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Aruwa CE, Sabiu S. Interplay of poultry-microbiome interactions - influencing factors and microbes in poultry infections and metabolic disorders. Br Poult Sci 2024:1-15. [PMID: 38920059 DOI: 10.1080/00071668.2024.2356666] [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: 01/31/2024] [Accepted: 03/06/2024] [Indexed: 06/27/2024]
Abstract
1. The poultry microbiome and its stability at every point in time, either free range or reared under different farming systems, is affected by several environmental and innate factors. The interaction of the poultry birds with their microbiome, as well as several inherent and extraneous factors contribute to the microbiome dynamics. A poor understanding of this could worsen poultry heath and result in disease/metabolic disorders.2. Many diseased states associated with poultry have been linked to dysbiosis state, where the microbiome experiences some perturbation. Dysbiosis itself is too often downplayed; however, it is considered a disease which could lead to more serious conditions in poultry. The management of interconnected factors by conventional and emerging technologies (sequencing, nanotechnology, robotics, 3D mini-guts) could prove to be indispensable in ensuring poultry health and welfare.3. Findings showed that high-throughput technological advancements enhanced scientific insights into emerging trends surrounding the poultry gut microbiome and ecosystem, the dysbiotic condition, and the dynamic roles of intrinsic and exogenous factors in determining poultry health. Yet, a combination of conventional, -omics based and other techniques further enhance characterisation of key poultry microbiome actors, their mechanisms of action, and roles in maintaining gut homoeostasis and health, in a bid to avert metabolic disorders and infections.4. In conclusion, there is an important interplay of innate, environmental, abiotic and biotic factors impacting on poultry gut microbiome homoeostasis, dysbiosis, and overall health. Associated infections and metabolic disorders can result from the interconnected nature of these factors. Emerging concepts (interkingdom or network signalling and neurotransmitter), and future technologies (mini-gut models, cobots) need to include these interactions to ensure accurate control and outcomes.
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Affiliation(s)
- C E Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
| | - S Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa
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2
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Makenov MT, Le LAT, Stukolova OA, Radyuk EV, Morozkin ES, Bui NTT, Zhurenkova OB, Dao MN, Nguyen CV, Luong MT, Nguyen DT, Fedorova MV, Valdokhina AV, Bulanenko VP, Akimkin VG, Karan LS. Detection of Filoviruses in Bats in Vietnam. Viruses 2023; 15:1785. [PMID: 37766193 PMCID: PMC10534609 DOI: 10.3390/v15091785] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
A new filovirus named Měnglà virus was found in bats in southern China in 2015. This species has been assigned to the new genus Dianlovirus and has only been detected in China. In this article, we report the detection of filoviruses in bats captured in Vietnam. We studied 248 bats of 15 species caught in the provinces of Lai Chau and Son La in northern Vietnam and in the province of Dong Thap in the southern part of the country. Filovirus RNA was found in four Rousettus leschenaultii and one Rousettus amplexicaudatus from Lai Chau Province. Phylogenetic analysis of the polymerase gene fragment showed that three positive samples belong to Dianlovirus, and two samples form a separate clade closer to Orthomarburgvirus. An enzyme-linked immunosorbent assay showed that 9% of Rousettus, 13% of Eonycteris, and 10% of Cynopterus bats had antibodies to the glycoprotein of marburgviruses.
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Affiliation(s)
- Marat T. Makenov
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Lan Anh T. Le
- Biomedicine Institute, Joint Vietnam-Russia Tropical Science and Technology Research Center, Hanoi 122000, Vietnam; (L.A.T.L.); (N.T.T.B.); (M.N.D.)
| | - Olga A. Stukolova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Ekaterina V. Radyuk
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Evgeny S. Morozkin
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Nga T. T. Bui
- Biomedicine Institute, Joint Vietnam-Russia Tropical Science and Technology Research Center, Hanoi 122000, Vietnam; (L.A.T.L.); (N.T.T.B.); (M.N.D.)
| | - Olga B. Zhurenkova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Manh N. Dao
- Biomedicine Institute, Joint Vietnam-Russia Tropical Science and Technology Research Center, Hanoi 122000, Vietnam; (L.A.T.L.); (N.T.T.B.); (M.N.D.)
| | - Chau V. Nguyen
- National Institute of Malariology, Parasitology and Entomology, Hanoi 110000, Vietnam;
| | - Mo T. Luong
- Southern Branch of Joint Vietnam-Russia Tropical Science and Technology Research Center, Ho Chi Minh City 740500, Vietnam; (M.T.L.); (D.T.N.)
| | - Dung T. Nguyen
- Southern Branch of Joint Vietnam-Russia Tropical Science and Technology Research Center, Ho Chi Minh City 740500, Vietnam; (M.T.L.); (D.T.N.)
| | - Marina V. Fedorova
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Anna V. Valdokhina
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Victoria P. Bulanenko
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Vasiliy G. Akimkin
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
| | - Lyudmila S. Karan
- Department of Molecular Diagnostics and Epidemiology, Central Research Institute of Epidemiology, 111123 Moscow, Russia; (M.T.M.); (O.A.S.); (E.V.R.); (O.B.Z.); (M.V.F.); (A.V.V.); (V.P.B.); (V.G.A.); (L.S.K.)
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3
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Matsvay A, Dyachkova M, Sai A, Burskaia V, Artyushin I, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Temminck's Stint Calicivirus: Evidence for a New Genus within Caliciviridae Family. Microorganisms 2022; 10:1540. [PMID: 36013958 PMCID: PMC9416405 DOI: 10.3390/microorganisms10081540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022] Open
Abstract
Caliciviridae is a family of viral pathogens that naturally infects vertebrates, including humans, and causes a range of highly contagious infectious diseases. Caliciviruses are not well studied because of the lack of a universal approach to their cultivation; however, the development of molecular genetics and bioinformatics methods can shed light on their genetic architecture and evolutionary relationships. Here, we present and characterize the complete genome sequence of calicivirus isolated from a sandpiper-Temminck's stint (Calidris temminckii), preliminarily named Temminck's stint calicivirus (TsCV). Its genome is a linear, non-segmented, single-stranded (+sense) RNA with genome organization typical of avian caliciviruses. Comparative studies have shown significant divergence of the nucleotide sequence of the TsCV genome, as well as the amino acid sequence of the major capsid protein from all publicly available genomic and protein sequences, with the highest genome sequence similarity to unclassified Ruddy turnstone calicivirus A (43.68%) and the lowest pairwise divergence of the major capsid protein with unclassified goose calicivirus (57.44%). Phylogenetic analysis, as well as a comparative analysis of the homologous proteins, showed evidence of another separate genus within the Caliciviridae family-previously proposed, but not yet accepted by International Committee on Taxonomy of Viruses (ICTV)-the Sanovirus genus, which combines seven previously unclassified genomic sequences of avian caliciviruses, including the newly discovered TsCV, which we propose to consider as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Marina Dyachkova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Anna Sai
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
| | - Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 143026 Moscow, Russia;
| | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - German Shipulin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, 119121 Moscow, Russia; (M.D.); (A.S.); (G.S.)
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Matsvay A, Dyachkova M, Mikhaylov I, Kiselev D, Say A, Burskaia V, Artyushin I, Khafizov K, Shipulin G. Complete Genome Sequence, Molecular Characterization and Phylogenetic Relationships of a Novel Tern Atadenovirus. Microorganisms 2021; 10:31. [PMID: 35056480 PMCID: PMC8781740 DOI: 10.3390/microorganisms10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery and study of viruses carried by migratory birds are tasks of high importance due to the host's ability to spread infectious diseases over significant distances. With this paper, we present and characterize the first complete genome sequence of atadenovirus from a tern bird (common tern, Sterna hirundo) preliminarily named tern atadenovirus 1 (TeAdV-1). TeAdV-1 genome is a linear double-stranded DNA molecule, 31,334 base pairs which contain 30 methionine-initiated open reading frames with gene structure typical for Atadenovirus genus, and the shortest known inverted terminal repeats (ITRs) within the Atadenovirus genus consisted of 25 bases. The nucleotide composition of the genome is characterized by a low G + C content (33.86%), which is the most AT-rich genome of known avian adenoviruses within Atadenovirus genus. The nucleotide sequence of the TeAdV-1 genome shows high divergence compared to known representatives of the Atadenovirus genus with the highest similarity to the duck atadenovirus 1 (53.7%). Phylogenetic analysis of the protein sequences of core genes confirms the taxonomic affiliation of the new representative to the genus Atadenovirus with the degree of divergence from the known representatives exceeding the interspecies distance within the genus. Thereby we proposed a novel TeAdV-1 to be considered as a separate species.
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Affiliation(s)
- Alina Matsvay
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Ivan Mikhaylov
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Daniil Kiselev
- Institute for Neurosciences of Montpellier, University of Montpellier, INSERM, 34091 Montpellier, France
| | - Anna Say
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
| | | | - Ilya Artyushin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, National Research University, 115184 Moscow, Russia
| | - German Shipulin
- Federal State Budgetary Institution "Centre for Strategic Planning and Management of Biomedical Health Risks" of the Federal Medical Biological Agency, 119121 Moscow, Russia
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Aruwa CE, Pillay C, Nyaga MM, Sabiu S. Poultry gut health - microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies. J Anim Sci Biotechnol 2021; 12:119. [PMID: 34857055 PMCID: PMC8638651 DOI: 10.1186/s40104-021-00640-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/01/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.
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Affiliation(s)
- Christiana Eleojo Aruwa
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Charlene Pillay
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Martin M Nyaga
- Next Generation Sequencing Unit, Division of Virology, Faculty of Heath Sciences, University of the Free State, Bloemfontein, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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6
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Makenov MT, Toure AH, Bayandin RB, Gladysheva AV, Shipovalov AV, Boumbaly S, Sacko N, Korneev MG, Yakovlev SA, Zhurenkova OB, Grigoreva YE, Fyodorova MV, Radyuk EV, Morozkin ES, Boiro MY, Matsvay A, Khafizov K, Karan LS. Ngari virus (Orthobunyavirus, Peribunyaviridae) in ixodid ticks collected from cattle in Guinea. Acta Trop 2021; 214:105790. [PMID: 33309594 DOI: 10.1016/j.actatropica.2020.105790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 11/27/2022]
Abstract
Ngari virus is a mosquito-borne virus belonging to the genus Orthobunyavirus (Peribunyaviridae family). This virus is pathogenic to humans and causes severe illness. Ngari virus is present in several African countries, including Madagascar. Here, we report the detection of Ngari virus in ixodid ticks collected from cows in Guinea. A tick survey was conducted in March-November of 2018 in six regions of Guinea. The sample comprised 710 pools, with a total of 2067 ticks belonging to five species collected from 197 cows. At the initial stage, we screened a subsample of tick pools of vector-borne viruses with a multiplex genus-specific primer panel. In the second stage of the study, we narrowed the search and screened all the samples by qPCR for the detection of Ngari virus. All positive samples were sequenced with primers flanking Ngari virus-specific fragments on the S and M segments. We found Ngari virus in 12 pools that were formed from engorged ticks collected from livestock in three villages of the Kindia and Kankan regions. Sequencing of the S and M segments confirmed that the detected viruses belong to Ngari virus, and the viruses were most similar to the strain Adrar, which was isolated in Mauritania. We detected viral RNA in ticks of the following species: Amblyomma variegatum, Rhipicephalus geigyi, and Rh. (Boophilus) spp. There is no evidence that ixodid ticks are competent vectors of the Ngari virus. Most likely, the ticks obtained the virus through blood from an infected host. The study of engorged ticks can be recommended as a simpler approach for the wide screening of the Ngari virus and subsequent testing of cattle and mosquitos in those locations where the PCR-positive ticks were collected.
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Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020; 12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Viruses are evolving at an alarming rate, spreading and inconspicuously adapting to cutting-edge therapies. Therefore, the search for rapid, informative and reliable diagnostic methods is becoming urgent as ever. Conventional clinical tests (PCR, serology, etc.) are being continually optimized, yet provide very limited data. Could high throughput sequencing (HTS) become the future gold standard in molecular diagnostics of viral infections? Compared to conventional clinical tests, HTS is universal and more precise at profiling pathogens. Nevertheless, it has not yet been widely accepted as a diagnostic tool, owing primarily to its high cost and the complexity of sample preparation and data analysis. Those obstacles must be tackled to integrate HTS into daily clinical practice. For this, three objectives are to be achieved: (1) designing and assessing universal protocols for library preparation, (2) assembling purpose-specific pipelines, and (3) building computational infrastructure to suit the needs and financial abilities of modern healthcare centers. Data harvested with HTS could not only augment diagnostics and help to choose the correct therapy, but also facilitate research in epidemiology, genetics and virology. This information, in turn, could significantly aid clinicians in battling viral infections.
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Affiliation(s)
- Daniel Kiselev
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- I.M. Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - Alina Matsvay
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
| | - Ivan Abramov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Vladimir Dedkov
- Pasteur Institute, Federal Service on Consumers’ Rights Protection and Human Well-Being Surveillance, 197101 Saint-Petersburg, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
| | - German Shipulin
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
| | - Kamil Khafizov
- FSBI “Center of Strategic Planning” of the Ministry of Health, 119435 Moscow, Russia; (D.K.); (A.M.); (I.A.); (G.S.)
- Moscow Institute of Physics and Technology, National Research University, 117303 Moscow, Russia
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8
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Canuti M, Munro HJ, Robertson GJ, Kroyer ANK, Roul S, Ojkic D, Whitney HG, Lang AS. New Insight Into Avian Papillomavirus Ecology and Evolution From Characterization of Novel Wild Bird Papillomaviruses. Front Microbiol 2019; 10:701. [PMID: 31031718 PMCID: PMC6473165 DOI: 10.3389/fmicb.2019.00701] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/20/2019] [Indexed: 11/24/2022] Open
Abstract
Viruses in the family Papillomaviridae have circular dsDNA genomes of approximately 5.7–8.6 kb that are packaged within non-enveloped, icosahedral capsids. The known papillomavirus (PV) representatives infect vertebrates, and there are currently more than 130 recognized PV species in more than 50 genera. We identified 12 novel avian papillomavirus (APV) types in wild birds that could represent five distinct species and two genera. Viruses were detected in paired oropharyngeal/cloacal swabs collected from six bird species, increasing the number of avian species known to harbor PVs by 40%. A new duck PV (DuPV-3) was found in mallard and American black duck (27.6% estimated prevalence) that was monophyletic with other known DuPVs. A single viral type was identified in Atlantic puffin (PuPV-1, 9.8% estimated prevalence), while a higher genetic diversity was found in other Charadriiformes. Specifically, three types [gull PV-1 (GuPV-1), -2, and -3] were identified in two gull species (estimated prevalence of 17% and 2.6% in American herring and great black-backed gull, respectively), and seven types [kittiwake PV-1 (KiPV-1) through -7] were found in black-legged kittiwake (81.3% estimated prevalence). Significantly higher DuPV-3 circulation was observed in spring compared to fall and in adults compared to juveniles. The studied host species’ tendencies to be in crowded environments likely affect infection rates and their migratory behaviors could explain the high viral diversity, illustrating how host behavior can influence viral ecology and distribution. For DuPV-3, GuPV-1, PuPV-1, and KiPV-2, we obtained the complete genomic sequences, which showed the same organization as other known APVs. Phylogenetic analyses showed evidence for virus–host co-divergence at the host taxonomic levels of family, order, and inter-order, but we also observed that host-specificity constraints are relaxed among highly related hosts as we found cross-species transmission within ducks and within gulls. Furthermore, the phylogeny of viruses infecting the Charadriiformes did not match the host phylogeny and gull viruses formed distinct monophyletic clades with kittiwake viruses, possibly reflecting past host-switching events. Considering the vast PV genotype diversity in other hosts and the large number of bird species, many more APVs likely remain to be discovered.
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Affiliation(s)
- Marta Canuti
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Hannah J Munro
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Gregory J Robertson
- Wildlife Research Division, Environment and Climate Change Canada, Mount Pearl, NL, Canada
| | - Ashley N K Kroyer
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sheena Roul
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, ON, Canada
| | - Hugh G Whitney
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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