijing 102206, People’s Republic of China
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Oyeniran KA, Martin DP, Lett JM, Rakotomalala MR, Azali HA, Varsani A. Movement of the A-strain maize streak virus in and out of Madagascar. Virology 2024; 600:110222. [PMID: 39265447 DOI: 10.1016/j.virol.2024.110222] [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: 05/28/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/14/2024]
Abstract
The maize streak virus belongs in the genus Mastrevirus, in the family Geminiviridae. The A-strain of the virus (MSV-A) is recognised as the principal causative agent of the most severe manifestation of maize streak disease (MSD). This disease continues to be a persistent limitation on maize output across sub-Saharan Africa and the nearby Indian Ocean islands. Irrespective of the causes behind the spread of MSV-A, we can determine the paths and speeds with which MSV-A spreads by analysing MSV genome sequence data along with information on when and where samples were taken. This information is valuable for identifying the geographical origins of viral strains that cause sporadic MSD epidemics in specific places and the geographical regions where viruses remain in reservoirs and contribute to prolonged epidemics during outbreaks. Our aim is to utilise these analyses to estimate the timing and origin of the MSV-A that arrived on the island of Madagascar in the Indian Ocean. Specifically, we employ model-based phylogeographic analyses on 524 complete MSV-A genome sequences, which consist of 56 newly obtained genomes from infected maize plants collected in Madagascar. These studies allow us to reconstruct the most likely paths of MSV-A to Madagascar. We found strong evidence for the existence of at least four separate movements of MSV-A variants from East and southern Africa to Madagascar. These movements took place between roughly 1979 (with a 95% highest probability density interval [HPD] ranging from 1976 to 1982) and 2003 (with a 95% HPD ranging from 2002 to 2003). While we inferred that MSV-A variants are spreading at an average rate of 38.9 km/year (with a 95% highest posterior density interval of 34.0-44.4) across their geographical range. Since their arrival in Madagascar, MSV-A variants have been migrating at an average rate of 47.6 km/year (with a 95% highest posterior density interval of 36.05-61.70). Human influences are likely significant contributors to both sporadic long-range movements of MSV-A between mainland Africa and Madagascar, as well as shorter to medium range movements within the island.
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Affiliation(s)
- Kehinde A Oyeniran
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa; Department of Biological Sciences, Bamidele Olumilua University of Education, Science and Technology, Ikere-Ekiti, Nigeria.
| | - Darren P Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, 7925, South Africa
| | | | | | | | - Arvind Varsani
- The Biodesign Centre for Fundamental and Applied Microbiomics, Centre for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, Cape Town 7700, South Africa
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35
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Jayanthi P, Geetanjali AS. Molecular characterization to study the genetic diversity of begomoviruses occurring in the major chilli growing areas of Tamil Nadu state of India. Int Microbiol 2024:10.1007/s10123-024-00580-0. [PMID: 39230779 DOI: 10.1007/s10123-024-00580-0] [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: 04/12/2024] [Revised: 08/06/2024] [Accepted: 08/13/2024] [Indexed: 09/05/2024]
Abstract
Chilli leaf curl disease (ChiLCD), which is a significant problem in chilli cultivation, is caused by begomoviruses that are transmitted by the whitefly Bemisia tabaci. This disease leads to severe impacts on crop yields. To determine the incidence of begomovirus in the chilli crop, infected chilli leaf samples exhibiting symptoms such as curling, yellowing, reduced leaf size, and overall stunted growth were collected from various districts of Tamil Nadu, namely, Coimbatore, Dharmapuri, Kancheepuram, Karur, Salem, Krishnagiri, Thoothukudi, Thiruvallur, Tiruchirappalli, Virudhunagar, Tiruvannamalai, Tenkasi, and Vellore, during the years 2018-2022. To determine the complete genome sequence of the begomoviruses, the rolling circle amplification (RCA) method was used to clone and sequence the begomovirus genomes from the chilli samples collected from various districts of Tamil Nadu. Here we characterized 17 DNA A genome sequences and 12 betasatellite sequences. BLAST results of the DNA A genome sequences revealed nucleotide identities ranging from 94.2 to 99.7% with five distinct begomovirus species of chilli, namely, chilli leaf curl Salem virus (HM007119), chilli leaf curl virus Bhavanisagar (NC_055130), chilli leaf curl Ahmedabad virus (MW795666), chilli leaf curl virus (NC_055131), and chilli leaf curl Sri Lanka virus (JN555600). BLAST results of the betasatellite sequences showed nucleotide identities of 96 to 98.8% with the tomato leaf curl Bangladesh betasatellite (MZ151286). In the present study, five distinct begomovirus species and one associated betasatellite were found to infect chilli crops in Tamil Nadu. This finding indicates a changing pattern of begomovirus occurrence in the different districts of Tamil Nadu. This study highlights the prevalence of chilli-infecting begomoviruses in the major chilli growing districts of Tamil Nadu, the identification of begomovirus species, and the significance of understanding and managing these viruses to safeguard chilli cultivation in the region.
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Affiliation(s)
- P Jayanthi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India
| | - A Swapna Geetanjali
- Department of Genetic Engineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India.
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36
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Lai HC, Neoh ZY, Tsai WS. Genetic Diversity and Pathogenicity Characterization of Tomato-Infecting Begomoviruses in Taiwan. PLANT DISEASE 2024; 108:2688-2700. [PMID: 38587795 DOI: 10.1094/pdis-12-22-2937-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The tomato yellow leaf curl disease (TYLCD) caused by whitefly (Bemisia tabaci)-transmitted begomoviruses (Geminiviridae) has constrained tomato production in Taiwan since 1981. Lisianthus enation leaf curl virus (LELCV), tomato leaf curl Taiwan virus (ToLCTV), and tomato yellow leaf curl Thailand virus (TYLCTHV) were the major viruses associated with TYLCD. In 2019 to 2020, we investigated TYLCD throughout Taiwan, with a 10 to 100% incidence on tomato fields. Begomovirus sequences were detected in 321 out of 506 collected samples by PCR with primers PAL1v1978B and PAR1c715H. In 2015 to 2016, 59 out of 99 samples collected in Hualien-Taitung areas were also found to have begomovirus sequences. Based on the analysis of 68 viral genomic sequences, six begomoviruses were identified, including LELCV, ToLCTV, TYLCTHV, tomato leaf curl Hsinchu virus, and two new begomoviruses, tentatively named tomato leaf curl Chiayi virus (ToLCCYV) and tomato leaf curl Nantou virus (ToLCNTV). Various isolates of LELCV and TYLCTHV were grouped into four and two strains, respectively. Recombinants were detected in LELCV-A, -C, and -D, ToLCCYV, ToLCNTV, and TYLCTHV-F. Based on virus-specific detection, the majority of TYLCD-associated viruses were mixed-infected by TYLCTHV-B with TYLCTHV-F, LELCV-A, -B, or -D, and/or ToLCTV. Meanwhile, viral DNA-B was mostly associated with TYLCTHV, and all identified DNA-Bs were highly homologous with previous TYLCTHV DNA-B. The pathogenicity of selected begomoviruses was confirmed through agroinfection and whitefly transmission. All tomato plants carrying Ty-1/3 and Ty-2 resistant genes were infected by all LELCV strains and ToLCCYV, although they appeared symptomless, suggesting these viruses could be managed through the use of the resistance pyramid.
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Affiliation(s)
- Hsuan-Chun Lai
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan
| | - Zhuan Yi Neoh
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan
| | - Wen-Shi Tsai
- Department of Plant Medicine, National Chiayi University, Chiayi City 600355, Taiwan
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Dai Z, Lu Q, Sun M, Chen H, Zhu R, Wang H. Identification of a Novel Parvovirus in the Arctic Wolf ( Canis lupus arctos). Pol J Microbiol 2024; 73:395-401. [PMID: 39268953 PMCID: PMC11395419 DOI: 10.33073/pjm-2024-035] [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: 06/07/2024] [Accepted: 08/06/2024] [Indexed: 09/15/2024] Open
Abstract
A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases.
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Affiliation(s)
- Ziyuan Dai
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Qiang Lu
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Mingzhong Sun
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Hongmei Chen
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Rong Zhu
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
| | - Huiqing Wang
- Department of Clinical Laboratory, Affiliated Hospital 6 of Nantong University, Yancheng Third People’s Hospital, Yancheng, China
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Saikia L, Medhi D, Bora S, Baishya L, Kataki M, Hazarika SC. An Outbreak of Bacillus cereus Emetic Toxin Mediated Food Poisoning After Consumption of Fried Rice in Assam. Indian J Microbiol 2024; 64:957-962. [PMID: 39282178 PMCID: PMC11399483 DOI: 10.1007/s12088-023-01167-5] [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: 04/29/2023] [Accepted: 11/28/2023] [Indexed: 09/18/2024] Open
Abstract
Bacillus cereus is an emerging food-borne pathogen responsible for two types of food poisoning: emetic and diarrhoeal type. Here we report an emetic type of food-borne illness attributable to Bacillus cereus. On 2nd February, 2021, 202 people suffered from pain in abdomen and vomiting after consuming the rice provided during a public gathering in Diphu, Assam. Culture of leftover fried rice showed growth of Bacillus cereus group of organisms. Molecular detection of enterotoxin and emetic toxin genes was done in the isolated strains by polymerase chain reaction. Multi locus sequence typing (MLST) and phylogenetic analysis was done to characterise the isolated strains. A total of five strains of Bacillus cereus were isolated. Ces gene was found in isolates GMC22 & GMC24 and other enterotoxins producing genes were found in isolates GMC23 and GMC24. MLST identified four sequence types (STs) (ST1051, ST1616, ST998 and ST1000). Phylogenetic analysis clustered ST-1051 assigned to the GMC22 strain into the previously defined clade I and was in close relation with ST-144, representing a new cereulide-producing emetic cluster. As Bacillus cereus is a common contaminant of foods, it is essential to evaluate the pathogenic potential of the bacteria for a definite link between causative agents and the illness. MLST can be used to characterize the Bacillus cereus strains isolated from outbreak samples in order to link the probable pathogens with the illness. In this outbreak, we suggest that ST-1051 is the strain responsible for the food-borne illness, which was predominantly of emetic type.
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Affiliation(s)
- Lahari Saikia
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, Assam 781032 India
| | - Devyashree Medhi
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, Assam 781032 India
| | - Simi Bora
- Department of Microbiology, Kokrajhar Medical College and Hospital, Kokrajhar, Assam 783370 India
| | - Lakshyasri Baishya
- Department of Microbiology, Gauhati Medical College and Hospital, Guwahati, Assam 781032 India
| | - Manjuri Kataki
- Department of Microbiology, Nagaon Medical College and Hospital, Nagaon, Assam 782001 India
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Shah PT, Wu Z, Ma R, Wu C. Genetic diversity, variation and recombination among the human papillomaviruses (HPVs) genomes isolated in China: a comparative genomic and phylogenetic analysis. Pathog Glob Health 2024; 118:505-518. [PMID: 39263878 PMCID: PMC11441022 DOI: 10.1080/20477724.2024.2401273] [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] [Indexed: 09/13/2024] Open
Abstract
Human papillomaviruses (HPVs) are widespread, sexually transmitted group of viruses that infect most individuals at some stage, causing genital warts and cancers. They are members of the Papillomaviridae family, which contains about 400 HPV types. China is among the high HPV burden countries with reported infections of multiple HPV types, accounting for 17.3% of global deaths and 18.2% of global new cases. Thus, understanding the genetic variation and geographic diversity characteristics of HPVs isolated in China is critical for global HPV prevention strategies. Thus, we analyzed the available HPV genome sequences isolated in China that grouped into two categories (alpha- and gamma-papillomaviruses) based on full-length genomes. The most common were HPV-16, -6, -58, and -52 respectively. In addition, four of the novel strains isolated in China, e.g. TG550, JDFY01, CH2, and L55 clustered with the HPV-mSK 159, 244, 201, and 200 respectively. Our phylogeographic network analysis indicated that the L55, TG550, and CH2 are genetically identical to the mSK 200, 046, and 201 respectively, while JDFY01 appeared separately, connected to the mSK-040 following five mutational steps. Also, we found ten recombination events among HPV-6/11 types within their E1, E2, E7, L1/L2 proteins, and Long Control Region ORFs. We achieved the consensus amino acid sequences of HPV proteins and found a conserved stretch of amino acids within E5A of all HPVs circulating in China. These findings offer valued insights into the genetic relationships, distribution, and evolution of the HPVs in China that may assist in adapting effective HPV preventive measures.
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Affiliation(s)
- Pir Tariq Shah
- Faculty of Medicine, School of Basic Medical Sciences, Dalian University of Technology, Dalian, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, China
| | - Zhenyong Wu
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ruilan Ma
- Radiotherapy Oncology Department, The Second Affiliated Hospital of the Dalian Medical University, Dalian, China
| | - Chengjun Wu
- Faculty of Medicine, School of Basic Medical Sciences, Dalian University of Technology, Dalian, China
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Campos AS, Franco AC, Godinho FM, Huff R, Candido DS, da Cruz Cardoso J, Hua X, Claro IM, Morais P, Franceschina C, de Lima Bermann T, dos Santos FM, Bauermann M, Selayaran TM, Ruivo AP, Santin C, Bonella J, Rodenbusch C, Ferreira JC, Weaver SC, Gewehr VR, Wallau GL, de Souza WM, Salvato RS. Molecular Epidemiology of Western Equine Encephalitis Virus, South America, 2023-2024. Emerg Infect Dis 2024; 30:1834-1840. [PMID: 39173662 PMCID: PMC11346983 DOI: 10.3201/eid3009.240530] [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] [Indexed: 08/24/2024] Open
Abstract
Western equine encephalitis virus (WEEV) is a mosquitoborne virus that reemerged in December 2023 in Argentina and Uruguay, causing a major outbreak. We investigated the outbreak using epidemiologic, entomological, and genomic analyses, focusing on WEEV circulation near the Argentina‒Uruguay border in Rio Grande do Sul state, Brazil. During November 2023‒April 2024, the outbreak in Argentina and Uruguay resulted in 217 human cases, 12 of which were fatal, and 2,548 equine cases. We determined cases on the basis of laboratory and clinical epidemiologic criteria. We characterized 3 fatal equine cases caused by a novel WEEV lineage identified through a nearly complete coding sequence analysis, which we propose as lineage C. Our findings highlight the importance of continued surveillance and equine vaccination to control future WEEV outbreaks in South America.
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Affiliation(s)
- Aline Scarpellini Campos
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Ana Claúdia Franco
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Fernanda M. Godinho
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Rosana Huff
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Darlan S. Candido
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Jader da Cruz Cardoso
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Xinyi Hua
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Ingra M. Claro
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Paola Morais
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Carolina Franceschina
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Thales de Lima Bermann
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Franciellen Machado dos Santos
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Milena Bauermann
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Tainá Machado Selayaran
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Amanda Pellenz Ruivo
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Cristiane Santin
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Juciane Bonella
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Carla Rodenbusch
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - José Carlos Ferreira
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Scott C. Weaver
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Vilar Ricardo Gewehr
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
| | - Gabriel Luz Wallau
- Secretaria de Saúde do Estado do Rio Grande do Sul, Porto Alegre, Brazil (A.S. Campos, F.M. Godinho, R. Huff, J. da Cruz Cardoso, P. Morais, C. Franceschina, F. Machado dos Santos, M. Bauermann, T.M. Selayaran, A.P. Ruivo, R.S. Salvato)
- Universidade Federal do Rio Grande do Sul, Porto Alegre (A.C. Franco, T. de L. Bermann, R.S. Salvato)
- Imperial College London, London, UK (D.S. Candido)
- University of Kentucky, Lexington, Kentucky, USA (X. Hua, I.M. Claro, W.M. de Souza)
- Secretaria de Agricultura do Estado do Rio Grande do Sul, Porto Alegre (C. Santin, J. Bonella, C. Rodenbusch, J.C. Ferreira, V.R. Gewehr)
- University of Texas Medical Branch, Galveston, Texas, USA (S.C. Weaver)
- Fundação Oswaldo Cruz, Recife, Brazil (G.L. Wallau)
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany (G.L. Wallau)
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Grecco S, Condon E, Bucafusco D, Bratanich AC, Panzera Y, Pérez R. Comparative genomics of canine parvovirus in South America: Diversification patterns in local populations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105633. [PMID: 38969193 DOI: 10.1016/j.meegid.2024.105633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/05/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
Canine parvovirus (CPV) is a significant pathogen in domestic dogs worldwide, causing a severe and often fatal disease. CPV comprises three antigenic variants (2a, 2b, and 2c) distributed unevenly among several phylogenetic groups. The present study compared genetic variability and evolutionary patterns in South American CPV populations. We collected samples from puppies suspected of CPV infection in the neighboring Argentina and Uruguay. Antigenic variants were preliminarily characterized using PCR-RFLP and partial vp2 sequencing. Samples collected in Argentina during 2008-2018 were mainly of the 2c variant. In the Uruguayan strains (2012-2019), the 2a variant wholly replaced the 2c from 2014. Full-length coding genome and vp2 sequences were compared with global strains. The 2c and 2a strains fell by phylogenetic analysis into two phylogroups (Europe I and Asia I). The 2c strains from Argentina and Uruguay clustered in the Europe I group, with strains from America, Europe, Asia, and Oceania. Europe I is widely distributed in South America in the dog population and is also being detected in the wildlife population. The 2a strains from Uruguay formed the distinct Asia I group with strains from Asia, Africa, America, and Oceania. This Asia I group is increasing its distribution in South America and worldwide. Our research reveals high genetic variability in adjacent synchronic samples and different evolutionary patterns in South American CPV. We also highlight the importance of ancestral migrations and local diversification in the evolution of global CPV strains.
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Affiliation(s)
- Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Emma Condon
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Danilo Bucafusco
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Virología. Av. Chorroarín 280, C1427CWO, Ciudad Autónoma de Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
| | - Ana Cristina Bratanich
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Virología. Av. Chorroarín 280, C1427CWO, Ciudad Autónoma de Buenos Aires, Argentina; CONICET - Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
| | - Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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Bhat S, Kattoor JJ, Sircar S, VinodhKumar OR, Thomas P, Ghosh S, Malik YS. Detection and Molecular Characterization of Porcine Teschoviruses in India: Identification of New Genotypes. Indian J Microbiol 2024; 64:963-972. [PMID: 39282184 PMCID: PMC11399526 DOI: 10.1007/s12088-023-01173-7] [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: 08/17/2023] [Accepted: 11/30/2023] [Indexed: 09/18/2024] Open
Abstract
Porcine Teschoviruses (PTVs) are ubiquitous enteric viral pathogens that infect pigs and wild boars worldwide. PTVs have been responsible for causing the severe clinical disease (Teschen disease) to asymptomatic infections. However, to date, limited information is available on large-scale epidemiological data and molecular characterization of PTVs in several countries. In this study, we report epidemiological data on PTVs based on screening of 534 porcine fecal samples from different states of India and a RT-PCR based detection of PTVs shows a percent positivity of 8.24% (44/534). The PTV prevalence varied among different regions of the country with the highest detection rates observed in the state of Karnataka (38.1%). Phylogenetic analysis based on VP1 gene reveals the presence of PTV genotype 6 and 13 along with some unassigned novel genotypes which did not cluster with any of the established PTV genotypes (PTV 1-PTV 13). Indian PTV 6 strains are genetically closest to the Spanish strains (85.7-94.4%) whereas PTV 13 and novel genotype strains were found to be more similar to the Chinese strains (88.1-99.1%). Using recombination detection software, no Indian PTVs found to be recombinant on VP1 gene and selection pressure analysis revealed the purifying selection in the several sites of the VP1 gene of PTVs. The Bayesian analysis of Indian PTVs shows 1.16 × 10-4 substitution/site/year as the mean evolutionary rate. Further, isolation of the novel PTV strains from India and more detailed investigation much needed to know the evolutionary history of PTV strains circulating in porcine populations in India.
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Affiliation(s)
- Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
| | - Jobin Jose Kattoor
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
- Animal Disease Diagnostic Laboratory, Purdue University, West Lafayette, IN 47907 USA
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
- Department of Animal Sciences, Washington State University, Pullman, WA 99164 USA
| | - O R VinodhKumar
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
| | - Prasad Thomas
- Division of Bacteriology and Mycology, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
| | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, P.O. 334, Basseterre, Saint Kitts and Nevis
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Bareilly, 243 122 India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141001 India
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Khan N, Kakakhel S, Malik A, Nigar K, Akhtar S, Khan AA, Khan A. Genetic substructure and host-specific natural selection trend across vaccine-candidate ORF-2 capsid protein of hepatitis-E virus. J Viral Hepat 2024; 31:524-534. [PMID: 38804127 DOI: 10.1111/jvh.13959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024]
Abstract
Hepatitis E virus is a primary cause of acute hepatitis worldwide. The present study attempts to assess the genetic variability and evolutionary divergence among HEV genotypes. A vaccine promising capsid-protein coding ORF-2 gene sequences of HEV was evaluated using phylogenetics, model-based population genetic methods and principal component analysis. The analyses unveiled nine distinct clusters as subpopulations for six HEV genotypes. HEV-3 genotype samples stratified into four different subgroups, while HEV-4 stratified into three additional subclusters. Rabbit-infectious HEV-3ra samples constitute a distinct cluster. Pairwise analysis identified marked genetic distinction of HEV-4c and HEV-4i subgenotypes compared to other genotypes. Numerous admixed, inter and intragenotype recombinant strains were detected. The MEME method identified several ORF-2 codon sites under positive selection. Some selection signatures lead to amino acid substitutions within ORF-2, resulting in altered physicochemical features. Moreover, a pattern of host-specific adaptive signatures was identified among HEV genotypes. The analyses conclusively depict that recombination and episodic positive selection events have shaped the observed genetic diversity among different HEV genotypes. The significant genetic diversity and stratification of HEV-3 and HEV-4 genotypes into subgroups, as identified in the current study, are noteworthy and may have implications for the efficacy of anti-HEV vaccines.
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Affiliation(s)
- Nasir Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Sehrish Kakakhel
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Kiran Nigar
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
| | - Suhail Akhtar
- Department of Biochemistry, A.T. Still University of Health Sciences, Kirksville, Missouri, USA
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan
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Xu D, Li J, Han L, Chen D, Bao W, Li L, Wang H, Shui J, Liang R, Liu Y, Liu Y, Cai K, Chen W. Epidemics and diversity of norovirus variants with acute gastroenteritis outbreak in Hongshan District, Wuhan City, China, 2021-2023. J Infect Public Health 2024; 17:102499. [PMID: 39067200 DOI: 10.1016/j.jiph.2024.102499] [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: 03/23/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Norovirus is the predominant pathogen causing foodborne illnesses and acute gastroenteritis (AGE) outbreaks worldwide, imposing a significant disease burden. This study aimed to investigate the epidemiological characteristics and genotypic diversity of norovirus outbreaks in Hongshan District, Wuhan City. METHODS A total of 463 AGE cases from 39 AGE-related outbreaks in Hongshan District between January 1, 2021, and June 30, 2023, were included in the study. Reverse transcription-polymerase chain reaction (RT-PCR) was used to identify norovirus types GI and GII in anal swab samples from all cases. Norovirus-positive samples were sequenced and analyzed for the open reading frame (ORF) 1/ORF2 hinge region. RESULTS 26 norovirus infectious outbreaks were reported among 39 acute diarrheal outbreaks, including 14 outbreaks in kindergartens, 8 in elementary schools, and 4 in universities. Based on clinical symptoms and epidemiological investigations, a total of 1295 individuals were identified as having been exposed to norovirus, yielding an attack rate of 35.75 %. A higher proportion of outbreaks was observed during the winter and spring seasons (38.46 %). Additionally, norovirus-positive samples were subjected to sequencing and analysis of the open reading frame (ORF) 1/ORF2 hinge region. Genotypic data for norovirus was successfully obtained from 18 (69.23 %) of the infectious outbreaks, revealing 10 distinct recombinant genotypes. GII.4 Sydney 2012 [P31] and GII.17[P17] were the predominant strains in 2021 and 2022, GII.3 [P12] emerged as the dominant strain in 2023. CONCLUSION Norovirus outbreaks in Hongshan District predominantly occurred in crowded educational institutions, with peaks in the cold season and a high attack rate in universities. GII.3 [P12] has become the locally predominant strain.
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Affiliation(s)
- Dandan Xu
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Jing Li
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China
| | - Lingyan Han
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Ding Chen
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Wubo Bao
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Li Li
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Huawei Wang
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Jinglin Shui
- Wuhan Hongshan Center for Disease Control and Prevention, Wuhan, Hubei 430065, China
| | - Ruyi Liang
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yang Liu
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yingle Liu
- The State Key Laboratory of Virology of China,Wuhan, Hubei 430072, China
| | - Kun Cai
- Hubei Provincial Center for Disease Control and Prevention, Wuhan, Hubei 430079, China.
| | - Weihong Chen
- Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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Zhao Y, Su X, He D. Codon Usage Analysis Reveals Distinct Evolutionary Patterns and Host Adaptation Strategies in Duck Hepatitis Virus 1 (DHV-1) Phylogroups. Viruses 2024; 16:1380. [PMID: 39339856 PMCID: PMC11437458 DOI: 10.3390/v16091380] [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: 06/22/2024] [Revised: 08/18/2024] [Accepted: 08/28/2024] [Indexed: 09/30/2024] Open
Abstract
Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.
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Affiliation(s)
| | | | - Dongchang He
- Department of Veterinary Medicine, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
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Munkhtsetseg A, Batmagnai E, Odonchimeg M, Ganbat G, Enkhmandakh Y, Ariunbold G, Dolgorsuren T, Odbileg R, Dulam P, Tuvshintulga B, Sugimoto C, Sakoda Y, Yamagishi J, Erdenechimeg D. Genome sequencing of canine distemper virus isolates from unvaccinated dogs in Mongolia. Vet J 2024; 308:106231. [PMID: 39209147 DOI: 10.1016/j.tvjl.2024.106231] [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: 04/05/2024] [Revised: 08/22/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
Canine distemper virus (CDV) triggers a severe, often fatal disease in dogs and wildlife known as canine distemper (CD). Prior research has noted significant genetic diversity and recombination among CDV isolates from different geographical regions, potentially contributing to vaccine failures. Despite this, no genetic characterization of Mongolian CDVs has been conducted. This study, isolated CDVs from three unvaccinated dogs: two 10-month-old mixed-breeds and an 18-month-old Samoyed. All exhibited CD symptoms and subsequently died. Virus isolation was conducted using Vero/dog SLAM cells, with genome sequencing performed via nanopore technology. The mixed-breed dogs were infected with non-recombinant CDV isolates, forming a sister clade to the Asia-1 lineage prevalent in Asia. The Samoyed was infected with a non-recombinant CDV isolate, classifying as Asia-4 lineage sporadically reported in some Asian countries. This sequencing data offers foundational information on genetic diversity, aiding CD control measure development and benefiting future Eurasia and Asian studies.
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Affiliation(s)
- Ariunbold Munkhtsetseg
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Enkhbaatar Batmagnai
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Myagmarsuren Odonchimeg
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Gombodash Ganbat
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Yondonjamts Enkhmandakh
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Gantulga Ariunbold
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Tsedenbal Dolgorsuren
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Raadan Odbileg
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | | | - Bumduuren Tuvshintulga
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia
| | - Chihiro Sugimoto
- Project for Strengthening the Practical Capacity of Public and Private Veterinarians, Japan International Cooperation Agency, Ulaanbaatar, Mongolia
| | - Yoshihiro Sakoda
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, GI-CoRE, Hokkaido University, Sapporo, Japan
| | - Dashzevge Erdenechimeg
- Laboratory of Virology, Institute of Veterinary Medicine, Mongolian University of Life Sciences Zaisan, Ulaanbaatar 17024, Mongolia.
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Lu Y, Zeng Y, Luo H, Qiao B, Meng Q, Dai Z, Chen N, Zhao L, Meng X, Zhang H, Xia J, Ping J. Molecular characteristic, evolution, and pathogenicity analysis of avian infectious bronchitis virus isolates associated with QX type in China. Poult Sci 2024; 103:104256. [PMID: 39288718 PMCID: PMC11421327 DOI: 10.1016/j.psj.2024.104256] [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: 05/06/2024] [Revised: 07/21/2024] [Accepted: 08/20/2024] [Indexed: 09/19/2024] Open
Abstract
Infectious bronchitis virus (IBV) is one of the major avian pathogens plaguing the global poultry industry. Although vaccination is the primary preventive measure for IBV infection, the emergence of virus variants with mutations and recombination has resulted in IBV circulating globally, presenting a challenge for IB control. Here, we isolated 3 IBV strains (CZ200515, CZ210840, and CZ211063) from suspected sick chickens vaccinated with IBV live attenuated vaccines (H120, 4/91, or QXL87). Phylogenetic analysis of the S1 gene sequence of the spike (S) revealed that the 3 isolates belonged to the QX-type (GI-19 lineage). Whole genome sequencing and recombination analysis indicated that CZ200515 and CZ210840 contained genetic material from 4/91 and Scyz3 (QX-type), possibly due to recombination between the circulating strain and the 4/91 vaccine strain, while no evidence of recombination was found in CZ211063. Pathogenicity analysis in 1-day-old specific pathogen-free (SPF) chickens demonstrated that all 3 isolates caused severe tissue damage and varying degrees of mortality. Virus cross-neutralization assay revealed decreased antigen relatedness between the isolates and the QX-type vaccine strain (QXL87). Amino acid sequence homology analysis of S1 revealed 5%-6.5% variances between the isolates and QXL87. Analysis of the S1 subunit structure revealed that mutations of amino acid residues in the hypervariable region (HVR) and the neutralizing epitope region resulted in antigenic variation in isolates by changing the antigen conformation. Our data indicate antigenicity variances between QX isolates and QXL87 vaccine strains, potentially resulting in immune evasion occurrences. Overall, these results offer crucial insights into the epidemiology and pathogenicity of QX-type IBV, facilitating improved selection and formulation of vaccines for disease management.
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Affiliation(s)
- Yuanlu Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yiran Zeng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haowei Luo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bingchen Qiao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Meng
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zijian Dai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Na Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lingcai Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianchen Meng
- Lihua Nanjing Industrial Research Institute Co. Ltd. Nanjing, 213168, China; Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009 China
| | - Haitao Zhang
- Lihua Nanjing Industrial Research Institute Co. Ltd. Nanjing, 213168, China
| | - Jun Xia
- Key Laboratory for Prevention and Control of Herbivorous Animal Diseases of the Ministry of Agriculture and Rural Affairs & Xinjiang Animal Disease Research Key Laboratory, Xinjiang Academy of Animal Sciences Institute of Veterinary Medicine, 830000, China.
| | - Jihui Ping
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
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Li C, Hu Y, Liu Y, Li N, Yi L, Tu C, He B. The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses. Virus Evol 2024; 10:veae062. [PMID: 39175838 PMCID: PMC11341201 DOI: 10.1093/ve/veae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 07/08/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024] Open
Abstract
Amphibians are an essential class in the maintenance of global ecosystem equilibrium, but they face serious extinction risks driven by climate change and infectious diseases. Unfortunately, the virus diversity harbored by these creatures has been rarely investigated. By profiling the virus flora residing in different tissues of 100 farmed black-spotted frogs (Rana nigromaculata) using a combination of DNA and RNA viromic methods, we captured 28 high-quality viral sequences covering at least 11 viral families. Most of these sequences were remarkably divergent, adding at least 10 new species and 4 new genera within the families Orthomyxoviridae, Adenoviridae, Nodaviridae, Phenuiviridae, and Picornaviridae. We recovered five orthomyxovirus segments, with three distantly neighboring two Chinese fish-related viruses. The recombination event of frog virus 3 occurred among the frog and turtle strains. The relative abundance and molecular detection revealed different tissue tropisms of these viruses, with the orthomyxovirus and adenoviruses being enteric and probably also neurotropic, but the new astrovirus and picornavirus being hepatophilic. These results expand the spectrum of viruses harbored by anurans, highlighting the necessity to continuously monitor these viruses and to investigate the virus diversity in a broader area with more diverse amphibian species.
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Affiliation(s)
- Chenxi Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 573 Yujinxiang Street, Jingyue District, Changchun, Jilin Province 130122, China
| | - Yazhou Hu
- Fisheries College, Hunan Agriculture University, No. 1 Nongda Road, Furong District, Changsha, Hunan Province 410128, China
| | - Yuhang Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 573 Yujinxiang Street, Jingyue District, Changchun, Jilin Province 130122, China
| | - Nan Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 573 Yujinxiang Street, Jingyue District, Changchun, Jilin Province 130122, China
| | - Le Yi
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 573 Yujinxiang Street, Jingyue District, Changchun, Jilin Province 130122, China
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 573 Yujinxiang Street, Jingyue District, Changchun, Jilin Province 130122, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, No. 12 Wenhui Road, Hanjiang District, Yangzhou, Jiangsu Province 225009, China
| | - Biao He
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, No. 573 Yujinxiang Street, Jingyue District, Changchun, Jilin Province 130122, China
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Kwak M, Troiano E, Kil EJ, Parrella G. High-throughput sequencing detected a virus-viroid complex in a single pokeweed plant. FRONTIERS IN PLANT SCIENCE 2024; 15:1435611. [PMID: 39239202 PMCID: PMC11374604 DOI: 10.3389/fpls.2024.1435611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/29/2024] [Indexed: 09/07/2024]
Abstract
In this study, total RNA high-throughput sequencing (HTS) of a single symptomatic Phytolacca americana plant enabled the obtention of a nearly complete genome of two new isolates of turnip yellows virus (TuYV), named TuYV-ITA1 and TuYV-ITA2, and revealed a mixed infection with a new variant of citrus exocortis viroid (CEVd), named CEVd-ITA1. The TuYV-ITA2 isolate diverged from the known virus isolates of TuYV and showed variability in the P0 and P5 readthrough domain. Recombination analysis revealed its recombinant nature between TuYV and an unidentified polerovirus. The putative recombination event was identified in the P5 readthrough domain of the TuYMV-ITA2 isolate. Our results thus represent the first report of TuYV in Italy and some molecular evidence for the possible natural co-existence of TuYV and CEVd in a new natural host for both infectious entities. This study is adding further knowledge about the role of weed plants as virus reservoirs, and thus additional biological and impact studies would be desirable to determine in particular the role of P. americana in the spread of TuYV and if this virus should be considered a new threat for the susceptible Italian crops.
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Affiliation(s)
- Myeonghwan Kwak
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | - Elisa Troiano
- Institute for Sustainable Plant Protection, National Research Council, Portici, Italy
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | - Giuseppe Parrella
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
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Ito T. First reports of several viruses and a viroid including a novel vitivirus in Japan, found through virome analysis of bulk grape genetic resources. Virus Genes 2024:10.1007/s11262-024-02101-7. [PMID: 39162928 DOI: 10.1007/s11262-024-02101-7] [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: 12/01/2023] [Accepted: 08/12/2024] [Indexed: 08/21/2024]
Abstract
Virome analysis was performed on 174 grape genetic resources from the National Agriculture and Food Research Organization, Japan. A total of 20 bulk samples was prepared by grouping the vines into batches of 6-10 plants. Each of the bulk samples was analyzed using high-throughput sequencing, which detected 27 viruses and 5 viroids, including six viruses and one viroid reported in Japan for the first time (grapevine viruses F, L, and T, grapevine Kizil Sapak virus, grapevine Syrah virus 1, grapevine satellite virus, and grapevine yellow speckle viroid 2). In addition, a novel vitivirus was detected with a maximum nucleotide sequence identity of only 58% to its closest relative, grapevine virus A (GVA). The genome of this novel virus was 7,461 nucleotides in length and encoded five open reading frames showing the typical genomic structure of vitiviruses. Phylogenetic trees of vitiviruses placed it in a distinct position nearest to GVA or grapevine virus F (GVF) in genomes and amino acids of deduced replication-associated protein (RAP) and coat protein (CP). The amino acid sequence identities of RAP and CP with GVA, GVF, and other vitiviruses were a maximum of 53% and 73%, respectively, which were significantly below the species demarcation threshold of 80% in the genus. The low identity and phylogenetic analyses indicate the discovery of a novel vitivirus species provisionally named grapevine virus P.
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Affiliation(s)
- Takao Ito
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Akitsu, Higashihiroshima, Hiroshima, 739-2494, Japan.
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