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Wu C, Fu Z, Xie C, Zhao J, He F, Jiao B, Jiao B. Epidemiological Characteristics and Genotypic Features of Rotavirus and Norovirus in Jining City, 2021-2022. Viruses 2024; 16:925. [PMID: 38932216 PMCID: PMC11209223 DOI: 10.3390/v16060925] [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: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Diarrhea, often caused by viruses like rotavirus (RV) and norovirus (NV), is a global health concern. This study focuses on RV and NV in Jining City from 2021 to 2022. Between 2021 and 2022, a total of 1052 diarrhea samples were collected. Real-Time Quantitative Fluorescent Reverse Transcriptase-PCR was used to detect RV-A, NV GI, and NV GII. For RV-A-positive samples, VP7 and VP4 genes were sequenced for genotype analysis, followed by the construction of evolutionary trees. Likewise, for NV-GII-positive samples, VP1 and RdRp genes were sequenced for genotypic analysis, and evolutionary trees were subsequently constructed. Between 2021 and 2022, Jining City showed varying detection ratios: RV-A alone (excluding co-infection of RV-A and NV GII) at 7.03%, NV GI at 0.10%, NV GII alone (excluding co-infection of RV-A and NV GII) at 5.42%, and co-infection of RV-A and NV GII at 1.14%. The highest RV-A ratios were shown in children ≤1 year and 2-5 years. Jining, Jinxiang County, and Liangshan County had notably high RV-A ratios at 24.37% (excluding co-infection of RV-A and NV GII) and 18.33% (excluding co-infection of RV-A and NV GII), respectively. Jining, Qufu, and Weishan had no RV-A positives. Weishan showed the highest NV GII ratios at 35.48% (excluding co-infection of RV-A and NV GII). Genotype analysis showed that, in 2021, G9P[8] and G2P[4] were dominant at 94.44% and 5.56%, respectively. In 2022, G8P[8], G9P[8], and G1P[8] were prominent at 75.86%, 13.79%, and 10.35%, respectively. In 2021, GII.3[P12], GII.4[P16], and GII.4[P31] constituted 71.42%, 14.29%, and 14.29%, respectively. In 2022, GII.3[P12] and GII.4[P16] accounted for 55.00% and 45.00%, respectively. RV-A and NV showed varying patterns for different time frames, age groups, and regions within Jining. Genotypic shifts were also observed in prevalent RV-A and NV GII strains in Jining City from 2021 to 2022. Ongoing monitoring of RV-A and NV is recommended for effective prevention and control.
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Affiliation(s)
- Changjing Wu
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining 272000, China; (C.W.); (C.X.); (J.Z.)
| | - Zhongyan Fu
- Department of Infectious Disease Control, Shandong Center for Disease Control and Prevention, Jinan 250001, China;
| | - Cuihua Xie
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining 272000, China; (C.W.); (C.X.); (J.Z.)
| | - Jian Zhao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining 272000, China; (C.W.); (C.X.); (J.Z.)
| | - Feifei He
- Computer Information Technology, Northern Arizona University, Flagstaff, AZ 86011, USA;
| | - Boyan Jiao
- Department of Laboratory, Jining Center for Disease Control and Prevention, Jining 272000, China; (C.W.); (C.X.); (J.Z.)
| | - Baihai Jiao
- Department of Medicine, School of Medicine, University of Connecticut Health Center, Farmington, CT 06032, USA
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Soliman RM, Nishioka K, Murakoshi F, Nakaya T. Use of live attenuated recombinant Newcastle disease virus carrying avian paramyxovirus 2 HN and F protein genes to enhance immune responses against species A rotavirus VP6 protein. Vet Res 2024; 55:16. [PMID: 38317245 PMCID: PMC10845738 DOI: 10.1186/s13567-024-01271-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
Numerous infectious diseases in cattle lead to reductions in body weight, milk production, and reproductive performance. Cattle are primarily vaccinated using inactivated vaccines due to their increased safety. However, inactivated vaccines generally result in weaker immunity compared with live attenuated vaccines, which may be insufficient in certain cases. Over the last few decades, there has been extensive research on the use of the Newcastle disease virus (NDV) as a live vaccine vector for economically significant livestock diseases. A single vaccination dose of NDV can sufficiently induce immunity; therefore, a booster vaccination dose is expected to yield limited induction of further immune response. We previously developed recombinant chimeric NDV (rNDV-2F2HN), in which its hemagglutinin-neuraminidase (HN) and fusion (F) proteins were replaced with those of avian paramyxovirus 2 (APMV-2). In vitro analysis revealed that rNDV-2F2HN expressing human interferon-gamma had potential as a cancer therapeutic tool, particularly for immunized individuals. In the present study, we constructed rNDV-2F2HN expressing the bovine rotavirus antigen VP6 (rNDV-2F2HN-VP6) and evaluated its immune response in mice previously immunized with NDV. Mice primarily inoculated with recombinant wild-type NDV expressing VP6 (rNDV-WT-VP6), followed by a booster inoculation of rNDV-2F2HN-VP6, showed a significantly stronger immune response than that in mice that received rNDV-WT-VP6 as both primary and booster inoculations. Therefore, our findings suggest that robust immunity could be obtained from the effects of chimeric rNDV-2F2HN expressing the same or a different antigen of a particular pathogen as a live attenuated vaccine vector.
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Affiliation(s)
- Rofaida Mostafa Soliman
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Animal Medicine (Infectious Diseases Division), Faculty of Veterinary Medicine, Damanhour University, Damanhour, El‑Beheira, Egypt
| | - Keisuke Nishioka
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Fumi Murakoshi
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Miyagi, Japan
| | - Takaaki Nakaya
- Department of Infectious Diseases, Kyoto Prefectural University of Medicine, Kyoto, Japan.
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Williams RAJ, Sánchez-Llatas CJ, Doménech A, Madrid R, Fandiño S, Cea-Callejo P, Gomez-Lucia E, Benítez L. Emerging and Novel Viruses in Passerine Birds. Microorganisms 2023; 11:2355. [PMID: 37764199 PMCID: PMC10536639 DOI: 10.3390/microorganisms11092355] [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: 07/21/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.
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Affiliation(s)
- Richard A. J. Williams
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
| | - Ana Doménech
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Ricardo Madrid
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Sergio Fandiño
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Pablo Cea-Callejo
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
| | - Esperanza Gomez-Lucia
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
- Deparment of Animal Health, Veterinary Faculty, Complutense University of Madrid, Av. Puerta de Hierro, s/n, 28040 Madrid, Spain
| | - Laura Benítez
- Department of Genetics, Physiology, and Microbiology, School of Biology, Complutense University of Madrid (UCM), C. de José Antonio Nováis, 12, 28040 Madrid, Spain; (C.J.S.-L.); (R.M.); (P.C.-C.); (L.B.)
- “Animal Viruses” Research Group, Complutense University of Madrid, 28040 Madrid, Spain; (A.D.); (S.F.); (E.G.-L.)
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Omotade TI, Babalola TE, Anyabolu CH, Japhet MO. Rotavirus and bacterial diarrhoea among children in Ile-Ife, Nigeria: Burden, risk factors and seasonality. PLoS One 2023; 18:e0291123. [PMID: 37699036 PMCID: PMC10497142 DOI: 10.1371/journal.pone.0291123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Diarrhoea is a leading cause of death among under-five children globally, with sub-Saharan Africa alone accounting for 1/3 episodes yearly. Viruses, bacteria and parasites may cause diarrhoea. Rotavirus is the most common viral aetiology of diarrhoea in children less than five years globally. In Nigeria, there is scarce data on the prevalence/importance, burden, clinical/risk factors and seasonality of rotavirus and bacteria and this study aims to determine the role of rotavirus and bacteria on diarrhoea cases in children less than five years in Ile-Ife, Nigeria. METHODS Socio-demographic data, environmental/risk factors and diarrhoiec stool samples were collected from children less than five years presenting with acute diarrhoea. Rotavirus was identified using ELISA. Bacteria pathogens were detected using cultural technique and typed using PCR. Diarrhoeagenic E. coli (DEC) isolates were subjected to antimicrobial susceptibility testing. Pathogen positive and negative samples were compared in terms of gender, age-group, seasonal distribution, and clinical/risk factors using chi-square with two-tailed significance. SPSS version 20.0.1 for Windows was used for statistical analysis. RESULTS At least one pathogen was detected from 63 (60.6%) children having gastroenteritis while 28 (44.4%) had multiple infections. Rotavirus was the most detected pathogen. Prevalence of rotavirus mono-infection was 22%, multiple infection with bacteria was 45%. Mono-infection prevalence of DEC, Shigella spp., and Salmonella spp. were 5.8% (6/104), 5.8% (6/104), and 2.9% (3/104) and co-infection with RVA were 23.1% (24/104), 21.2% (22/104) and 10.6% (11/104) respectively. All rotaviral infections were observed in the dry season. The pathotypes of DEC detected were STEC and EAEC. Parent earnings and mid-upper arm circumference measurement have statistical correlation with diarrhoea (p = 0.034; 0.035 respectively). CONCLUSION In this study, rotavirus was more prevalent than bacteria and occurred only in the dry season. Among bacteria aetiologies, DEC was the most common detected. Differences in seasonal peaks of rotavirus and DEC could be employed in diarrhoea management in Nigeria and other tropical countries to ensure optimal limited resources usage in preventing diarrhoea transmission and reducing indiscriminate use of antibiotics.
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Affiliation(s)
| | - Toluwani Ebun Babalola
- Department of Paediatrics, Obafemi Awolowo University Teaching Hospital (OAUTHC), Ile-Ife, Osun State, Nigeria
| | - Chineme Henry Anyabolu
- Department of Paediatrics, Obafemi Awolowo University Teaching Hospital (OAUTHC), Ile-Ife, Osun State, Nigeria
| | - Margaret Oluwatoyin Japhet
- Faculty of Science, Department of Microbiology, Obafemi Awolowo University, Ile-Ife, Osun State, Nigeria
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Ayaz Kök S, Üstün S, Taşkent Sezgin H. Diagnosis of Ruminant Viral Diseases with Loop-Mediated Isothermal Amplification. Mol Biotechnol 2023; 65:1228-1241. [PMID: 36719638 PMCID: PMC9888337 DOI: 10.1007/s12033-023-00674-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
Infectious diseases in livestock industry are major problems for animal health, food safety, and the economy. Zoonotic diseases from farm animals are significant threat to human population as well. These are notifiable diseases listed by the World Organization for Animal Health (OIE). Rapid diagnostic methods can help keep infectious diseases under control in herds. Loop-mediated isothermal amplification (LAMP) is a simple and rapid nucleic acid amplification method that is studied widely for detection of many infectious diseases in the field. LAMP allows biosensing of target DNA or RNA under isothermal conditions with high specificity in a short period of time. An untrained user can analyze results based on color change or turbidity. Here we review LAMP assays to diagnose OIE notifiable ruminant viral diseases in literature highlighting properties of LAMP method considering what is expected from an efficient, field usable diagnostic test.
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Affiliation(s)
- Sanem Ayaz Kök
- Biotechnology Interdisciplinary Program, İzmir Institute of Technology, Gülbahçe, Urla, İzmir, Turkey, 35430
- New Era Biotechnology, Teknopark İzmir, Gülbahçe, Urla, İzmir, Turkey, 35430
| | - Selcen Üstün
- Bioengineering Department, İzmir Institute of Technology, Gülbahçe, Urla, İzmir, Turkey, 35430
| | - Hümeyra Taşkent Sezgin
- Biotechnology Interdisciplinary Program, İzmir Institute of Technology, Gülbahçe, Urla, İzmir, Turkey, 35430.
- New Era Biotechnology, Teknopark İzmir, Gülbahçe, Urla, İzmir, Turkey, 35430.
- Bioengineering Department, İzmir Institute of Technology, Gülbahçe, Urla, İzmir, Turkey, 35430.
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6
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Adam E. Equine rotaviruses - an update from Kentucky. Vet Rec 2023; 192:e3139. [PMID: 37265275 DOI: 10.1002/vetr.3139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Emma Adam of the Gluck Equine Research Center at the University of Kentucky in the USA provides an update on rotaviruses, particularly the group B equine rotavirus identified in 2021.
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Affiliation(s)
- Emma Adam
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40546, USA
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Amit LN, John JL, Mori D, Chin AZ, Mosiun AK, Ahmed K. Increase in rotavirus prevalence with the emergence of genotype G9P[8] in replacement of genotype G12P[6] in Sabah, Malaysia. Arch Virol 2023; 168:173. [PMID: 37269384 DOI: 10.1007/s00705-023-05803-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/19/2023] [Indexed: 06/05/2023]
Abstract
Rotaviruses are major causative agents of acute diarrhea in children under 5 years of age in Malaysia. However, a rotavirus vaccine has not been included in the national vaccination program. To date, only two studies have been carried out in the state of Sabah, Malaysia, although children in this state are at risk of diarrheal diseases. Previous studies showed that 16%-17% of cases of diarrhea were caused by rotaviruses and that equine-like G3 rotavirus strains are predominant. Because the prevalence of rotaviruses and their genotype distribution vary over time, this study was conducted at four government healthcare facilities from September 2019 through February 2020. Our study revealed that the proportion of rotavirus diarrhea increased significantly to 37.2% (51/137) after the emergence of the G9P[8] genotype in replacement of the G12P[8] genotype. Although equine-like G3P[8] strains remain the predominant rotaviruses circulating among children, the Sabahan G9P[8] strain belonged to lineage VI and was phylogenetically related to strains from other countries. A comparison of the Sabahan G9 strains with the G9 vaccine strains used in the RotaSiil and Rotavac vaccines revealed several mismatches in neutralizing epitopes, indicating that these vaccines might not be effective in Sabahan children. However, a vaccine trial may be necessary to understand the precise effects of vaccination.
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Affiliation(s)
- Lia Natasha Amit
- Department of Pathology and Microbiology, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Jecelyn Leaslie John
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Daisuke Mori
- Department of Pathology and Microbiology, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Abraham Zefong Chin
- Department of Community and Family Medicine, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Andau Konodan Mosiun
- Kunak District Health Office, Ministry of Health Malaysia, Kunak, Sabah, Malaysia
| | - Kamruddin Ahmed
- Department of Pathology and Microbiology, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia.
- Borneo Medical and Health Research Centre, Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia.
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Tran H, Friendship R, Poljak Z. Classification of group A rotavirus VP7 and VP4 genotypes using random forest. Front Genet 2023; 14:1029185. [PMID: 37323680 PMCID: PMC10267748 DOI: 10.3389/fgene.2023.1029185] [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: 09/08/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023] Open
Abstract
Introduction: Group A rotaviruses are major pathogens in causing severe diarrhea in young children and neonates of many different species of animals worldwide and group A rotavirus sequence data are becoming increasingly available over time. Different methods exist that allow for rotavirus genotyping, but machine learning methods have yet to be explored. Usage of machine learning algorithms such as random forest alongside alignment-based methodology may allow for both efficient and accurate classification of circulating rotavirus genotypes through the dual classification system. Methods: Random forest models were trained on positional features obtained from pairwise and multiple sequence alignment and cross-validated using methods of repeated 10-fold cross-validation thrice and leave one- out cross validation. Models were then validated on unseen data from the testing datasets to observe real-world performance. Results: All models were found to perform strongly in classification of VP7 and VP4 genotypes with high overall accuracy and kappa values during model training (0.975-0.992, 0.970-0.989) and during model testing (0.972-0.996, 0.969-0.996), respectively. Models trained on multiple sequence alignment generally had slightly higher overall accuracy and kappa values than models trained on pairwise sequence alignment method. In contrast, pairwise sequence alignment models were found to be generally faster than multiple sequence alignment models in computational speed when models do not need to be retrained. Models that used repeated 10-fold cross-validation thrice were also found to be much faster in model computational speed than models that used leave-one-out cross validation, with no noticeable difference in overall accuracy and kappa values between the cross-validation methods. Discussion: Overall, random forest models showed strong performance in the classification of both group A rotavirus VP7 and VP4 genotypes. Application of these models as classifiers will allow for rapid and accurate classification of the increasing amounts of rotavirus sequence data that are becoming available.
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Casey-Moore MC, Mijatovic-Rustempasic S, Jaimes J, Perkins C, Riley AM, Cortese MM, Gautam R, Bowen MD. Coding-Complete Genome Sequences of G6P[14] Rotavirus Strain Detected in a Human Stool Specimen within the United States. Microbiol Resour Announc 2023:e0000823. [PMID: 37140434 DOI: 10.1128/mra.00008-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
In this study, we report the detection of a G6P[14] rotavirus strain from a human stool sample within the United States. The full genotype constellation of the G6P[14] strain was identified as G6-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3.
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Affiliation(s)
- Mary C Casey-Moore
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Slavica Mijatovic-Rustempasic
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jose Jaimes
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Charity Perkins
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ann Marie Riley
- Infectious Disease Diagnostic Laboratory, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Margaret M Cortese
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rashi Gautam
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael D Bowen
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Genomic Constellation of Human Rotavirus G8 Strains in Brazil over a 13-Year Period: Detection of the Novel Bovine-like G8P[8] Strains with the DS-1-like Backbone. Viruses 2023; 15:v15030664. [PMID: 36992373 PMCID: PMC10056101 DOI: 10.3390/v15030664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/06/2023] Open
Abstract
Rotavirus (RVA) G8 is frequently detected in animals, but only occasionally in humans. G8 strains, however, are frequently documented in nations in Africa. Recently, an increase in G8 detection was observed outside Africa. The aims of the study were to monitor G8 infections in the Brazilian human population between 2007 and 2020, undertake the full-genotype characterization of the four G8P[4], six G8P[6] and two G8P[8] RVA strains and conduct phylogenetic analysis in order to understand their genetic diversity and evolution. A total of 12,978 specimens were screened for RVA using ELISA, PAGE, RT-PCR and Sanger sequencing. G8 genotype represented 0.6% (15/2434) of the entirely RVA-positive samples. G8P[4] comprised 33.3% (5/15), G8P[6] 46.7% (7/15) and G8P[8] 20% (3/15). All G8 strains showed a short RNA pattern. All twelve selected G8 strains displayed a DS-1-like genetic backbone. The whole-genotype analysis on a DS-1-like backbone identified four different genotype-linage constellations. According to VP7 analysis, the Brazilian G8P[8] strains with the DS-1-like backbone strains were derived from cattle and clustered with newly DS-1-like G1/G3/G9/G8P[8] strains and G2P[4] strains. Brazilian IAL-R193/2017/G8P[8] belonged to a VP1/R2.XI lineage and were grouped with bovine-like G8P[8] strains with the DS-1-like backbone strains detected in Asia. Otherwise, the Brazilian IAL-R558/2017/G8P[8] possess a “Distinct” VP1/R2 lineage never previously described and grouped apart from any of the DS-1-like reference strains. Collectively, our findings suggest that the Brazilian bovine-like G8P[8] strains with the DS-1-like backbone strains are continuously evolving and likely reassorting with local RVA strains rather than directly relating to imports from Asia. The Brazilian G8P[6]-DS-1-like strains have been reassorted with nearby co-circulating American strains of the same DS-1 genotype constellation. However, phylogenetic analyses revealed that these strains have some genetic origin from Africa. Finally, rather than being African-born, Brazilian G8P[4]-DS-1-like strains were likely imported from Europe. None of the Brazilian G8 strains examined here exhibited signs of recent zoonotic reassortment. G8 strains continued to be found in Brazil according to their intermittent and localized pattern, thus, does not suggest that a potential emergence is taking place in the country. Our research demonstrates the diversity of G8 RVA strains in Brazil and adds to the understanding of G8P[4]/P[6]/P[8] RVA genetic diversity and evolution on a global scale.
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Johne R, Tausch SH, Schilling-Loeffler K, Ulrich RG. Genome sequence analysis of a novel rotavirus strain indicates a broad genetic diversity of rotavirus A in shrews. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 107:105392. [PMID: 36494067 DOI: 10.1016/j.meegid.2022.105392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Rotavirus A (RVA) is an etiologic agent of diarrhea in humans and animals. It shows a high degree of genetic heterogeneity. Although distinct associations of RVA genotypes with certain host species are common, interspecies-transmission has also been described. Recently, RVA strains, which are genetically distinct and cluster basally to all other RVA strains in phylogenetic trees, have been identified in common shrews (Sorex araneus). Here, the genome sequence analysis of another RVA strain (RVA/Common Shrew-wt/GER/KS11-0893/2010/G42P[58]) from a common shrew from Germany is described. Generally, the strain shows low sequence identities to established strains, which is reflected by the assessment of the novel genotypes G42-P[58]-I32-R28-C24-M24-A39-N28-T28-E32-H28 to its genome segments. Specifically, the strain is phylogenetically distant from previously described RVA strains of common shrews, whereas it is more closely related to other avian and mammalian RVA strains including those from Asian house shrews (Suncus murinus). The results indicate that a broad variety of diverse RVA strains can be found in shrews suggesting a significant role of these animals in rotavirus evolution.
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Affiliation(s)
- Reimar Johne
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Katja Schilling-Loeffler
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany; Partner site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research (DZIF), Südufer 10, 17493 Greifswald-Insel Riems, Germany
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12
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Potential zoonotic swine enteric viruses: The risk ignored for public health. Virus Res 2022; 315:198767. [PMID: 35421434 DOI: 10.1016/j.virusres.2022.198767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 12/28/2022]
Abstract
Swine could serve as a natural reservoir for a large variety of viruses, including potential zoonotic enteric viruses. The presence of viruses with high genetic similarity between porcine and human strains may result in the emergence of zoonotic or xenozoonotic infections. Furthermore, the globalization and intensification of swine industries exacerbate the transmission and evolution of zoonotic viruses among swine herds and individuals working in swine-related occupations. To effectively prevent the public health risks posed by zoonotic swine enteric viruses, designing, and implementing a comprehensive measure for early diagnosis, prevention, and mitigation, requires interdisciplinary a collaborative ''One Health" approach from veterinarians, environmental and public health professionals, and the swine industry. In this paper, we reviewed the current knowledge of selected potential zoonotic swine enteric viruses and explored swine intensive production and its associated public health risks.
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13
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Sadiq A, Bostan N, Aziz A. Effect of rotavirus genetic diversity on vaccine impact. Rev Med Virol 2022; 32:e2259. [PMID: 34997676 DOI: 10.1002/rmv.2259] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/05/2021] [Indexed: 11/07/2022]
Abstract
Group A rotaviruses (RVAs) are the leading cause of gastroenteritis, causing 0.2 million deaths and several million hospitalisations globally each year. Four rotavirus vaccines (RotarixTM , RotaTeqTM , Rotavac® and ROTASIIL® ) have been pre-qualified by the World Health Organization (WHO), but the two newly pre-qualified vaccines (Rotavac® and ROTASIIL® ) are currently only in use in Palestine and India, respectively. In 2009, WHO strongly proposed that rotavirus vaccines be included in the routine vaccination schedule of all countries around the world. By the end of 2019, a total of 108 countries had administered rotavirus vaccines, and 10 countries have currently been approved by Gavi for the introduction of rotavirus vaccine in the near future. With 39% of global coverage, rotavirus vaccines have had a substantial effect on diarrhoeal morbidity and mortality in different geographical areas, although efficacy appears to be higher in high income settings. Due to the segmented RNA genome, the pattern of RVA genotypes in the human population is evolving through interspecies transmission and/or reassortment events for which the vaccine might be less effective in the future. However, despite the relative increase in some particular genotypes after rotavirus vaccine use, the overall efficacy of rotavirus mass vaccination worldwide has not been affected. Some of the challenges to improve the effect of current rotavirus vaccines can be solved in the future by new rotavirus vaccines and by vaccines currently in progress.
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Affiliation(s)
- Asma Sadiq
- Department of Biosciences, Molecular Virology Laboratory, COMSATS University, Islamabad, Pakistan
| | - Nazish Bostan
- Department of Biosciences, Molecular Virology Laboratory, COMSATS University, Islamabad, Pakistan
| | - Aamir Aziz
- Sarhad University of Science and Information Technology, Institute of Biological Sciences, Sarhad University, Peshawar, Pakistan
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14
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Recent advances in rotavirus reverse genetics and its utilization in basic research and vaccine development. Arch Virol 2021; 166:2369-2386. [PMID: 34216267 PMCID: PMC8254061 DOI: 10.1007/s00705-021-05142-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/27/2021] [Indexed: 11/29/2022]
Abstract
Rotaviruses are segmented double-stranded RNA viruses with a high frequency of gene reassortment, and they are a leading cause of global diarrheal deaths in children less than 5 years old. Two-thirds of rotavirus-associated deaths occur in low-income countries. Currently, the available vaccines in developing countries have lower efficacy in children than those in developed countries. Due to added safety concerns and the high cost of current vaccines, there is a need to develop cost-effective next-generation vaccines with improved safety and efficacy. The reverse genetics system (RGS) is a powerful tool for investigating viral protein functions and developing novel vaccines. Recently, an entirely plasmid-based RGS has been developed for several rotaviruses, and this technological advancement has significantly facilitated novel rotavirus research. Here, we review the recently developed RGS platform and discuss its application in studying infection biology, gene reassortment, and development of vaccines against rotavirus disease.
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15
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Wa-1 Equine-Like G3P[8] Rotavirus from a Child with Diarrhea in Colombia. Viruses 2021; 13:v13061075. [PMID: 34199978 PMCID: PMC8226935 DOI: 10.3390/v13061075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022] Open
Abstract
Rotavirus A (RVA) has been considered the main cause of diarrheal disease in children under five years in emergency services in both developed and developing countries. RVA belongs to the Reoviridae family, which comprises 11 segments of double-stranded RNA (dsRNA) as a genomic constellation that encodes for six structural and five to six nonstructural proteins. RVA has been classified in a binary system with Gx[Px] based on the spike protein (VP4) and the major outer capsid glycoprotein (VP7), respectively. The emerging equine-like G3P[8] DS-1-like strains reported worldwide in humans have arisen an important concern. Here, we carry out the complete genome characterization of a previously reported G3P[8] strain in order to recognize the genetic diversity of RVA circulating among infants in Colombia. A near-full genome phylogenetic analysis was done, confirming the presence of the novel equine-like G3P[8] with a Wa-like backbone for the first time in Colombia. This study demonstrated the importance of surveillance of emerging viruses in the Colombian population; furthermore, additional studies must focus on the understanding of the spread and transmission dynamic of this important RVA strain in different areas of the country.
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Aggarwal S, Hassan E, Baldridge MT. Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses. Viruses 2021; 13:975. [PMID: 34070283 PMCID: PMC8225081 DOI: 10.3390/v13060975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022] Open
Abstract
Every year, millions of children are infected with viruses that target the gastrointestinal tract, causing acute gastroenteritis and diarrheal illness. Indeed, approximately 700 million episodes of diarrhea occur in children under five annually, with RNA viruses norovirus, rotavirus, and astrovirus serving as major causative pathogens. Numerous methodological advancements in recent years, including the establishment of novel cultivation systems using enteroids as well as the development of murine and other animal models of infection, have helped provide insight into many features of viral pathogenesis. However, many aspects of enteric viral infections remain elusive, demanding further study. Here, we describe the different in vitro and in vivo tools available to explore different pathophysiological attributes of human enteric RNA viruses, highlighting their advantages and limitations depending upon the question being explored. In addition, we discuss key areas and opportunities that would benefit from further methodological progress.
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Affiliation(s)
- Somya Aggarwal
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
| | - Ebrahim Hassan
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Cárcamo-Calvo R, Muñoz C, Buesa J, Rodríguez-Díaz J, Gozalbo-Rovira R. The Rotavirus Vaccine Landscape, an Update. Pathogens 2021; 10:520. [PMID: 33925924 PMCID: PMC8145439 DOI: 10.3390/pathogens10050520] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Rotavirus is the leading cause of severe acute childhood gastroenteritis, responsible for more than 128,500 deaths per year, mainly in low-income countries. Although the mortality rate has dropped significantly since the introduction of the first vaccines around 2006, an estimated 83,158 deaths are still preventable. The two main vaccines currently deployed, Rotarix and RotaTeq, both live oral vaccines, have been shown to be less effective in developing countries. In addition, they have been associated with a slight risk of intussusception, and the need for cold chain maintenance limits the accessibility of these vaccines to certain areas, leaving 65% of children worldwide unvaccinated and therefore unprotected. Against this backdrop, here we review the main vaccines under development and the state of the art on potential alternatives.
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Affiliation(s)
- Roberto Cárcamo-Calvo
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
| | - Carlos Muñoz
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Roberto Gozalbo-Rovira
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
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18
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Tecnologias para a autoeficácia materna na prevenção da diarreia infantil: ensaio clínico. ACTA PAUL ENFERM 2021. [DOI: 10.37689/acta-ape/2021ao03232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach. Viruses 2020; 12:v12121432. [PMID: 33322135 PMCID: PMC7764520 DOI: 10.3390/v12121432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.
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20
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Murunga N, P Otieno G, Maia M, N Agoti C. Effectiveness of Rotarix ® vaccine in Africa in the first decade of progressive introduction, 2009-2019: systematic review and meta-analysis. Wellcome Open Res 2020; 5:187. [PMID: 33215049 PMCID: PMC7658728 DOI: 10.12688/wellcomeopenres.16174.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2020] [Indexed: 11/30/2022] Open
Abstract
Background: Randomized controlled trials of licensed oral rotavirus group A (RVA) vaccines, indicated lower efficacy in developing countries compared to developed countries. We investigated the pooled effectiveness of Rotarix
® in Africa in 2019, a decade since progressive introduction began in 2009. Methods: A systematic search was conducted in PubMed to identify studies that investigated the effectiveness of routine RVA vaccination in an African country between 2009 and 2019. A meta-analysis was undertaken to estimate pooled effectiveness of the full-dose versus partial-dose of Rotarix
® (RV1) vaccine and in different age groups. Pooled odds ratios were estimated using random effects model and the risk of bias assessed using Newcastle-Ottawa scale. The quality of the evidence was assessed using GRADE. Results: By December 2019, 39 (72%) countries in Africa had introduced RVA vaccination, of which 34 were using RV1. Thirteen eligible studies from eight countries were included in meta-analysis for vaccine effectiveness (VE) of RVA by vaccine dosage (full or partial) and age categories. Pooled RV1 VE against RVA associated hospitalizations was 44% (95% confidence interval (CI) 28-57%) for partial dose versus 58% (95% CI 50-65%) for full dose. VE was 61% (95% CI 50-69%), 55% (95% CI 32-71%), 56% (95% CI 43-67%), and 61% (95% CI 42-73%) for children aged <12 months, 12-23 months, <24 months and 12-59 months, respectively. Conclusion: RV1 vaccine use has resulted in a significant reduction in severe diarrhoea in African children and its VE is close to the efficacy findings observed in clinical trials. RV1 VE point estimate was higher for children who received full dose than those who received partial dose, and its protection lasted beyond the first year of life.
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Affiliation(s)
- Nickson Murunga
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Public Health, School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Marta Maia
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Public Health, School of Health and Human Sciences, Pwani University, Kilifi, Kenya
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21
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Kurenzvi L, Sebunya TK, Coetzee T, Paganotti GM, Teye MV. Prevalence of Cryptosporidium parvum, Giardia intestinalis and molecular characterization of group A rotavirus associated with diarrhea in children below five years old in Gaborone, Botswana. Pan Afr Med J 2020; 37:159. [PMID: 33425192 PMCID: PMC7757325 DOI: 10.11604/pamj.2020.37.159.25392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/26/2020] [Indexed: 11/11/2022] Open
Abstract
Introduction Cryptosporidium, Giardia and rotaviruses are amongst the leading causes of acute gastroenteritis in children ≤5 years worldwide. The purpose of this study was to determine the occurrence of Cryptosporidium parvum, Giardia intestinalis and molecular characteristics of rotaviruses after Rotarix® introduction in Botswana. Methods in this case study, 200 diarrheic stool specimens and 100 control samples from children under five years old were collected between March and November, 2017. Samples were analyzed by modified Ziehl Neelsen staining technique for cryptosporidium, wet mount procedure for Giardia and negative samples were confirmed by immunochromatographic assay. Specimens were analyzed for rotavirus by ELISA, PAGE, RT-PCR, sequencing of VP7 and VP4 antigen followed by phylogenetic analysis. Results prevalence rates of 20.5%, 16.5% and 11.0% in diarrhea cases were observed for Cryptosporidium parvum, Giardia intestinalis and rotavirus, respectively. Four percent of diarrheic specimens had multiple infections. The predominant rotavirus genotype was GIP[8] (7/15) followed by G2P[4] (2/15) and G3P[8] (1/15). Twenty percent of specimens were non-typeable. One mixed strain, G1+G2P[4,8] (2/15), was detected. Phylogenetic analysis of VP4 and VP7 sequences clustered Botswana rotavirus strains within G1 lineages 1 and 2, G3 lineage 1, P[8] lineage 3 and P[4] lineage 5 together with Southern African strains. Conclusion this study provides important information on occurrence and demographic risk groups for Cryptosporidium parvum, Giardia intestinalis and rotavirus in young children as well as genetic diversity of rotaviruses after vaccine introduction in Botswana. Constant monitoring of circulating rotavirus strains is essential in assessing effectiveness of current vaccines in Botswana.
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Affiliation(s)
- Lineage Kurenzvi
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Teresa Kibirige Sebunya
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Tidimalo Coetzee
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Giacomo Maria Paganotti
- Botswana-University of Pennsylvania Partnership, Gaborone, Botswana.,Division of Infectious Diseases, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA.,Department of Biomedical Sciences, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Mathias Vondee Teye
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
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Murunga N, P. Otieno G, Maia M, N. Agoti C. Effectiveness of Rotarix® vaccine in Africa in the first decade of progressive introduction, 2009-2019: systematic review and meta-analysis. Wellcome Open Res 2020; 5:187. [DOI: 10.12688/wellcomeopenres.16174.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Randomized controlled trials of licensed oral rotavirus group A (RVA) vaccines, indicated lower efficacy in developing countries compared to developed countries. We investigated the pooled effectiveness of Rotarix® in Africa in 2019, a decade since progressive introduction began in 2009. Methods: A systematic search was conducted in PubMed to identify studies that investigated the effectiveness of routine RVA vaccination in an African country between 2009 and 2019. A meta-analysis was undertaken to estimate pooled effectiveness of the full-dose versus partial-dose of Rotarix® (RV1) vaccine and in different age groups. Pooled odds ratios were estimated using random effects model and the risk of bias assessed using Newcastle-Ottawa scale. The quality of the evidence was assessed using GRADE. Results: By December 2019, 39 (72%) countries in Africa had introduced RVA vaccination, of which 34 were using RV1. Thirteen eligible studies from eight countries were included in meta-analysis for vaccine effectiveness (VE) of RVA by vaccine dosage (full or partial) and age categories. Pooled RV1 VE against RVA associated hospitalizations was 44% (95% confidence interval (CI) 28-57%) for partial dose versus 58% (95% CI 50-65%) for full dose. VE was 61% (95% CI 50-69%), 55% (95% CI 32-71%), 56% (95% CI 43-67%), and 61% (95% CI 42-73%) for children aged <12 months, 12-23 months, <24 months and 12-59 months, respectively. Conclusion: RV1 vaccine use has resulted in a significant reduction in severe diarrhoea in African children and its VE is close to the efficacy findings observed in clinical trials. RV1 VE point estimate was higher for children who received full dose than those who received partial dose, and its protection lasted beyond the first year of life.
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Overview of the Development, Impacts, and Challenges of Live-Attenuated Oral Rotavirus Vaccines. Vaccines (Basel) 2020; 8:vaccines8030341. [PMID: 32604982 PMCID: PMC7565912 DOI: 10.3390/vaccines8030341] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/26/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022] Open
Abstract
Safety, efficacy, and cost-effectiveness are paramount to vaccine development. Following the isolation of rotavirus particles in 1969 and its evidence as an aetiology of severe dehydrating diarrhoea in infants and young children worldwide, the quest to find not only an acceptable and reliable but cost-effective vaccine has continued until now. Four live-attenuated oral rotavirus vaccines (LAORoVs) (Rotarix®, RotaTeq®, Rotavac®, and RotaSIIL®) have been developed and licensed to be used against all forms of rotavirus-associated infection. The efficacy of these vaccines is more obvious in the high-income countries (HIC) compared with the low- to middle-income countries (LMICs); however, the impact is far exceeding in the low-income countries (LICs). Despite the rotavirus vaccine efficacy and effectiveness, more than 90 countries (mostly Asia, America, and Europe) are yet to implement any of these vaccines. Implementation of these vaccines has continued to suffer a setback in these countries due to the vaccine cost, policy, discharging of strategic preventive measures, and infrastructures. This review reappraises the impacts and effectiveness of the current live-attenuated oral rotavirus vaccines from many representative countries of the globe. It examines the problems associated with the low efficacy of these vaccines and the way forward. Lastly, forefront efforts put forward to develop initial procedures for oral rotavirus vaccines were examined and re-connected to today vaccines.
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Gutierrez MB, Fialho AM, Maranhão AG, Malta FC, de Andrade JDSR, de Assis RMS, Mouta SDSE, Miagostovich MP, Leite JPG, Machado Fumian T. Rotavirus A in Brazil: Molecular Epidemiology and Surveillance during 2018-2019. Pathogens 2020; 9:pathogens9070515. [PMID: 32605014 PMCID: PMC7400326 DOI: 10.3390/pathogens9070515] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 02/06/2023] Open
Abstract
Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use of Rotarix™ in the country has reduced childhood mortality and morbidity due to AGE. Even though both marketed vaccines are widely distributed, the surveillance of RVA causing AGE and the monitoring of circulating genotypes are important tools to keep tracking the epidemiological scenario and vaccines impact. Thus, our study investigated RVA epidemiological features, viral load and G and P genotypes circulation in children and adults presenting AGE symptoms in eleven states from three out of five regions in Brazil. By using TaqMan®-based one-step RT-qPCR, we investigated a total of 1536 stool samples collected from symptomatic inpatients, emergency department visits and outpatients from January 2018 to December 2019. G and P genotypes of RVA-positive samples were genetically characterized by multiplex RT-PCR or by nearly complete fragment sequencing. We detected RVA in 12% of samples, 10.5% in 2018 and 13.7% in 2019. A marked winter/spring seasonality was observed, especially in Southern Brazil. The most affected age group was children aged >24-60 months, with a positivity rate of 18.8% (p < 0.05). Evaluating shedding, we found a statistically lower RVA viral load in stool samples collected from children aged up to six months compared to the other age groups (p < 0.05). The genotype G3P[8] was the most prevalent during the two years (83.7% in 2018 and 65.5% in 2019), and nucleotide sequencing of some strains demonstrated that they belonged to the emergent equine-like G3P[8] genotype. The dominance of an emergent genotype causing AGE reinforces the need for continuous epidemiological surveillance to assess the impact of mass RVA immunization as well as to monitor the emergence of novel genotypes.
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25
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Beserra LAR, Barbosa CM, Berg M, Brandão PE, Soares RM, Gregori F. Genome constellations of rotavirus a isolated from avian species in Brazil, 2008-2015. Braz J Microbiol 2020; 51:1363-1375. [PMID: 32378061 DOI: 10.1007/s42770-020-00259-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/09/2020] [Indexed: 10/24/2022] Open
Abstract
Rotaviruses are members of the family Reoviridae and are a common cause of acute diarrhea in many mammalian and avian species. They are non-enveloped icosahedral particles and their genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). Genotypes are defined based upon the diversity found in these genes and viral characterization plays a central role on epidemiological studies and prevention. Here we investigate the distribution of Brazilian RVAs genotypes in 8 chicken samples collected between 2008 and 2015 from different regions by RT-PCR, partial (Sanger) nucleotide sequencing and phylogenetic analysis from all rotavirus genes. Although the identified genotypes were typical from avian host species, when analyzed together, they form novel genetic constellations: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. This study highlights that avian rotaviruses are widespread among commercial farms in Brazil, and the co-circulation of at least two different genomic constellations indicates that may present a way bigger genetic variability, that can be increased by the possible transmission events from other birds, lack of specific preventive measures, as well as the different viral evolution mechanisms.
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Affiliation(s)
- Laila A R Beserra
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo, SP, CEP 05508-270, Brazil.
| | - Carla M Barbosa
- Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Dr. Prof. Lineu Prestes, 1374, São Paulo, SP, CEP 05508 900, Brazil
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences (SLU). BVF, Virologi, Box 7028, 75007, Uppsala, Sweden
| | - Paulo E Brandão
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo, SP, CEP 05508-270, Brazil
| | - Rodrigo M Soares
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo, SP, CEP 05508-270, Brazil
| | - Fabio Gregori
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, São Paulo, SP, CEP 05508-270, Brazil
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Human Enteric Circulating Viruses and Co-infections Among Hospitalized Children with Severe Acute Gastroenteritis in Chihuahua, Mexico, During 2010 - 2011. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.95010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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27
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Stubbs SCB, Quaye O, Acquah ME, Adadey SM, Kean IRL, Gupta S, Blacklaws BA. Full genomic characterization of a porcine rotavirus strain detected in an asymptomatic piglet in Accra, Ghana. BMC Vet Res 2020; 16:11. [PMID: 31924206 PMCID: PMC6954506 DOI: 10.1186/s12917-019-2226-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/25/2019] [Indexed: 12/03/2022] Open
Abstract
Background The introduction of rotavirus A vaccination across the developing world has not proved to be as efficacious as first hoped. One cause of vaccine failure may be infection by zoonotic rotaviruses that are very variable antigenically from the vaccine strain. However, there is a lack of genomic information about the circulating rotavirus A strains in farm animals in the developing world that may be a source of infection for humans. We therefore screened farms close to Accra, Ghana for animals sub-clinically infected with rotavirus A and then sequenced the virus found in one of these samples. Results 6.1% of clinically normal cows and pigs tested were found to be Rotavirus A virus antigen positive in the faeces. A subset of these (33.3%) were also positive for virus RNA. The most consistently positive pig sample was taken forward for metagenomic sequencing. This gave full sequence for all open reading frames except segment 5 (NSP1), which is missing a single base at the 5′ end. The virus infecting this pig had genome constellation G5-P[7]-I5-R1-C1-M1-A8-N1-T7-E1-H1, a known porcine genotype constellation. Conclusions Farm animals carry rotavirus A infection sub-clinically at low frequency. Although the rotavirus A genotype discovered here has a pig-like genome constellation, a number of the segments most closely resembled those isolated from humans in suspected cases of zoonotic transmission. Therefore, such viruses may be a source of variable gene segments for re-assortment with other viruses to cause vaccine breakdown. It is recommended that further human and pig strains are characterized in West Africa, to better understand this dynamic.
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Affiliation(s)
- Samuel C B Stubbs
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Volta Road, P. O. Box LG 54, Legon, Accra, Ghana.
| | - Maame Ekua Acquah
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Volta Road, P. O. Box LG 54, Legon, Accra, Ghana
| | - Samuel Mawuli Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Volta Road, P. O. Box LG 54, Legon, Accra, Ghana
| | - Iain R L Kean
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Srishti Gupta
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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28
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Islam A, Hossain ME, Haider N, Rostal MK, Mukharjee SK, Ferdous J, Miah M, Rahman M, Daszak P, Rahman MZ, Epstein JH. Molecular characterization of group A rotavirus from rhesus macaques (Macaca mulatta) at human-wildlife interfaces in Bangladesh. Transbound Emerg Dis 2019; 67:956-966. [PMID: 31765042 DOI: 10.1111/tbed.13431] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/29/2023]
Abstract
Group A rotavirus (RVA) is an important cause of diarrhoea in people, especially children, and animals globally. Due to the segmented nature of the RVA genome, animal RVA strains have the potential to adapt to the human host through reassortment with other co-infecting human viruses. Macaques share food and habitat with people, resulting in close interaction between these two species. This study aimed to detect and characterize RVA in rhesus macaques (Macaca mulatta) in Bangladesh. Faecal samples (N = 454) were collected from apparently healthy rhesus macaques from nine different sites in Bangladesh between February and March 2013. The samples were tested by one-step, real-time, reverse transcriptase-polymerase chain reaction (PCR). Four percent of samples (n = 20; 95% CI 2.7%-6.7%) were positive for RVA. RVA positive samples were further characterized by nucleotide sequence analysis of two structural protein gene fragments, VP4 (P genotype) and VP7 (G genotype). G3, G10, P[3] and P[15] genotypes were identified and were associated as G3P[3], G3P[15] and G10P[15]. The phylogenetic relationship between macaque RVA strains from this study and previously reported human strains indicates possible transmission between humans and macaques in Bangladesh. To our knowledge, this is the first report of detection and characterization of rotaviruses in rhesus macaques in Bangladesh. These data will not only aid in identifying viral sharing between macaques, human and other animals, but will also improve the development of mitigation measures for the prevention of future rotavirus outbreaks.
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Affiliation(s)
- Ariful Islam
- EcoHealth Alliance, New York, NY, USA.,Centre for Integrative Ecology, School of Life and Environmental Science, Deakin University, Geelong, Vic., Australia
| | - Mohammad Enayet Hossain
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Najmul Haider
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK
| | | | - Sanjoy Kumar Mukharjee
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jinnat Ferdous
- EcoHealth Alliance, New York, NY, USA.,Institute of Epidemiology, Disease Control and Research (IEDCR), Dhaka, Bangladesh
| | - Mojnu Miah
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafizur Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | - Mohammed Ziaur Rahman
- International Centre for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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29
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Roczo-Farkas S, Kirkwood CD, Cowley D, Barnes GL, Bishop RF, Bogdanovic-Sakran N, Boniface K, Donato CM, Bines JE. The Impact of Rotavirus Vaccines on Genotype Diversity: A Comprehensive Analysis of 2 Decades of Australian Surveillance Data. J Infect Dis 2019; 218:546-554. [PMID: 29790933 DOI: 10.1093/infdis/jiy197] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/03/2018] [Indexed: 12/28/2022] Open
Abstract
Background Introduction of rotavirus vaccines into national immunization programs (NIPs) could result in strain selection due to vaccine-induced selective pressure. This study describes the distribution and diversity of rotavirus genotypes before and after rotavirus vaccine introduction into the Australian NIP. State-based vaccine selection facilitated a unique comparison of diversity in RotaTeq and Rotarix vaccine states. Methods From 1995 to 2015, the Australian Rotavirus Surveillance Program conducted genotypic analysis on 13051 rotavirus-positive samples from children <5 years of age, hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined using serological and heminested multiplex reverse-transcription polymerase chain reaction assays. Results G1P[8] was the dominant genotype nationally in the prevaccine era (1995-2006). Following vaccine introduction (2007-2015), greater genotype diversity was observed with fluctuating genotype dominance. Genotype distribution varied based on the vaccine implemented, with G12P[8] dominant in states using RotaTeq, and equine-like G3P[8] and G2P[4] dominant in states and territories using Rotarix. Conclusions The increased diversity and differences in genotype dominance observed in states using RotaTeq (G12P[8]), and in states and territories using Rotarix (equine-like G3P[8] and G2P[4]), suggest that these vaccines exert different immunological pressures that influence the diversity of rotavirus strains circulating in Australia.
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Affiliation(s)
- Susie Roczo-Farkas
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Daniel Cowley
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Graeme L Barnes
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville
| | - Ruth F Bishop
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nada Bogdanovic-Sakran
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Karen Boniface
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Celeste M Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Julie E Bines
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
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30
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Beck-Friis T, Andersson M, Gustavsson L, Lindh M, Westin J, Andersson LM. Burden of rotavirus infection in hospitalized elderly individuals prior to the introduction of rotavirus vaccination in Sweden. J Clin Virol 2019; 119:1-5. [PMID: 31421292 DOI: 10.1016/j.jcv.2019.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/22/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Rotavirus gastroenteritis (GE) in the elderly has been much less studied than in children. OBJECTIVES The aim of this study was to determine the morbidity and mortality for elderly hospitalized patients with rotavirus GE prior to the introduction of rotavirus vaccination in Sweden, and to investigate the epidemiology of rotavirus genotypes in these patients. STUDY DESIGN All patients 60 years or older who were hospitalized at Sahlgrenska University Hospital, Gothenburg, Sweden, and were rotavirus positive in a clinical diagnostic test from 2009 to 2016, were included. Medical records were reviewed and rotavirus genotyping real-time PCR was performed. RESULTS One hundred and fifty-nine patients were included, corresponding to an annual incidence of hospitalization due to rotavirus GE of 16/100 000 inhabitants aged 60 years or older. G2P[4] was the most common genotype, followed by G1P[8] and G4P[8]. The majority of patients had community-onset of symptoms and no or few pre-existing health disorders. Four patients (2.5%) died within 30 days of sampling. Patients with hospital-onset rotavirus GE had a longer median length of stay following diagnosis compared with patients with community-onset of symptoms (19 vs. 5 days, p = 0.001) and higher 30-day mortality (8.6% (3/35) vs. < 1% (1/124), p = 0.03). CONCLUSIONS Hospitalization due to rotavirus GE among the elderly seems to mainly affect otherwise healthy individuals and is associated with low 30-day mortality.
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Affiliation(s)
- Thomas Beck-Friis
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Diagnosvägen 21, 41650 Gothenburg, Sweden.
| | - Maria Andersson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Diagnosvägen 21, 41650 Gothenburg, Sweden
| | - Lars Gustavsson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Diagnosvägen 21, 41650 Gothenburg, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Diagnosvägen 21, 41650 Gothenburg, Sweden
| | - Johan Westin
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Diagnosvägen 21, 41650 Gothenburg, Sweden
| | - Lars-Magnus Andersson
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Diagnosvägen 21, 41650 Gothenburg, Sweden
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31
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de Barros BDCV, Chagas EN, Bezerra LW, Ribeiro LG, Duarte Júnior JWB, Pereira D, da Penha Junior ET, Silva JR, Bezerra DAM, Bandeira RS, Pinheiro HHC, Guerra SDFDS, Guimarães RJDPSE, Mascarenhas JDP. Rotavirus A in wild and domestic animals from areas with environmental degradation in the Brazilian Amazon. PLoS One 2018; 13:e0209005. [PMID: 30562373 PMCID: PMC6298726 DOI: 10.1371/journal.pone.0209005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 11/28/2018] [Indexed: 12/28/2022] Open
Abstract
Acute gastroenteritis is one of the main causes of mortality in humans and young animals. Domestic and mainly wild animals such as bats, small rodents and birds are highly diversified animals in relation to their habitats and ecological niches and are widely distributed geographically in environments of forest fragmentation in some areas of the Amazon, being considered important sources for viruses that affect humans and other animals. Due to the anthropical activities, these animals changed their natural habitat and adapted to urbanized environments, thus representing risks to human and animal health. Although the knowledge of the global diversity of enteric viruses is scarce, there are reports demonstrating the detection of rotavirus in domestic animals and animals of productive systems, such as bovines and pigs. The present study investigated the prevalence of Rotavirus A in 648 fecal samples of different animal species from the northeastern mesoregion of the state of Pará, Brazil, which is characterized as an urbanized area with forest fragments. The fecal specimens were collected from October 2014 to April 2016 and subjected to a Qualitative Real-Time Polymerase Chain Reaction (RT-qPCR), using the NSP3 gene as a target. It was observed that 27.5% (178/648) of the samples presented positive results for RVA, with 178 samples distributed in birds (23.6%), canines (21.35%), chiropterans (17.98%), bovines (14.6%), horses (8.43%), small rodents (6.74%), pigs (3.93%) and felines (3.37%), demonstrating the circulation of RVA in domestic animals and suggesting that such proximity could cause transmissions between different species and the occurrence of rearrangements in the genome of RVA as already described in the literature, associated to the traces of environmental degradation in the studied areas.
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Affiliation(s)
| | | | | | | | | | - Diego Pereira
- Amazon Metropolitan University Center, Belém, Pará, Brazil
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Babji S, Arumugam R, Priyahemavathy R, Sriraman A, Sarvanabhavan A, Manickavasagam P, Simon A, Aggarwal I, Moses PD, Arora R, Kang G. Genotype distribution of Group A rotavirus from southern India, 2005-2016. Vaccine 2017; 36:7816-7819. [PMID: 28844408 DOI: 10.1016/j.vaccine.2017.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 10/18/2022]
Abstract
Diarrheal disease due to Group A rotaviruses remain a leading cause of mortality and morbidity in the less developed parts of the world. India has started a phased roll out of rotavirus vaccine in the national immunization program. This analysis summarizes the rotavirus genotype strain distribution pre-vaccine introduction in Vellore, India from December 2005 to June 2016. Rotavirus was responsible for 32% of all diarrheal admission to the hospital. G2P[4] was the predominant strain in the initial years and was gradually replaced by G1P[8]. The emergence of G9P[4] replacing G9P[8], and the detection of G12 strains over several years were documented. There was no clear seasonality of disease. These data form the baseline to monitor genotype distribution post-vaccine introduction in Tamil Nadu.
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Affiliation(s)
- Sudhir Babji
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
| | - Rajesh Arumugam
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - R Priyahemavathy
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Archana Sriraman
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | - Anna Simon
- Department of Child Health, Christian Medical College, Vellore, India
| | - Indira Aggarwal
- Department of Child Health, Christian Medical College, Vellore, India
| | - Prabhakar D Moses
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Rashmi Arora
- Epidemiology and Communicable Diseases Division, Indian Council of Medical Research, New Delhi, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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Mohanty E, Dwibedi B, Kar SK, Acharya AS. Epidemiological features and genetic characterization of virus strains in rotavirus associated gastroenteritis in children of Odisha in Eastern India. INFECTION GENETICS AND EVOLUTION 2017; 53:77-84. [PMID: 28438670 DOI: 10.1016/j.meegid.2017.04.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/22/2017] [Accepted: 04/14/2017] [Indexed: 12/18/2022]
Abstract
We have studied the clinical characteristics, severity and seasonality of rotavirus infection and prevalent genotypes in 652 non-rota vaccinated children in Odisha in eastern India. P genotypes were analysed for their association with host blood group antigens. P type of the virus is determined by the VP8* gene, and specific recognition of A - type of Histo - blood group antigen by P[14]VP8* has been reported. VP4, VP7 and VP6 genes of commonly identified G1P[8] strain were compared with genes of the same strain isolated from other parts of India, elsewhere and strains used for Rotarix and Rotateq vaccines. In 54.75% of children with gastroenteritis, rota virus was found. 9.65% of children had moderate, 78.07% severe, and 12.28% very severe disease as assessed using the Vesikari scoring system. The incidence of infection was highest during winter months. There was no association between any blood group and specific P genotypes. G1P[8] was the commonest cause of gastroenteritis, followed by G1P[11], G3P[8], G9P[8], G2P[4], G2P[6], G9P[4], G9P[11] and G1P[6]. Predominant G genotypes identified were G1 (72.9%), G9 (10.81%), G2 (8.10%) and G3 (8.10%). Sequence analysis of the VP7 gene, placed the G1P[8] strain in lineage 1 and of VP6 gene placed nine G1P[8] strains in subgroup II and one in subgroup I. The VP7 gene segment of two Odisha G1P[8] strains were found to cluster relatively close to the VP7 sequences of Rotarix vaccine. Antigenic differences were found with vaccine strains. Ten G1P[8] strains sequenced for the VP4 gene had 91-93% nucleotide and 92-96% amino acid identity with Rotateq vaccine P[8]). Rotarix vaccine VP4 had 89-91% nucleotide and 90-92% amino acid identity. Our findings indicate genetic variability of rotavirus strains circulating in the region and are significant, given the introduction of rota vaccination in the State.
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Affiliation(s)
- Eileena Mohanty
- Viral Diagnostic and Research Laboratory, Regional Medical Research Centre, Indian Council of Medical Research, Bhubaneswar 751023, Odisha, India
| | - Bhagirathi Dwibedi
- Viral Diagnostic and Research Laboratory, Regional Medical Research Centre, Indian Council of Medical Research, Bhubaneswar 751023, Odisha, India.
| | - S K Kar
- Viral Diagnostic and Research Laboratory, Regional Medical Research Centre, Indian Council of Medical Research, Bhubaneswar 751023, Odisha, India
| | - A S Acharya
- Viral Diagnostic and Research Laboratory, Regional Medical Research Centre, Indian Council of Medical Research, Bhubaneswar 751023, Odisha, India
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