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Huang CW, Chen LH, Lee DH, Liu YP, Li WC, Lee MS, Chen YP, Lee F, Chiou CJ, Lin YJ. Evolutionary history of H5 highly pathogenic avian influenza viruses (clade 2.3.4.4c) circulating in Taiwan during 2015-2018. INFECTION GENETICS AND EVOLUTION 2021; 92:104885. [PMID: 33932612 DOI: 10.1016/j.meegid.2021.104885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/20/2021] [Accepted: 04/24/2021] [Indexed: 12/13/2022]
Abstract
The highly pathogenic avian influenza (HPAI) virus A/goose/Guangdong/1/96 H5N1 (Gs/GD) lineage has been transmitted globally and has caused deaths in wild birds, poultry, and humans. Clade 2.3.4.4c, one of the subclades of the Gs/GD lineage, spread through Taiwan in late 2014 and become an endemic virus. We analyzed 239 newly sequenced HPAI clade H5Nx isolates to explore the phylogenetic relationships, divergence times, and evolutionary history of Taiwan HPAI H5Nx viruses from 2015 to 2018. Overall, 15 reassortant genotypes were identified among H5N2, H5N3, and H5N8 viruses. Maximum likelihood and Bayesian phylogenies based on homologous hemagglutinin (HA) and matrix protein (MP) genes suggest that Taiwan HPAI H5Nx viruses share a most recent common ancestor that has diversified since October 2014 and is closely related to two HPAI H5N8 viruses identified from wild birds in Japan. Two waves of HPAI caused by multiple reassortants were identified, the first occurring in late 2014 and the second beginning in late 2016. The first wave consisted of seven H5Nx reassortants that spread through Taiwan. In the second wave, eight novel reassortants were detected which had newly introduced internal genes, mostly derived from the avian influenza virus gene pool maintained in wild birds in Asia. Phylodynamic reconstruction using the Bayesian Skygrid model revealed varied fluctuating patterns of relative genetic diversity among reassortants. The mean evolutionary rate also varied among reassortants and subtypes. The neuraminidase (NA) gene evolved faster than the HA gene in H5N2 viruses, while HA evolved faster than NA in H5N8 viruses. The HA mean evolutionary rate ranged from 6.10 × 10-3 to 7.73 × 10-3 and from 5.81 × 10-3 to 9.45 × 10-3 substitutions/site/year for H5N2 and H5N8 viruses, respectively. The continuous circulation of HPAI H5Nx variants and the emergence of novel reassortants in Taiwan highlight that the surveillance, biosecurity, and management systems of poultry farms need to be improved and carefully executed.
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Affiliation(s)
- Chih-Wei Huang
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Li-Hsuan Chen
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA.
| | - Yu-Pin Liu
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Wan-Chen Li
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Ming-Shiuh Lee
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Yen-Ping Chen
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Fan Lee
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Chwei-Jang Chiou
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
| | - Yu-Ju Lin
- Animal Health Research Institute, Council of Agriculture, New Taipei City, Taiwan.
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Alvarez-Munoz S, Upegui-Porras N, Gomez AP, Ramirez-Nieto G. Key Factors That Enable the Pandemic Potential of RNA Viruses and Inter-Species Transmission: A Systematic Review. Viruses 2021; 13:537. [PMID: 33804942 PMCID: PMC8063802 DOI: 10.3390/v13040537] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/17/2021] [Accepted: 03/20/2021] [Indexed: 12/27/2022] Open
Abstract
Viruses play a primary role as etiological agents of pandemics worldwide. Although there has been progress in identifying the molecular features of both viruses and hosts, the extent of the impact these and other factors have that contribute to interspecies transmission and their relationship with the emergence of diseases are poorly understood. The objective of this review was to analyze the factors related to the characteristics inherent to RNA viruses accountable for pandemics in the last 20 years which facilitate infection, promote interspecies jump, and assist in the generation of zoonotic infections with pandemic potential. The search resulted in 48 research articles that met the inclusion criteria. Changes adopted by RNA viruses are influenced by environmental and host-related factors, which define their ability to adapt. Population density, host distribution, migration patterns, and the loss of natural habitats, among others, have been associated as factors in the virus-host interaction. This review also included a critical analysis of the Latin American context, considering its diverse and unique social, cultural, and biodiversity characteristics. The scarcity of scientific information is striking, thus, a call to local institutions and governments to invest more resources and efforts to the study of these factors in the region is key.
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Affiliation(s)
| | | | | | - Gloria Ramirez-Nieto
- Microbiology and Epidemiology Research Group, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (S.A.-M.); (N.U.-P.); (A.P.G.)
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Mateus-Anzola J, Gaytan-Cruz L, Montoya-Carrillo C, Ivan Sánchez-Betancourt J, Zarza H, Segura-Velázquez R, Ojeda-Flores R. Molecular identification and phylogenetic characterization of influenza A virus at a wildlife-livestock interface in Mexico. Transbound Emerg Dis 2020; 68:3563-3573. [PMID: 33350099 DOI: 10.1111/tbed.13962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/22/2022]
Abstract
Influenza A virus (IAV) outbreaks constitute a constant threat to public health and pose a remarkable impact on socio-economic systems worldwide. Interactions between wild and domestic birds, humans and swine can lead to spillover events. Backyard livestock systems in proximity to wetlands represent high-risk areas for viral spread. However, some gaps remain in our knowledge of IAV transmission at the wildlife-livestock interface in Mexico. Hence, the study aimed at molecular identification and phylogenetic characterization of IAV in the wild duck-backyard livestock interface at a wetland of Mexico. A total of 875 animals were tested by real-time RT-PCR (qRT-PCR). We detected IAV in 3.68% of the wild ducks sampled during the winter season 2016-2017. Nonetheless, the samples obtained from backyard poultry and swine tested negative. The highest IAV frequency (11.10%) was found in the Mexican duck (Anas diazi). Subtypes H1N1, H3N2 and H5N2 were detected. Phylogenetic analyses revealed that IAV detected in wild birds from the Lerma wetlands was mostly related to swine and poultry IAV strains previously isolated in the United States and Mexico. Except, the UIFMVZ377/H5N2 related to North American waterbirds. In conclusion, the co-circulation of three IAV subtypes in wild ducks close to backyard farms in Mexico, as well as the local identification of influenza viruses genetically related to Mexican and North American IAV strains, highlights the importance of the Lerma marshes for influenza surveillance given the close interaction among wild birds, poultry, pigs and humans.
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Affiliation(s)
- Jessica Mateus-Anzola
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Liliana Gaytan-Cruz
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Cecilia Montoya-Carrillo
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Ivan Sánchez-Betancourt
- Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Heliot Zarza
- Departamento de Ciencias Ambientales, CBS, Universidad Autónoma Metropolitana Unidad Lerma, México, México
| | - René Segura-Velázquez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Unidad de Investigación, Ciudad de México, México
| | - Rafael Ojeda-Flores
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
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Affiliation(s)
- C Heffernan
- London International Development Centre, 36 Gordon Square, London W1H 20D, United Kingdom.
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Meyer A, Dinh TX, Nhu TV, Pham LT, Newman S, Nguyen TTT, Pfeiffer DU, Vergne T. Movement and contact patterns of long-distance free-grazing ducks and avian influenza persistence in Vietnam. PLoS One 2017. [PMID: 28632789 PMCID: PMC5478089 DOI: 10.1371/journal.pone.0178241] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Presence of ducks, and in particular of free-grazing ducks, has consistently been shown to be one of the most important risk factors for highly pathogenic avian influenza outbreaks which has compromised poultry production in South-East Asia since the early 2000s and continues to threaten public health, farmers’ livelihood and food security. Although free-grazing duck production has been practised for decades in South-East Asia, there are few published studies describing this production system, which is suspected to play an important role in the maintenance of avian influenza viruses. This study aimed at describing quantitatively the long-distance free-grazing duck production system in South Vietnam, characterising the movement and contact patterns of the duck flocks, and identifying potential associations between farming practices, movement and contact patterns and the circulation of avian influenza viruses. We conducted interviews among stakeholders involved in the free-grazing duck production system (duck farmers, transporters and rice paddy owners) in combination with a virological cross-sectional survey in South Vietnam. Results show that both direct and indirect contacts between free-grazing duck flocks were frequent and diverse. The flocks were transported extensively across district and province boundaries, mainly by boat but also by truck or on foot. A third of the investigated flocks had a positive influenza A virology test, indicating current circulation of avian influenza viruses, but none were positive for H5 subtypes. The age and size of the flock as well as its location at the time of sampling were associated with the risk of influenza A circulation in the flocks. These findings should be considered when developing risk assessment models of influenza virus spread aimed at informing the development of improved biosecurity practices leading to enhanced animal health, sustainable animal production and reliable income for farmers.
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Affiliation(s)
- Anne Meyer
- Veterinary Epidemiology, Economics and Public Health Group, Royal Veterinary College, London, United-Kingdom
- * E-mail:
| | | | - Thu Van Nhu
- National Institute for Animal Sciences, Hanoi, Vietnam
| | - Long Thanh Pham
- Department of Animal Health, Ministry of Agriculture and Rural Development, Hanoi, Vietnam
| | - Scott Newman
- Emergency Centre for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Thuy Thi Thanh Nguyen
- Emergency Centre for Transboundary Animal Diseases, Food and Agriculture Organization of the United Nations, Hanoi, Vietnam
| | - Dirk Udo Pfeiffer
- Veterinary Epidemiology, Economics and Public Health Group, Royal Veterinary College, London, United-Kingdom
- School of Veterinary Medicine, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Timothée Vergne
- Veterinary Epidemiology, Economics and Public Health Group, Royal Veterinary College, London, United-Kingdom
- MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle) Group, Institut de Recherche pour le Développement (IRD-224, CNRS-5290, Université de Montpellier 2), Montpellier, France
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Rashid PMA, Saeed NM, Dyary HO. Genetic characterization and phylogenic analysis of H5N1 avian influenza virus detected in peafowl in Kirkuk province, Iraq. J Med Virol 2017; 89:1179-1185. [PMID: 28036106 DOI: 10.1002/jmv.24762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 11/09/2022]
Abstract
A highly pathogenic avian influenza (HPAI), H5N1, was detected for the first time in peafowls in Kirkuk province, Iraq in 2015. Genetic analysis of the Kirkuk H5N1 indicated molecular markers for avian-type receptors. The Kirkuk H5N1 hemagglutinin gene had an infrequent amino acid cleavage site (SPQREKRRKRGLF), and neuraminidase genes showed sensitive molecular markers for antiviral drugs. Additionally, the phylogenetic analysis found that the Kirkuk H5N1 belonged to subclade 2.3.2.1c. Our results showed that the 2015 H5N1 from the Iraqi city of Kirkuk exhibited new genetic characterization and was different from the 2006 H5N1 isolate from Iraq.
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Affiliation(s)
- Peshnyar M A Rashid
- Molecular Diagnostic Laboratory, Slemani Veterinary Directorate, As Sulaymaniyah, Kurdistan region, Iraq
| | - Nahla M Saeed
- Basic Sciences Department, College of Veterinary Medicine, University of Sulaimani, As Sulaymaniyah, Kurdistan region, Iraq
| | - Hiewa Othman Dyary
- Basic Sciences Department, College of Veterinary Medicine, University of Sulaimani, As Sulaymaniyah, Kurdistan region, Iraq
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Paul MC, Goutard FL, Roulleau F, Holl D, Thanapongtharm W, Roger FL, Tran A. Quantitative assessment of a spatial multicriteria model for highly pathogenic avian influenza H5N1 in Thailand, and application in Cambodia. Sci Rep 2016; 6:31096. [PMID: 27489997 PMCID: PMC4977984 DOI: 10.1038/srep31096] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/13/2016] [Indexed: 11/26/2022] Open
Abstract
The Highly Pathogenic Avian Influenza H5N1 (HPAI) virus is now considered endemic in several Asian countries. In Cambodia, the virus has been circulating in the poultry population since 2004, with a dramatic effect on farmers' livelihoods and public health. In Thailand, surveillance and control are still important to prevent any new H5N1 incursion. Risk mapping can contribute effectively to disease surveillance and control systems, but is a very challenging task in the absence of reliable disease data. In this work, we used spatial multicriteria decision analysis (MCDA) to produce risk maps for HPAI H5N1 in poultry. We aimed to i) evaluate the performance of the MCDA approach to predict areas suitable for H5N1 based on a dataset from Thailand, comparing the predictive capacities of two sources of a priori knowledge (literature and experts), and ii) apply the best method to produce a risk map for H5N1 in poultry in Cambodia. Our results showed that the expert-based model had a very high predictive capacity in Thailand (AUC = 0.97). Applied in Cambodia, MCDA mapping made it possible to identify hotspots suitable for HPAI H5N1 in the Tonlé Sap watershed, around the cities of Battambang and Kampong Cham, and along the Vietnamese border.
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Affiliation(s)
- Mathilde C. Paul
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- EPIA, INRA, 63122 Saint Genès Champanelle, France
| | - Flavie L. Goutard
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- CIRAD, UPR AGIRs, 10900 Bangkok, Thaïland
- Kasetsart University, 10900 Bangkok, Thailand
| | - Floriane Roulleau
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | - Davun Holl
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | | | - François L. Roger
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- CIRAD, UPR AGIRs, 10900 Bangkok, Thaïland
- Kasetsart University, 10900 Bangkok, Thailand
| | - Annelise Tran
- CIRAD, UPR AGIRs, F-34398, Montpellier, France
- CIRAD, UMR TETIS, F-34398, Montpellier, France
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Osbjer K, Berg M, Sokerya S, Chheng K, San S, Davun H, Magnusson U, Olsen B, Zohari S. Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia. Transbound Emerg Dis 2016; 64:1557-1568. [PMID: 27484711 DOI: 10.1111/tbed.12547] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Indexed: 11/27/2022]
Abstract
Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low-income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene-based rRT-PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full-length genome sequencing confirmed triple reassortant H3N2 in all IAV-positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South-East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden.
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Affiliation(s)
- K Osbjer
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - M Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - S Sokerya
- Centre for Livestock and Agriculture Development, Phnom Penh, Cambodia
| | - K Chheng
- National Institute of Public Health, Phnom Penh, Cambodia
| | - S San
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | - H Davun
- National Veterinary Research Institute, Phnom Penh, Cambodia
| | - U Magnusson
- Division of Reproduction, Department of Clinical Sciences, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - B Olsen
- Infectious Diseases, Zoonosis Science Center, Department of Medical Sciences and IMBIM, Uppsala University (UU), Uppsala, Sweden
| | - S Zohari
- Department of Microbiology, National Veterinary Institute, Uppsala, Sweden
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Wei K, Li Y, Chen H, Zhang Q. Genomic Surveillance Elucidates HCV 1a Phylodynamics and Molecular Evolution. Evol Biol 2016. [DOI: 10.1007/s11692-016-9379-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Wei K, Liu X. Phylogenetic Analysis and Functional Characterization of the Influenza A H5N1 PB2 Gene. Transbound Emerg Dis 2015; 64:374-388. [PMID: 25990872 DOI: 10.1111/tbed.12376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Indexed: 12/23/2022]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses are endemic in poultry and cause continued inter-species transmission to human in Asia, such as China and Vietnam, leading to pandemic concerns and socio-economic challenges. Phylogenetic analysis of H5N1 viruses isolated from China and Vietnam during 2001-2012 showed that several geographically distinct sublineages have become established in these two countries. Subsequently, we reassigned HPAI H5N1 viruses into three distinct groups to reveal the intrasubtype reassortment. Apart from six reassortants detected here, we found that several viral strains showed signals for homologous recombination within PB2 and PB1 genes, suggestive of the fluidity of the H5N1 virus gene pool. Furthermore, sequenced-based analyses revealed that the viral polymerase displayed a higher level of genetic polymorphism but associated with lower substitution rate when compared with those of other gene segments. In addition, the selection pressure analysis indicated that purifying selection was predominant in eight genomic segments especially in the polymerase complex. However, the site-by-site analysis helped to detect 14 positively selected sites in the PB1, PA, HA, NA, MP and NS proteins. Despite the fact that PB2 protein of H5N1 viruses was highly conserved at the amino acid level, eleven adaptive mutations were still observed in the protein. Further comparative structural analysis of the K627E mutation indicated that there were no structural differences between the variants, which possessed either PB2-627E or PB2-627K. Transcriptomic analysis suggested the non-mitochondrial PB2 protein of H5N1 virus that forms a stable complex with the mitochondrial antiviral signalling protein (MAVS, also known as IPS-1, VISA or Cardif) can induce interferon-beta (IFN-β) expression, but the substitution (PB2-K627E) is not the sole determinant of the RIG-I-like receptors (RLR) signalling components induction in Calu-3 cells.
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Affiliation(s)
- K Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - X Liu
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
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Wei K, Lin Y, Li Y, Chen Y. Tracking the Evolution in Phylogeny, Structure and Function of H5N1 Influenza Virus PA Gene. Transbound Emerg Dis 2014; 63:548-63. [PMID: 25476417 DOI: 10.1111/tbed.12301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 01/24/2023]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 viruses have severely affected the poultry industry of Vietnam and Indonesia. The outbreaks of HPAI H5N1 viruses continue to pose a serious threat to public health, which have profound impacts on public health. In this study, we presented phylogenetic evidences for five reassortants among HPAI H5N1 viruses sampled from Vietnam and Indonesia during 2003-2013 and found that reassortment events occurred more frequently in the three gene segments (PB1, PA and HA) than in the remaining five gene segments (PB2, NA, NP, NS and MP). The sequence-based analyses have revealed that the PA protein displays high levels of DNA sequence polymorphism and variability than other internal proteins. Seven positive selection sites were detected in PA proteins, which ranked second only to the surface glycoproteins. Structure-based comparative analysis of PA proteins showed a remarkable sequence conservation between the high-pathogenic, low-pathogenic and reassortant viruses, indicating that PA appears to be a potential antiviral target. Furthermore, by analysing the published data, we compared the differential expression of genes involved in RIG-I- and MAVS-mediated intracellular type I interferon (IFN)-inducing pathway between the VN3028IIcl2-infected, IDN3006-infected and IDN3006/PA-infected groups. Our analyses indicated that the inhibitory effect of the PA protein on MAVS was not strong. In addition, transcriptional levels of 33 mitochondrial proteins involved in the induction of apoptosis have significantly increased, suggesting that PA may play an important role in apoptosis signalling pathway.
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Affiliation(s)
- K Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Y Lin
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Y Li
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou, China
| | - Y Chen
- School of Medicine, Tsinghua University, Beijing, China
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Wei K, Pan S. Maize protein phosphatase gene family: identification and molecular characterization. BMC Genomics 2014; 15:773. [PMID: 25199535 PMCID: PMC4169795 DOI: 10.1186/1471-2164-15-773] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Protein phosphatases (PPs) play critical roles in various cellular processes through the reversible protein phosphorylation that dictates many signal transduction pathways among organisms. Recently, PPs in Arabidopsis and rice have been identified, while the whole complement of PPs in maize is yet to be reported. RESULTS In this study, we have identified 159 PP-encoding genes in the maize genome. Phylogenetic analyses categorized the ZmPP gene family into 3 classes (PP2C, PTP, and PP2A) with considerable conservation among classes. Similar intron/exon structural patterns were observed in the same classes. Moreover, detailed gene structures and duplicative events were then researched. The expression profiles of ZmPPs under different developmental stages and abiotic stresses (including salt, drought, and cold) were analyzed using microarray and RNA-seq data. A total of 152 members were detected in 18 different tissues representing distinct stages of maize plant developments. Under salt stress, one gene was significantly up-expressed in seed root (SR) and one gene was down-expressed in primary root (PR) and crown root (CR), respectively. As for drought stress condition, 13 genes were found to be differentially expressed in leaf, out of which 10 were up-regulated and 3 exhibited down-regulation. Additionally, 13 up-regulated and 3 down-regulated genes were found in cold-tolerant line ETH-DH7. Furthermore, real-time PCR was used to confirm the expression patterns of ZmPPs. CONCLUSIONS Our results provide new insights into the phylogenetic relationships and characteristic functions of maize PPs and will be useful in studies aimed at revealing the global regulatory network in maize abiotic stress responses, thereby contributing to the maize molecular breeding with enhanced quality traits.
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Affiliation(s)
- Kaifa Wei
- School of Biological Sciences and Biotechnology, Minnan Normal University, Zhangzhou 363000, China.
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