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Weber N, Nagy M, Markotter W, Schaer J, Puechmaille SJ, Sutton J, Dávalos LM, Dusabe MC, Ejotre I, Fenton MB, Knörnschild M, López-Baucells A, Medellin RA, Metz M, Mubareka S, Nsengimana O, O'Mara MT, Racey PA, Tuttle M, Twizeyimana I, Vicente-Santos A, Tschapka M, Voigt CC, Wikelski M, Dechmann DK, Reeder DM. Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats. Biol Lett 2023; 19:20230358. [PMID: 37964576 PMCID: PMC10646460 DOI: 10.1098/rsbl.2023.0358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
Africa experiences frequent emerging disease outbreaks among humans, with bats often proposed as zoonotic pathogen hosts. We comprehensively reviewed virus-bat findings from papers published between 1978 and 2020 to evaluate the evidence that African bats are reservoir and/or bridging hosts for viruses that cause human disease. We present data from 162 papers (of 1322) with original findings on (1) numbers and species of bats sampled across bat families and the continent, (2) how bats were selected for study inclusion, (3) if bats were terminally sampled, (4) what types of ecological data, if any, were recorded and (5) which viruses were detected and with what methodology. We propose a scheme for evaluating presumed virus-host relationships by evidence type and quality, using the contrasting available evidence for Orthoebolavirus versus Orthomarburgvirus as an example. We review the wording in abstracts and discussions of all 162 papers, identifying key framing terms, how these refer to findings, and how they might contribute to people's beliefs about bats. We discuss the impact of scientific research communication on public perception and emphasize the need for strategies that minimize human-bat conflict and support bat conservation. Finally, we make recommendations for best practices that will improve virological study metadata.
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Affiliation(s)
- Natalie Weber
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
| | - Martina Nagy
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Wanda Markotter
- Centre for Viral Zoonoses, Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Juliane Schaer
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Sébastien J. Puechmaille
- ISEM, University of Montpellier, Montpellier, France
- Institut Universitaire de France, Paris, France
- Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | | | - Liliana M. Dávalos
- Department of Ecology and Evolution and Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, USA
| | | | - Imran Ejotre
- Institute of Biology, Humboldt University, Berlin, Germany
- Muni University, Arua, Uganda
| | - M. Brock Fenton
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Mirjam Knörnschild
- Museum für Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
- Evolutionary Ethology, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Rodrigo A. Medellin
- Institute of Ecology, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Samira Mubareka
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | | | - M. Teague O'Mara
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Bat Conservation International Austin, TX, USA
- Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, USA
| | - Paul A. Racey
- Centre for Ecology and Conservation, University of Exeter, Exeter, UK
| | - Merlin Tuttle
- Merlin Tuttle's Bat Conservation, Austin, TX USA
- Department of Integrative Biology, University of Texas, Austin, USA
| | | | - Amanda Vicente-Santos
- Graduate Program in Population Biology, Ecology and Emory University, Atlanta, GA, USA
- Department of Biology, University of Oklahoma, Norman, OK, USA
| | - Marco Tschapka
- University of Ulm, Institute of Evolutionary Ecology and Conservation Genomics, Ulm, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | | | - Martin Wikelski
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dina K.N. Dechmann
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Biology, University of Konstanz, Konstanz, Germany
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Mashaly MES, Alkasaby NM, Bakr A, Zaki MES, Montasser K. Viral pathogens of acute gastroenteritis in Egyptian children: role of the parechovirus. BMC Infect Dis 2022; 22:584. [PMID: 35768762 PMCID: PMC9245302 DOI: 10.1186/s12879-022-07562-5] [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] [Received: 02/10/2022] [Accepted: 06/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AND AIM Human parechovirus (HPeV) has emerged as a pathogen associated with acute gastroenteritis (AGE). AIM To detect the presence of HPeV in the stool samples from Egyptian children with AGE seeking care and the possibility of its co-infection with other enteric viruses. METHODOLOGY One hundred stool samples were collected from children attending Mansoura University Children's Hospital with AGE. HPeV and astrovirus were detected by reverse transcriptase-polymerase chain reaction (RT-PCR). At the same time, detection of rotavirus antigen and norovirus was achieved by enzyme-linked immunosorbent assay and rapid immunochromatographic method, respectively. RESULTS The most frequently detected virus was rotavirus (39%), followed by norovirus (27%), HPeV (19%), and astrovirus (12%). Interestingly, the single infection with HPeV was 5%. Among the 19 HPeV positive samples, the co-infection of HPeV with other enteric viruses was detected in 9(43.9%) for rotavirus, 7(36.8%) for norovirus, 2(10.5%) for astrovirus, in 3(15.8%) for rotavirus and norovirus and 1(5.3%) for norovirus and astrovirus. Regarding the clinical presentation, there was no significant difference between children infected with HPeV alone and those infected with viruses other than HPeV alone; fever (p = 0.3), vomiting (p = 0.12), abdominal pain (p = 0.12), and grades of severity (P = 0.82). HPeV alone infected children were of mild severity (60%), and their main presenting symptom was fever (60%). CONCLUSIONS Detection of HPeV as a single viral pathogen in the stool of some children with AGE showed that this virus could be a causative agent of AGE in Egyptian children. Therefore, HPeV could be included as one of the viruses screened for AGE diagnosis in children in Egypt.
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Affiliation(s)
| | - Nashwa M Alkasaby
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Asmaa Bakr
- Pediatric Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Maysaa El Sayed Zaki
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Karim Montasser
- Clinical Pathology Department, Helwn Faculty of Medicine, Helwn University, Cairo, Egypt
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Durairaj K, Trinh TTT, Yun SY, Yeo SJ, Sung HW, Park H. Molecular Characterization and Pathogenesis of H6N6 Low Pathogenic Avian Influenza Viruses Isolated from Mallard Ducks (Anas platyrhynchos) in South Korea. Viruses 2022; 14:v14051001. [PMID: 35632743 PMCID: PMC9143286 DOI: 10.3390/v14051001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
The subtype H6N6 has been identified worldwide following the increasing frequency of avian influenza viruses (AIVs). These AIVs also have the ability to bind to human-like receptors, thereby increasing the risk of animal-human transmission. In September 2019, an H6N6 avian influenza virus—KNU2019-48 (A/Mallard (Anas platyrhynchos)/South Korea/KNU 2019-48/2019(H6N6))—was isolated from Anas platyrhynchos in South Korea. Phylogenetic analysis results revealed that the hemagglutinin (HA) gene of this strain belongs to the Korean lineage, whereas the neuraminidase (NA) and polymerase basic protein 1 (PB1) genes belong to the Chinese lineage. Outstanding internal proteins such as PB2, polymerase acidic protein, nucleoprotein, matrix protein, and non-structural protein belong to the Vietnamese lineage. Additionally, a monobasic amino acid (PRIETR↓GLF) at the HA cleavage site; non-deletion of the stalk region (residue 59–69) in the NA gene; and E627 in the PB2 gene indicate that the KNU2019-48 isolate is a typical low-pathogenic avian influenza (LPAI) virus. The nucleotide sequence similarity analysis of HA revealed that the highest homology (97.18%) of this isolate is to that of A/duck/Jiangxi/01.14 NCJD125-P/2015(H6N6), and the amino acid sequence of NA (97.38%) is closely related to that of A/duck/Fujian/10.11_FZHX1045-C/2016 (H6N6). An in vitro analysis of the KNU2019-48 virus shows a virus titer of not more than 2.8 Log10 TCID 50/mL until 72 h post-infection, whereas in the lungs, the virus is detected at 3 dpi (days post-infection). The isolated KNU2019-48 (H6N6) strain is the first reported AIV in Korea, and the H6 subtype virus has co-circulated in China, Vietnam, and Korea for half a decade. Overall, our study demonstrates that Korean H6N6 strain PB1-S375N, PA-A404S, and S409N mutations are infectious in humans and might contribute to the enhanced pathogenicity of this strain. Therefore, we emphasize the importance of continuous and intensive surveillance of the H6N6 virus not only in Korea but also worldwide.
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Affiliation(s)
- Kaliannan Durairaj
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (K.D.); (S.-Y.Y.)
| | - Thuy-Tien Thi Trinh
- Institute of Endemic Diseases, Medical Research Center, Department of Tropical Medicine and Parasitology, Seoul National University, Seoul 03080, Korea;
| | - Su-Yeon Yun
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (K.D.); (S.-Y.Y.)
| | - Seon-Ju Yeo
- Department of Tropical Medicine and Parasitology, Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul 03080, Korea
- Correspondence: (S.-J.Y.); (H.-W.S.); (H.P.)
| | - Haan-Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (S.-J.Y.); (H.-W.S.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 570-749, Korea; (K.D.); (S.-Y.Y.)
- Correspondence: (S.-J.Y.); (H.-W.S.); (H.P.)
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Virome of Bat Guano from Nine Northern California Roosts. J Virol 2021; 95:JVI.01713-20. [PMID: 33115864 DOI: 10.1128/jvi.01713-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/17/2020] [Indexed: 12/12/2022] Open
Abstract
Bats are hosts to a large variety of viruses, including many capable of cross-species transmissions to other mammals, including humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and from a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Nearly complete or complete genomes of a novel parvovirus, astrovirus, nodavirus, circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses, and densoviruses, and more partial genomes of a novel alphacoronavirus and a bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found, likely reflecting their wide distribution among different bats. Unexpectedly, a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR; these possibly originated from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent, indicating that numerous viruses still remain to be characterized, even from such a heavily investigated order as Chiroptera.IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using an unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species, likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected, whose presence are likely the result of contamination from defecation and urination atop guano and which reflect the close interaction of these mammals in the wild.
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Genetic characteristics and pathogenicity of novel reassortant H6 viruses isolated from wild birds in China. Vet Microbiol 2021; 254:108978. [PMID: 33454600 DOI: 10.1016/j.vetmic.2021.108978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 01/03/2021] [Indexed: 02/08/2023]
Abstract
During our routine surveillance, we isolated seven H6 avian influenza virus (AIV) strains, including three H6N1 strains, three H6N2 strains, and one H6N8 strain, from 3667 fresh fecal samples that were collected from wild bird habitats in China from March 2017 and May 2019. Phylogenetic analysis revealed that these viruses formed five different genotypes and have undergone complicate reassortment during their evolution by acquiring genes from AIVs of both Eurasian and North American lineages that have been previously detected in migrating waterfowl and poultry. Viral pathogenesis in mice showed that these H6 viruses replicated efficiently in both the nasal turbinates and lungs of mice without pre-adaptation, but none of them were lethal for mice. We studied the genetic characteristic and biological property of novel reassortant H6 viruses isolated from wild birds in China. It also highlights the need for continued surveillance of H6 AIVs circulating in nature.
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Nadan S, Taylor MB, Page NA. Circulation of classic and recombinant human astroviruses detected in South Africa: 2009 to 2014. J Clin Virol 2020; 135:104719. [PMID: 33388529 DOI: 10.1016/j.jcv.2020.104719] [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: 08/19/2020] [Revised: 11/13/2020] [Accepted: 12/17/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Astroviruses (AstVs) are associated with diarrhoeal and extra-intestinal infections in human, animal and avian species. A prevalence of 7% was reported in selected regions in SA while AstVs detected from clinical stool specimens were almost identical phylogenetically to strains identified in environmental and water samples. This study investigated the molecular diversity of astroviruses circulating between 2009 and 2014 in South Africa (SA). METHODS Astroviruses detected in stool specimens collected from hospitalised children were investigated retrospectively. Astroviruses were characterised using type-specific RT-PCR, partial nucleotide sequence analyses in ORF1 and ORF2 and whole genome sequencing. Different genotypes were compared with clinical features to investigate genotype-related associations. The Vesikari severity scale (VSS) was evaluated for scoring astrovirus diarrhoeal infections. RESULTS Of 405 astroviruses detected, 49.9 % (202/405) were characterised into 32 genotypes comprising 66.3 % (134/202) putative-recombinants and 33.7 % (68/202) classic strains. No trends by year of collection, age or site were observed. Whole genome analysis in eight strains revealed that genotypes assigned by partial nucleotide sequence analyses to five astroviruses were incorrect. Bivariate analyses showed there were no significant associations between genotypes and clinical symptoms or severity of infection. A comparison of Vesikari parameters with astrovirus-positive proxy values demonstrated that Vesikari scores for duration of diarrhoea and admission temperatures would result in a milder infection rating in astrovirus-positive cases. CONCLUSIONS Diverse genotypes co-circulated with putative-recombinants predominating. Astrovirus classification was complicated by the lack of a consistent characterisation system and reliable reference database. The VSS should be used cautiously to rate astrovirus diarrhoea. While surveillance in communities and out-patient clinics must be continued, screening for human astroviruses in alternate hosts is needed to determine the reservoir species.
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Affiliation(s)
- Sandrama Nadan
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa.
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa; National Health Laboratory Services, Tshwane Academic Division, Pretoria, South Africa
| | - Nicola A Page
- Centre for Enteric Diseases, National Institute for Communicable Disease, Private Bag X4, Sandringham, 2131, South Africa; Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, 0031, South Africa
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El Sayed Zaki M, Mashaly GES, Alsayed MAL, Nomir MM. Molecular study of human astrovirus in Egyptian children with acute gastroenteritis. Germs 2020; 10:167-173. [PMID: 33134194 DOI: 10.18683/germs.2020.1202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/15/2020] [Indexed: 11/08/2022]
Abstract
Introduction Human astrovirus (HAstV) has been increasingly identified as an important cause of acute gastroenteritis in young children. Limited information is available about the prevalence and genotype distribution of classic HAstV causing acute gastroenteritis in Egyptian children. Methods Stool samples were collected from 100 infants and children attending the gastroenterology outpatient clinic in Mansoura University Children Hospital and suffering from acute gastroenteritis during the period extending from January 2018 to January 2019. Samples were tested for HAstV using reverse transcription PCR. Genotyping was performed using type-specific reverse transcription nested PCR. Results Among 100 children included in this study, the detection rate of HAstV was 11% (11 patients). There was a significant difference regarding age between cases positive and negative for HAstV (p=0.005). There was a higher prevalence of HAstV in children aged one year or younger. Significant association was detected between HAstV positive cases and rural residence (p=0.002), summer season (p=0.025) and fever (p=0.017). The HAstV genotypes detected were HAstV-8 (8/11, 72.7%), HAstV-3 (2/11, 18.2%) and HAstV-2 (1/11, 9.1%). Conclusions This study suggests that HAstV is a common pathogen causing gastroenteritis in Egyptian children especially in rural areas. The most frequent HAstV genotype in our study was HAstV-8.
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Affiliation(s)
| | - Ghada El-Saeed Mashaly
- MD, Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Mona Abdel Latif Alsayed
- MD, Lecturer of Pediatrics and Pediatric Gastroenterology and Hepatology, Pediatric Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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