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Ciuoderis K, Usuga J, Pérez-Restrepo LS, Gonzalez-Ramirez M, Carvajal L, Cardona A, Moreno I, Diaz A, Peña M, Hernández-Ortiz JP, Osorio JE. Genomic diversity and evolutionary dynamics of Influenza A viruses in Colombian swine: implications for one health surveillance and control. Emerg Microbes Infect 2024; 13:2368202. [PMID: 38970562 PMCID: PMC11229761 DOI: 10.1080/22221751.2024.2368202] [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: 05/05/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024]
Abstract
Influenza A viruses (IAV) impose significant respiratory disease burdens in both swine and humans worldwide, with frequent human-to-swine transmission driving viral evolution in pigs and highlighting the risk at the animal-human interface. Therefore, a comprehensive One Health approach (interconnection among human, animal, and environmental health) is needed for IAV prevention, control, and response. Animal influenza genomic surveillance remains limited in many Latin American countries, including Colombia. To address this gap, we genetically characterized 170 swine specimens from Colombia (2011-2017). Whole genome sequencing revealed a predominance of pandemic-like H1N1 lineage, with a minority belonging to H3N2 and H1N2 human seasonal-like lineage and H1N1 early classical swine lineages. Significantly, we have identified reassortant and recombinant viruses (H3N2, H1N1) not previously reported in Colombia. This suggests a broad genotypic viral diversity, likely resulting from reassortment between classical endemic viruses and new introductions established in Colombia's swine population (e.g. the 2009 H1N1 pandemic). Our study highlights the importance of a One Health approach in disease control, particularly in an ecosystem where humans are a main source of IAV to swine populations, and emphasizes the need for continued surveillance and enhanced biosecurity measures. The co-circulation of multiple subtypes in regions with high swine density facilitates viral exchange, underscoring the importance of monitoring viral evolution to inform vaccine selection and public health policies locally and globally.
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MESH Headings
- Animals
- Swine
- Colombia/epidemiology
- Orthomyxoviridae Infections/virology
- Orthomyxoviridae Infections/veterinary
- Orthomyxoviridae Infections/epidemiology
- Swine Diseases/virology
- Swine Diseases/epidemiology
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/classification
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/classification
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Evolution, Molecular
- Genetic Variation
- Phylogeny
- One Health
- Humans
- Influenza A virus/genetics
- Influenza A virus/classification
- Influenza A virus/isolation & purification
- Whole Genome Sequencing
- Genome, Viral
- Epidemiological Monitoring
- Reassortant Viruses/genetics
- Reassortant Viruses/classification
- Reassortant Viruses/isolation & purification
- Influenza A Virus, H1N2 Subtype/genetics
- Influenza A Virus, H1N2 Subtype/isolation & purification
- Influenza A Virus, H1N2 Subtype/classification
- Influenza, Human/virology
- Influenza, Human/epidemiology
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Affiliation(s)
- Karl Ciuoderis
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jaime Usuga
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | | | | | - Leidi Carvajal
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Andrés Cardona
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Isabel Moreno
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
| | - Andrés Diaz
- Pig Improvement Company, Hendersonville, NC, USA
| | - Mario Peña
- PorkColombia Association, Bogotá, Colombia
| | - Juan P. Hernández-Ortiz
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
- Faculty of Life Sciences, Universidad Nacional de Colombia, Medellín, Colombia
| | - Jorge E. Osorio
- GHI One Health Colombia, Universidad Nacional de Colombia, Medellín, Colombia
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Global Health Institute, University of Wisconsin, Madison, WI, USA
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Adlhoch C, Alm E, Enkirch T, Lamb F, Melidou A, Willgert K, Marangon S, Monne I, Stegeman JA, Delacourt R, Baldinelli F, Broglia A. Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. EFSA J 2024; 22:e8735. [PMID: 38576537 PMCID: PMC10988447 DOI: 10.2903/j.efsa.2024.8735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
Avian influenza viruses (AIV) remain prevalent among wild bird populations in the European Union and European Economic Area (EU/EEA), leading to significant illness in and death of birds. Transmission between bird and mammal species has been observed, particularly in fur animal farms, where outbreaks have been reported. While transmission from infected birds to humans is rare, there have been instances of exposure to these viruses since 2020 without any symptomatic infections reported in the EU/EEA. However, these viruses continue to evolve globally, and with the migration of wild birds, new strains carrying potential mutations for mammalian adaptation could be selected. If avian A(H5N1) influenza viruses acquire the ability to spread efficiently among humans, large-scale transmission could occur due to the lack of immune defences against H5 viruses in humans. The emergence of AIV capable of infecting mammals, including humans, can be facilitated by various drivers. Some intrinsic drivers are related to virus characteristics or host susceptibility. Other drivers are extrinsic and may increase exposure of mammals and humans to AIV thereby stimulating mutation and adaptation to mammals. Extrinsic drivers include the ecology of host species, such as including wildlife, human activities like farming practices and the use of natural resources, climatic and environmental factors. One Health measures to mitigate the risk of AIV adapting to mammals and humans focus on limiting exposure and preventing spread. Key options for actions include enhancing surveillance targeting humans and animals, ensuring access to rapid diagnostics, promoting collaboration between animal and human sectors, and implementing preventive measures such as vaccination. Effective communication to different involved target audiences should be emphasised, as well as strengthening veterinary infrastructure, enforcing biosecurity measures at farms, and reducing wildlife contact with domestic animals. Careful planning of poultry and fur animal farming, especially in areas with high waterfowl density, is highlighted for effective risk reduction.
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Milićević V, Glišić D, Sapundžić ZZ, Milovanović B, Maletić J, Jezdimirović N, Kureljušić B. Seroprevalence of Viral Enzootic Diseases in Swine Backyard Farms in Serbia. Animals (Basel) 2023; 13:3409. [PMID: 37958164 PMCID: PMC10649762 DOI: 10.3390/ani13213409] [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: 08/23/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Contrary to pig farming in developed Western countries, in a large part of the world, pigs are still traditionally kept in small backyard farms, usually for family needs. Their main characteristics are low biosecurity, swill feeding, natural breeding and uncontrolled trade. Given the high number of backyard farms in Serbia and the risk they are thought to pose to intensive pig farming, the main aim of this study was to evaluate the prevalence of major viral diseases of swine among traditionally kept pigs in small holdings with low biosecurity. For this investigation, 222 serum samples from 69 backyard holdings were randomly selected and tested for antibodies to Porcine Reproductive and Respiratory Syndrome virus (PRRSV), Aujeszky's disease virus (ADV), Porcine Parvovirus (PPV) and Swine influenza Virus (SIV) by enzyme-linked immunosorbent assay (ELISA). The herd-level seroprevalence of PRRS, Aujeszky's disease and PPV was 2.9%, 27.5% and 37.7%, respectively. Swine influenza seroconversion was not confirmed in any of the tested holdings. Despite widely distributed PPV and AD in backyard farms in Serbia, almost 50% of them are still negative for all the tested diseases. The backyard farms must be monitored, and owners must be educated as their role in eradication programs and obtaining country-free status may be crucial.
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Affiliation(s)
- Vesna Milićević
- Institute of Veterinary Medicine of Serbia, Janisa Janulisa 14, 11000 Belgrade, Serbia; (D.G.); (Z.Z.S.); (B.M.); (J.M.); (N.J.); (B.K.)
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Donachie D, Ewann F, Poudevigne F. Animal Agrocrime: An Overlooked Biological Threat. Health Secur 2023; 21:415-420. [PMID: 37527212 PMCID: PMC10541920 DOI: 10.1089/hs.2022.0144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Affiliation(s)
- Daniel Donachie
- Daniel Donachie, BVMS, MRCVS, is Programme Manager – Emergency Management, Preparedness and Resilience Department, World Organisation for Animal Health, Paris, France
| | - Fanny Ewann
- Fanny Ewann, PhD, is a Specialized Officer, Bioterrorism Prevention Unit, CBRNE & Vulnerable Target Sub-Directorate, International Criminal Police Organization (INTERPOL), Lyon, France
| | - Frédéric Poudevigne
- Frédéric Poudevigne, DMV, MSc, is an Emergency Management Specialist, Emergency Management Center, Food and Agriculture Organization of the United Nations, Rome, Italy
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5
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Zeller MA, Ma J, Wong FY, Tum S, Hidano A, Holt H, Chhay T, Sorn S, Koeut D, Seng B, Chao S, Ng GGK, Yan Z, Chou M, Rudge JW, Smith GJD, Su YCF. The genomic landscape of swine influenza A viruses in Southeast Asia. Proc Natl Acad Sci U S A 2023; 120:e2301926120. [PMID: 37552753 PMCID: PMC10438389 DOI: 10.1073/pnas.2301926120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/07/2023] [Indexed: 08/10/2023] Open
Abstract
Swine are a primary source for the emergence of pandemic influenza A viruses. The intensification of swine production, along with global trade, has amplified the transmission and zoonotic risk of swine influenza A virus (swIAV). Effective surveillance is essential to uncover emerging virus strains; however gaps remain in our understanding of the swIAV genomic landscape in Southeast Asia. More than 4,000 nasal swabs were collected from pigs in Cambodia, yielding 72 IAV-positive samples by RT-qPCR and 45 genomic sequences. We unmasked the cocirculation of multiple lineages of genetically diverse swIAV of pandemic concern. Genomic analyses revealed a novel European avian-like H1N2 swIAV reassortant variant with North American triple reassortant internal genes, that emerged approximately seven years before its first detection in pigs in 2021. Using phylogeographic reconstruction, we identified south central China as the dominant source of swine viruses disseminated to other regions in China and Southeast Asia. We also identified nine distinct swIAV lineages in Cambodia, which diverged from their closest ancestors between two and 15 B.P., indicating significant undetected diversity in the region, including reverse zoonoses of human H1N1/2009 pandemic and H3N2 viruses. A similar period of cryptic circulation of swIAVs occurred in the decades before the H1N1/2009 pandemic. The hidden diversity of swIAV observed here further emphasizes the complex underlying evolutionary processes present in this region, reinforcing the importance of genomic surveillance at the human-swine interface for early warning of disease emergence to avoid future pandemics.
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Affiliation(s)
- Michael A. Zeller
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Jordan Ma
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Foong Ying Wong
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Sothyra Tum
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Arata Hidano
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Hannah Holt
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Ty Chhay
- Livestock Development for Community Livelihood, Phnom Penh120108, Cambodia
| | - San Sorn
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Dina Koeut
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Bunnary Seng
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Sovanncheypo Chao
- National Animal Health and Production Research Institute, General Directorate of Animal Health and Production, Phnom Penh120608, Cambodia
| | - Giselle G. K. Ng
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Zhuang Yan
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
| | - Monidarin Chou
- University of Health Sciences, Phnom Penh120210, Cambodia
| | - James W. Rudge
- Department of Global Health and Development, London School of Hygiene & Tropical Medicine, LondonWC1E 7HT, United Kingdom
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore169857, Singapore
- SingHealth Duke-NUS Global Health Institute,SingHealth Duke-NUS Academic Medical Centre, Singapore169857, Singapore
- Duke Global Health Institute, Duke University, Durham, NC27708
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore169857, Singapore
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6
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Makovska I, Dhaka P, Chantziaras I, Pessoa J, Dewulf J. The Role of Wildlife and Pests in the Transmission of Pathogenic Agents to Domestic Pigs: A Systematic Review. Animals (Basel) 2023; 13:1830. [PMID: 37889698 PMCID: PMC10251848 DOI: 10.3390/ani13111830] [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: 04/19/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 10/29/2023] Open
Abstract
Wild animals and pests are important reservoirs and vectors of pathogenic agents that can affect domestic pigs. Rapid globalization, anthropogenic factors, and increasing trends toward outdoor pig production facilitate the contact between domestic pigs and wildlife. However, knowledge on the transmission pathways between domestic pigs and the aforementioned target groups is limited. The present systematic review aims to collect and analyze information on the roles of different wild animal species and pests in the spread of pathogens to domesticated pigs. Overall, 1250 peer-reviewed manuscripts published in English between 2010 and 2022 were screened through the PRISMA framework using PubMed, Scopus, and Web of Science databases. A total of 84 studies reporting possible transmission routes of different pathogenic agents were included. A majority of the studies (80%) focused on the role of wild boars in the transmission of pathogenic agents to pig farms. Studies involving the role of rodents (7%), and deer (6%) were the next most frequent, whereas the role of insects (5%), wild carnivores (5%), wild birds (4%), cats (2%), and badgers (1%) were less available. Only 3.5% of studies presented evidence-based transmission routes from wildlife to domestic pigs. Approximately 65.5% of the included studies described possible risks/risk factors for pathogens' transmission based on quantitative data, whereas 31% of the articles only presented a hypothesis or qualitative analysis of possible transmission routes or risk factors and/or contact rates. Risk factors identified include outdoor farms or extensive systems and farms with a low level of biosecurity as well as wildlife behavior; environmental conditions; human activities and movements; fomites, feed (swill feeding), water, carcasses, and bedding materials. We recommend the strengthening of farm biosecurity frameworks with special attention to wildlife-associated parameters, especially in extensive rearing systems and high-risk zones as it was repeatedly found to be an important measure to prevent pathogen transmission to domestic pigs. In addition, there is a need to focus on effective risk-based wildlife surveillance mechanisms and to raise awareness among farmers about existing wildlife-associated risk factors for disease transmission.
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Affiliation(s)
- Iryna Makovska
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (P.D.); (I.C.); (J.P.); (J.D.)
| | - Pankaj Dhaka
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (P.D.); (I.C.); (J.P.); (J.D.)
- Centre for One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India
| | - Ilias Chantziaras
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (P.D.); (I.C.); (J.P.); (J.D.)
| | - Joana Pessoa
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (P.D.); (I.C.); (J.P.); (J.D.)
| | - Jeroen Dewulf
- Veterinary Epidemiology Unit, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; (P.D.); (I.C.); (J.P.); (J.D.)
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7
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Chauhan RP, Fogel R, Limson J. Overview of Diagnostic Methods, Disease Prevalence and Transmission of Mpox (Formerly Monkeypox) in Humans and Animal Reservoirs. Microorganisms 2023; 11:1186. [PMID: 37317160 DOI: 10.3390/microorganisms11051186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
Mpox-formerly monkeypox-is a re-emerging zoonotic virus disease, with large numbers of human cases reported during multi-country outbreaks in 2022. The close similarities in clinical symptoms that Mpox shares with many orthopoxvirus (OPXV) diseases make its diagnosis challenging, requiring laboratory testing for confirmation. This review focuses on the diagnostic methods used for Mpox detection in naturally infected humans and animal reservoirs, disease prevalence and transmission, clinical symptoms and signs, and currently known host ranges. Using specific search terms, up to 2 September 2022, we identified 104 relevant original research articles and case reports from NCBI-PubMed and Google Scholar databases for inclusion in the study. Our analyses observed that molecular identification techniques are overwhelmingly being used in current diagnoses, especially real-time PCR (3982/7059 cases; n = 41 studies) and conventional PCR (430/1830 cases; n = 30 studies) approaches being most-frequently-used to diagnose Mpox cases in humans. Additionally, detection of Mpox genomes, using qPCR and/or conventional PCR coupled to genome sequencing methods, offered both reliable detection and epidemiological analyses of evolving Mpox strains; identified the emergence and transmission of a novel clade 'hMPXV-1A' lineage B.1 during 2022 outbreaks globally. While a few current serologic assays, such as ELISA, reported on the detection of OPXV- and Mpox-specific IgG (891/2801 cases; n = 17 studies) and IgM antibodies (241/2688 cases; n = 11 studies), hemagglutination inhibition (HI) detected Mpox antibodies in human samples (88/430 cases; n = 6 studies), most other serologic and immunographic assays used were OPXV-specific. Interestingly, virus isolation (228/1259 cases; n = 24 studies), electron microscopy (216/1226 cases; n = 18 studies), and immunohistochemistry (28/40; n = 7 studies) remain useful methods of Mpox detection in humans in select instances using clinical and tissue samples. In animals, OPXV- and Mpox-DNA and antibodies were detected in various species of nonhuman primates, rodents, shrews, opossums, a dog, and a pig. With evolving transmission dynamics of Mpox, information on reliable and rapid detection methods and clinical symptoms of disease is critical for disease management.
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Affiliation(s)
- Ravendra P Chauhan
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
| | - Ronen Fogel
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
| | - Janice Limson
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa
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8
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Lee S, Ntakiyisumba E, Seol JW, Won G. Risk factors influencing swine influenza A virus infection in South Korea: A systematic review and meta-analysis of prevalence and seroprevalence. Front Vet Sci 2022; 9:1003351. [PMID: 36246324 PMCID: PMC9559919 DOI: 10.3389/fvets.2022.1003351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The past and current burden of swine influenza A viruses (swIAV) must be estimated since pigs act as mixing vessels and are considered a potential source of newly emerging IAV variants. The objective of this systematic review and meta-analysis was to integrate data on the prevalence and seroprevalence of swIAV in South Korean domestic pigs and evaluate important risk factors that influence these outcomes. Eight databases were searched for studies that evaluated the prevalence and seroprevalence of swIAV in South Korean pigs using a specified search string; twenty-seven eligible studies were identified after application of a set of pre-determined inclusion criteria by three authors. The reported prevalence and seroprevalence were pooled separately in proportions between 0 and 1, using a random-effect meta-analysis. To identify and quantify potential sources of heterogeneity, subgroup, and meta-regression analyses were conducted using covariates (publication type, swIAV subtype, growth stage of pigs, sampling region, publication year, sampling season, facility, detection method, sample type, and sample size). The overall prevalence and seroprevalence in domestic pigs were 0.05 [95% confidence intervals (CIs): 0.05-0.12] and 0.35 (95% CIs: 0.14-0.63), respectively. To identify the impact of covariates on effect size, a suitable meta-regression model was determined using predictor importance estimates with corrected Akaike information criterion values. Consequently, the best-fit model included two covariates, publication year and sample size, which were significantly associated with high heterogeneity in the subgroup analysis. Furthermore, data visualization depicted a significant non-linear association between swIAV prevalence and seroprevalence and specific growth stages of pigs. These findings suggest that the periodic monitoring of pigs at different growth stages in large farms may help to establish the status of swIAV-spread across species in the region, and thereby minimize pandemic risk.
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Affiliation(s)
| | | | | | - Gayeon Won
- College of Veterinary Medicine, Jeonbuk National University, Iksan, South Korea
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9
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Characterization of a Near Full-Length Hepatitis E Virus Genome of Subtype 3c Generated from Naturally Infected South African Backyard Pigs. Pathogens 2022; 11:pathogens11091030. [PMID: 36145462 PMCID: PMC9506134 DOI: 10.3390/pathogens11091030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Eight genotypes of the hepatitis E virus (Orthohepevirus A; HEV) designated HEV-1 to HEV-8 have been reported from various mammalian hosts. Notably, domestic pigs and wild boars are the natural reservoirs of HEV-3 and HEV-4 genotypes with zoonotic propensity. Since HEV infection in domestic pigs is usually subclinical, it may remain undetected, facilitating zoonotic spillover of HEV to the exposed human populations. A previous study from our group in 2021, using deep sequencing of a pooled saliva sample, generated various swine enteric virus genomes, including a near full-length swine HEV genome (7040 nt; 97.7% genome coverage) from five-month-old grower pigs at a backyard pig farm in the uMgungundlovu District, KwaZulu-Natal, South Africa. In the present study, we describe the further characterization, including genotyping and subtyping of the swine HEV isolate using phylogenetics and ‘HEVnet Typing Tool’. Our analyses confirmed that the South African swine HEV genome characterized in this study belonged to HEV genotype 3 subtype 3c (HEV-3c). While HEV-3c infections in domestic pigs have been previously reported from Brazil, Germany, Italy, and the Netherlands, they only generated partial genome sequences of open reading frame 1 (ORF1) and/or ORF2. To our knowledge, this is the first near full-length swine HEV-3c genome generated from naturally infected domestic pigs (Sus scrofa domesticus) in South Africa. However, due to the gap in the information on the HEV-3c genome sequences in various geographical locations worldwide, including South Africa, the epidemiology of the South African swine HEV genome characterized in this study remains inconclusive. Molecular and genomic surveillance of HEV in domestic pig populations in South Africa would be useful to determine their prevalence, circulating subtypes, and zoonosis risk.
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Gaudino M, Chiapponi C, Moreno A, Zohari S, O’Donovan T, Quinless E, Sausy A, Oliva J, Salem E, Fusade-Boyer M, Meyer G, Hübschen JM, Saegerman C, Ducatez MF, Snoeck CJ. Evolutionary and temporal dynamics of emerging influenza D virus in Europe (2009-22). Virus Evol 2022; 8:veac081. [PMID: 36533151 PMCID: PMC9752663 DOI: 10.1093/ve/veac081] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/25/2022] [Accepted: 08/31/2022] [Indexed: 07/30/2023] Open
Abstract
Influenza D virus (IDV) is an emerging influenza virus that was isolated for the first time in 2011 in the USA from swine with respiratory illness. Since then, IDV has been detected worldwide in different animal species, and it was also reported in humans. Molecular epidemiological studies revealed the circulation of two major clades, named D/OK and D/660. Additional divergent clades have been described but have been limited to specific geographic areas (i.e. Japan and California). In Europe, IDV was detected for the first time in France in 2012 and subsequently also in Italy, Luxembourg, Ireland, the UK, Switzerland, and Denmark. To understand the time of introduction and the evolutionary dynamics of IDV on the continent, molecular screening of bovine and swine clinical samples was carried out in different European countries, and phylogenetic analyses were performed on all available and newly generated sequences. Until recently, D/OK was the only clade detected in this area. Starting from 2019, an increase in D/660 clade detections was observed, accompanied by an increase in the overall viral genetic diversity and genetic reassortments. The time to the most recent common ancestor (tMRCA) of all existing IDV sequences was estimated as 1995-16 years before its discovery, indicating that the virus could have started its global spread in this time frame. Despite the D/OK and D/660 clades having a similar mean tMRCA (2007), the mean tMRCA for European D/OK sequences was estimated as January 2013 compared to July 2014 for European D/660 sequences. This indicated that the two clades were likely introduced on the European continent at different time points, as confirmed by virological screening findings. The mean nucleotide substitution rate of the hemagglutinin-esterase-fusion (HEF) glycoprotein segment was estimated as 1.403 × 10-3 substitutions/site/year, which is significantly higher than the one of the HEF of human influenza C virus (P < 0.0001). IDV genetic drift, the introduction of new clades on the continent, and multiple reassortment patterns shape the increasing viral diversity observed in the last years. Its elevated substitution rate, diffusion in various animal species, and the growing evidence pointing towards zoonotic potential justify continuous surveillance of this emerging influenza virus.
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Affiliation(s)
- Maria Gaudino
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Chiara Chiapponi
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna ‘Bruno Ubertini’, Brescia 25124, Italy
| | - Ana Moreno
- Department of Virology, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna ‘Bruno Ubertini’, Brescia 25124, Italy
| | - Siamak Zohari
- Department of microbiology, National Veterinary Institute, Uppsala SE-751 89, Sweden
| | - Tom O’Donovan
- Central Veterinary Research Laboratory, Celbridge, Co. Kildare W23 X3PH, Ireland
| | - Emma Quinless
- Central Veterinary Research Laboratory, Celbridge, Co. Kildare W23 X3PH, Ireland
| | - Aurélie Sausy
- Clinical and Applied Virology Group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
| | - Justine Oliva
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Elias Salem
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | | | - Gilles Meyer
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse 31076, France
| | - Judith M Hübschen
- Clinical and Applied Virology Group, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette L-4354, Luxembourg
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11
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Zhang X, Chen S, Li X, Zhang L, Ren L. Flavonoids as Potential Antiviral Agents for Porcine Viruses. Pharmaceutics 2022; 14:pharmaceutics14091793. [PMID: 36145539 PMCID: PMC9501777 DOI: 10.3390/pharmaceutics14091793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Flavonoids are types of natural substances with phenolic structures isolated from a variety of plants. Flavonoids have antioxidant, anti-inflammatory, anticancer, and antiviral activities. Although most of the research or applications of flavonoids are focused on human diseases, flavonoids also show potential applicability against porcine virus infection. This review focuses on the recent progress in antiviral mechanisms of potential flavonoids against the most common porcine viruses. The mechanism discussed in this paper may provide a theoretical basis for drug screening and application of natural flavonoid compounds and flavonoid-containing herbs to control porcine virus infection and guide the research and development of pig feed additives.
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12
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Metagenomic Analysis of RNA Fraction Reveals the Diversity of Swine Oral Virome on South African Backyard Swine Farms in the uMgungundlovu District of KwaZulu-Natal Province. Pathogens 2022; 11:pathogens11080927. [PMID: 36015047 PMCID: PMC9416320 DOI: 10.3390/pathogens11080927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/31/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Numerous RNA viruses have been reported in backyard swine populations in various countries. In the absence of active disease surveillance, a persistent knowledge gap exists on the diversity of RNA viruses in South African backyard swine populations. This is the first study investigating the diversity of oral RNA virome of the backyard swine in South Africa. We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Total viral RNA was extracted and used for the library preparation for deep sequencing using the Illumina HiSeq X instrument. The FASTQ files containing paired-end reads were analyzed using Genome Detective v 1.135. The assembled nucleotide sequences were analyzed using the PhyML phylogenetic tree. The genome sequence analysis identified a high diversity of swine enteric viruses in the saliva samples obtained from BSF2 and BSF3, while only a few viruses were identified in the saliva obtained from BSF1. The swine enteric viruses belonged to various animal virus families; however, two fungal viruses, four plant viruses, and five unclassified RNA viruses were also identified. Specifically, viruses of the family Astroviridae, according to the number of reads, were the most prevalent. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained. The occurrence of various swine enteric viruses in swine saliva suggests a high risk of diarrhoeic diseases in the backyard swine. Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations. We recommend the implementation of biosecurity to ensure sustainable backyard swine farming while safeguarding public health.
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Chauhan RP, Gordon ML. An overview of influenza A virus genes, protein functions, and replication cycle highlighting important updates. Virus Genes 2022; 58:255-269. [PMID: 35471490 DOI: 10.1007/s11262-022-01904-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
Abstract
The recent research findings on influenza A virus (IAV) genome biology prompted us to present a comprehensive overview of IAV genes, protein functions, and replication cycle. The eight gene segments of the IAV genome encode 17 proteins, each having unique functions contributing to virus fitness in the host. The polymerase genes are essential determinants of IAV pathogenicity and virulence; however, other viral components also play crucial roles in the IAV replication, transmission, and adaptation. Specific adaptive mutations within polymerase (PB2, PB1, and PA) and glycoprotein-hemagglutinin (HA) and neuraminidase (NA) genes, may facilitate interspecies transmission and adaptation of IAV. The HA-NA interplay is essential for establishing the IAV infection; the low pH triggers the inactivation of HA-receptor binding, leading to significantly lower NA activities, indicating that the enzymatic function of NA is dependent on HA binding. While the HA and NA glycoproteins are required to initiate infection, M1, M2, NS1, and NEP proteins are essential for cytoplasmic trafficking of viral ribonucleoproteins (vRNPs) and the assembly of the IAV virions. The mechanisms that enable IAV to exploit the host cell resources to advance the infection are discussed. A comprehensive understanding of IAV genome biology is essential for developing antivirals to combat the IAV disease burden.
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Affiliation(s)
- Ravendra P Chauhan
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa
| | - Michelle L Gordon
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban, 4001, South Africa.
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