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Mejías-Molina C, Pico-Tomàs A, Martínez-Puchol S, Itarte M, Torrell H, Canela N, Borrego CM, Corominas L, Rusiñol M, Bofill-Mas S. Wastewater-based epidemiology applied at the building-level reveals distinct virome profiles based on the age of the contributing individuals. Hum Genomics 2024; 18:10. [PMID: 38303015 PMCID: PMC10832175 DOI: 10.1186/s40246-024-00580-1] [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: 11/21/2023] [Accepted: 01/24/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Human viruses released into the environment can be detected and characterized in wastewater. The study of wastewater virome offers a consolidated perspective on the circulation of viruses within a population. Because the occurrence and severity of viral infections can vary across a person's lifetime, studying the virome in wastewater samples contributed by various demographic segments can provide valuable insights into the prevalence of viral infections within these segments. In our study, targeted enrichment sequencing was employed to characterize the human virome in wastewater at a building-level scale. This was accomplished through passive sampling of wastewater in schools, university settings, and nursing homes in two cities in Catalonia. Additionally, sewage from a large urban wastewater treatment plant was analysed to serve as a reference for examining the collective excreted human virome. RESULTS The virome obtained from influent wastewater treatment plant samples showcased the combined viral presence from individuals of varying ages, with astroviruses and human bocaviruses being the most prevalent, followed by human adenoviruses, polyomaviruses, and papillomaviruses. Significant variations in the viral profiles were observed among the different types of buildings studied. Mamastrovirus 1 was predominant in school samples, salivirus and human polyomaviruses JC and BK in the university settings while nursing homes showed a more balanced distribution of viral families presenting papillomavirus and picornaviruses and, interestingly, some viruses linked to immunosuppression. CONCLUSIONS This study shows the utility of building-level wastewater-based epidemiology as an effective tool for monitoring the presence of viruses circulating within specific age groups. It provides valuable insights for public health monitoring and epidemiological studies.
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Affiliation(s)
- Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain.
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | | | - Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Helena Torrell
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Núria Canela
- Centre for Omic Sciences (COS), Joint Unit Universitat Rovira I Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Eurecat, Centre Tecnològic de Catalunya, Reus, Catalonia, Spain
| | - Carles M Borrego
- Catalan Institute for Water Research (ICRA), Girona, Spain
- Group of Molecular Microbial Ecology, Institute of Aquatic Ecology, University of Girona, Girona, Catalonia, Spain
| | | | - Marta Rusiñol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Barcelona, Catalonia, Spain
- The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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Rubio-Mora E, Carrascoso GR, Rodríguez JG. Sapovirus infection as another cause of persistent viral diarrhea: case series and review of the literature. Eur J Clin Microbiol Infect Dis 2024; 43:55-59. [PMID: 37924444 DOI: 10.1007/s10096-023-04695-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023]
Abstract
Human sapovirus (HuSaV) is a common cause of gastroenteritis worldwide and is responsible for approximately 4% of acute gastroenteritis episodes in Europe. As reported with norovirus, patients with immunocompromised states are at increased risk of developing HuSaV infection, which can lead to persistent diarrhea and chronic viral shedding in some individuals. Chronic infections are incompletely investigated in these patients, and, due to the lack of specific treatment for HuSaV infection, different clinical approaches were carried out in order to provide further evidence on clinical evolution of these patients with different treatments. In this retrospective study, we report five immunocompromised pediatric patients with recurrent diarrhea caused by HuSaV and long-term viral shedding. Stool samples were analyzed by real-time PCR and tested for enteropathogenic viruses and bacteria and protozoa. Among transplant recipients, reduction of immunosuppressant therapy led to clinical improvement and relief of symptoms, maintaining a balance between managing the infection and preventing graft rejection. Nitazoxanide for 14 days was only used in one of these patients, showing to be an effective therapy to achieve reduction in time to resolution of symptoms. Neither nitazoxanide nor modification of immunosuppressant therapy could avoid recurrences. Further investigations are needed to develop new approaches that can both clear the infection and avoid persistent diarrhea in these patients.
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Affiliation(s)
- Eduardo Rubio-Mora
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046, Madrid, Spain.
| | - Guillermo Ruiz Carrascoso
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046, Madrid, Spain
| | - Julio García Rodríguez
- Servicio de Microbiología y Parasitología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046, Madrid, Spain
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Jung S, Yeo D, Wang Z, Woo S, Seo Y, Hossain MI, Rhee MS, Choi C. Improvement of nested reverse transcription-polymerase chain reaction (RT-PCR) with high specificity and sensitivity detection of sapovirus in food matrix. J Virol Methods 2022; 309:114609. [PMID: 36028003 DOI: 10.1016/j.jviromet.2022.114609] [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: 07/14/2022] [Revised: 08/17/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022]
Abstract
Sapovirus (SaV) is a causative agent of human gastroenteritis in both community outbreaks and sporadic cases worldwide. Shellfish accumulate a variety of pathogens during filter feeding. In particular, the contamination of shellfish by SaV has caused several outbreaks. As reported previously, nested RT-PCR (nRT-PCR) has been widely used in clinical samples, but has not proven suitable for food samples, such as oysters. This study aimed to identify a primer set for the detection of SaV with high specificity and sensitivity in food samples. To accomplish this, primers were improved in RNA-dependent RNA polymerase (RdRp) regions of SaV whole genome sequences. The sensitivity of the improved nRT-PCR was 100-1000 times higher than that of previous nRT-PCR and > 10 times higher than that of the previous real-time RT-PCR assay. Notably, cross-reaction with other viruses or food matrices was not observed by the specificity test. This study improved the reliable primer set to detect SaV in various food matrices with high sensitivity.
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Affiliation(s)
- Soontag Jung
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Daseul Yeo
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Zhaoqi Wang
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Seoyoung Woo
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Yeeun Seo
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Md Iqbal Hossain
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Changsun Choi
- Department of Food and Nutrition, Chung-Ang University, 4726 Seodongdaero, Daedeok-myeon, Anseong-si, Gyeonggi-do 17546, Republic of Korea.
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Gelaw A, Liebert UG. Molecular Detection of Enteric Viruses in Under-Five Children with Diarrhea in Debre Tabor, Northwest Ethiopia. Infect Drug Resist 2022; 15:1981-1994. [PMID: 35480057 PMCID: PMC9035461 DOI: 10.2147/idr.s364142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background Viral gastroenteritis belongs to the major public health problems of infant and children worldwide. The largest proportion of morbidity and mortality occurs in Sub-Saharan Africa. Purpose Aimed to assess the burden and genetic diversity of enteric viruses among children with diarrhea. Patients and Methods A cross-sectional study was undertaken from December 2015 to April 2016 in Debre Tabor. A total of thirty-eight children, who presented with diarrhea at Debre Tabor health centers, were included. Fecal samples were collected and screened for enteric viruses by RT-PCR. Data were analyzed using SPSS software. Descriptive summary techniques were used to display the findings. Results Out of thirty-eight children screened, 52.6% were positive for at least one enteric virus. Six (30.0%) of the children had mixed enteric virus infections. Human adenovirus (HAdV) 7 (18.4%) was predominant followed by noroviruses (NoVs) 5 (13.2%), enterovirus (EV) 5 (13.2%), rotavirus A (RVA) 4 (10.5%), human astrovirus (HAstV) 2 (5.3%), and human parechovirus (HPeV) 1 (2.6%). Overall, nineteen different types of enteric virus genotypes were identified. Diverse adenovirus within species A (HAdV-12,-31), B (HAdV-3), C (HAdV-2), and F (HAdV-4) were detected. Norovirus II (GII.4 and GII.6) and norovirus I (GI.2, GI.3, and GI.5) genotypes were found. Sapovirus genotypes within genogroup II (GII.1, GII.5, and GII.6) were identified. Wild-type rotavirus G9 and P[8] genotypes were detected in one of the rotavirus positive samples. Non-polio enteroviruses within species A (coxsackie A virus (CAV) 5, CAV6, and CAV14) and C (enterovirus (EV-C) 99) were also identified. In two of the fecal samples classic HAstV-2 was detected. Conclusion Diverse enteric viruses were detected in fecal samples from under-five children with diarrhea. The detection of heterogeneous enteric viruses in this small data set highlights the need for extended multicenter studies to describe the burden and genetic diversity of enteric virus.
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Affiliation(s)
- Aschalew Gelaw
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences University of Gondar, Gondar, Ethiopia
- Institute of Virology, Leipzig University, Leipzig, Germany
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, Leipzig, Germany
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Makhaola K, Lechiile K, Moyo S, Goldfarb DM, Pernica JM, Kebaabetswe LP. Molecular Characterization of Sapovirus from Children with Gastroenteritis in Botswana. JOURNAL OF CLINICAL VIROLOGY PLUS 2022. [DOI: 10.1016/j.jcvp.2022.100077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Zweigart MR, Becker-Dreps S, Bucardo F, González F, Baric RS, Lindesmith LC. Serological Humoral Immunity Following Natural Infection of Children with High Burden Gastrointestinal Viruses. Viruses 2021; 13:2033. [PMID: 34696463 PMCID: PMC8538683 DOI: 10.3390/v13102033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 12/14/2022] Open
Abstract
Acute gastroenteritis (AGE) is a major cause of morbidity and mortality worldwide, resulting in an estimated 440,571 deaths of children under age 5 annually. Rotavirus, norovirus, and sapovirus are leading causes of childhood AGE. A successful rotavirus vaccine has reduced rotavirus hospitalizations by more than 50%. Using rotavirus as a guide, elucidating the determinants, breath, and duration of serological antibody immunity to AGE viruses, as well as host genetic factors that define susceptibility is essential for informing development of future vaccines and improving current vaccine candidates. Here, we summarize the current knowledge of disease burden and serological antibody immunity following natural infection to inform further vaccine development for these three high-burden viruses.
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Affiliation(s)
- Mark R. Zweigart
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA; (M.R.Z.); (S.B.-D.)
| | - Sylvia Becker-Dreps
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA; (M.R.Z.); (S.B.-D.)
- Department of Family Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Filemón Bucardo
- Department of Microbiology, National Autonomous University of Nicaragua, León 21000, Nicaragua; (F.B.); (F.G.)
| | - Fredman González
- Department of Microbiology, National Autonomous University of Nicaragua, León 21000, Nicaragua; (F.B.); (F.G.)
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA; (M.R.Z.); (S.B.-D.)
| | - Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA; (M.R.Z.); (S.B.-D.)
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7
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Sapoviruses detected from acute gastroenteritis outbreaks and hospitalized children in Taiwan. J Formos Med Assoc 2021; 120:1591-1601. [DOI: 10.1016/j.jfma.2020.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 10/11/2020] [Accepted: 11/25/2020] [Indexed: 12/17/2022] Open
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Abstract
PURPOSE OF REVIEW Sapovirus, a genus in the Caliciviridae family alongside norovirus, is increasingly recognized as an important cause of childhood diarrhea. Some challenges exist in our ability to better understand sapovirus infections, including the inability to grow sapovirus in cell culture, which has hindered diagnosis and studies of immunity. Another challenge is that individuals with sapovirus infection are commonly coinfected with other enteric pathogens, complicating our ability to attribute the diarrhea episode to a single pathogen. RECENT FINDINGS Development of molecular methods for sapovirus detection has increased our ability to measure disease prevalence. The prevalence of sapovirus varies between 1 and 17% of diarrhea episodes worldwide, with the highest burden in young children and older adults. Further, epidemiological studies have used novel approaches to account for the presence of coinfections with other enteric pathogens; one multisite cohort study of children under two years of age found that sapovirus had the second-highest attributable incidence among all diarrheal pathogens studied. SUMMARY Especially in settings where rotavirus vaccines have been introduced, efforts to reduce the overall burden of childhood diarrhea should focus on the reduction of sapovirus transmission and disease burden.
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de Oliveira-Tozetto S, Santiso-Bellón C, Ferrer-Chirivella JM, Navarro-Lleó N, Vila-Vicent S, Rodríguez-Díaz J, Buesa J. Epidemiological and Genetic Characterization of Sapovirus in Patients with Acute Gastroenteritis in Valencia (Spain). Viruses 2021; 13:v13020184. [PMID: 33530573 PMCID: PMC7911121 DOI: 10.3390/v13020184] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/16/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023] Open
Abstract
Sapovirus is a common cause of acute gastroenteritis in all age groups. Sapovirus infections are seldom investigated in Spain, and its epidemiology in the country is not well known. The use of molecular diagnostic procedures has allowed a more frequent detection of sapoviruses in patients with diarrhea. A total of 2545 stool samples from patients with acute gastroenteritis attended from June 2018 to February 2020 at the Clinic University Hospital in Valencia, Spain, were analyzed by reverse transcription (RT) and real-time multiplex PCR (RT-PCR) to investigate the etiology of enteric infections. Sapovirus was the second enteric virus detected with a positive rate of 8%, behind norovirus (12.2%) and ahead of rotavirus (7.1%), astrovirus (4.9%) and enteric adenoviruses (2.9%). Most sapovirus infections occurred in infants and young children under 3 years of age (74%) with the highest prevalence in autumn and early winter. Coinfections were found in 25% of the patients with sapovirus diarrhea, mainly with other enteric viruses. Genotyping demonstrated the circulation of seven different genotypes during the study period, with a predominance of genotypes GI.1, GI.2, and GII.1. Phylogenetic analysis showed that genogroup GII strains form a cluster separated from genogroup GI and GV, being genotype GV.1 strains related to genotype GI.1 and GI.2 strains.
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Affiliation(s)
- Sibele de Oliveira-Tozetto
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Cristina Santiso-Bellón
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Correspondence: (C.S.-B.); (J.B.)
| | - Josep M. Ferrer-Chirivella
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
| | - Noemi Navarro-Lleó
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Susana Vila-Vicent
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, 46010 Valencia, Spain; (S.d.O.-T.); (N.N.-L.); (S.V.-V.); (J.R.-D.)
- Microbiology Service, INCLIVA Health Research Institute, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain;
- Correspondence: (C.S.-B.); (J.B.)
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Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions. Viruses 2020; 12:v12050516. [PMID: 32392864 PMCID: PMC7290424 DOI: 10.3390/v12050516] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/22/2022] Open
Abstract
Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.
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Sapovirus detection and quantification in fecal samples from allogeneic hematopoietic stem cell transplant recipients. Virusdisease 2020; 31:374-377. [PMID: 32904858 DOI: 10.1007/s13337-020-00583-1] [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: 12/09/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Sapovirus are important agents of acute gastroenteritis (AGE) and they are associated with outbreaks and sporadic cases worldwide. They infect people of all ages, but mainly children, the elderly and immunocompromised individuals are affected. The aim of this study was investigate sapovirus and to determine viral loads in fecal samples from patient undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). Fecal samples were submitted to extraction of the genetic material using a commercial kit, and RT-qPCR TaqMan was used for sapovirus screening and determination of viral loads, using a standard curve with serial dilutions of a recombinant plasmid. Positive samples were sequence by Sanger method. Sapovirus was detected in one patient, 5.3% (1/19). Viral excretion lasted for 16 days. Viral load varied from 1.73 × 106 to 8.97 × 106 GC/g. One of the positive samples was characterized as GI.1 genotype. This is the first study to determine sapovirus loads in samples from allo-HSCT and to identify GI.1 genotype in immunocompromised patients.
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Makhaola K, Moyo S, Kebaabetswe LP. Distribution and Genetic Variability of Sapoviruses in Africa. Viruses 2020; 12:v12050490. [PMID: 32349380 PMCID: PMC7291139 DOI: 10.3390/v12050490] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
In this review, we describe the distribution and genetic diversity of sapoviruses detected among humans, animals and the environment in African countries. Databases were searched for studies conducted in African countries and published between Jan 2005 and Mar 2019. Only studies where RT- PCR was used for initial detection were included in the systematic review. We identified 27 studies from 14 African countries with 18 focused on human sapoviruses, two on animal sapoviruses and seven on sapoviruses observed in the environment. Samples. The overall estimated pooled prevalence of human sapovirus infections among symptomatic and asymptomatic individuals was similar at 5.0% (95% Confidence Interval (CI): 3.0–7.0) and 2.0% (95% CI: 1.0–3.0), respectively. In environmental samples sapovirus detection rates ranged from 0% to 90% while in animal studies it was 1.7% to 34.8%. Multiple causes of gastroenteritis, sensitivity of detection method used, diversity of sapovirus strains and rotavirus vaccine coverage rate are some of the factors that could have contributed to the wide range of sapovirus detection rates that were reported. The studies reported human genogroups GI, GII, and GIV, with genogroup GI being the most prevalent. Some potential novel strains were detected from animal samples. Most studies genotyped a small portion of either the capsid and/or polymerase region. However, this is a limitation as it does not allow for detection of recombinants that occur frequently in sapoviruses. More studies with harmonized genotyping protocols that cover longer ranges of the sapovirus genome are needed to provide more information on the genomic characterization of sapoviruses circulating in African countries. Further investigations on animal to human transmission for sapoviruses are needed as inter-species transmissions have been documented for other viruses.
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Affiliation(s)
- Kgomotso Makhaola
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology & Infectious Diseases, Harvard T.H Chan School of Public Health, Boston, MA 02115, USA
| | - Lemme P. Kebaabetswe
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
- Correspondence:
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Molecular detection and characterisation of sapoviruses and noroviruses in outpatient children with diarrhoea in Northwest Ethiopia. Epidemiol Infect 2020; 147:e218. [PMID: 31364546 PMCID: PMC6625200 DOI: 10.1017/s0950268819001031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Childhood morbidity and mortality of diarrhoeal diseases are high, particularly in low-income countries and noroviruses and sapoviruses are among the most frequent causes worldwide. Their epidemiology and diversity remain not well studied in many African countries. To assess the positivity rate and the diversity of sapoviruses and noroviruses in Northwest Ethiopia, during November 2015 and April 2016, a total of 450 faecal samples were collected from outpatient children aged <5 years who presented with diarrhoea. Samples were screened for noroviruses and sapoviruses by real-time RT-PCR. Partial VP1 genes were sequenced, genotyped and phylogenetically analysed. Norovirus and sapovirus stool positivity rate was 13.3% and 10.0%, respectively. Noroviruses included GII.4 (35%), GII.6 (20%), GII.17 (13.3%), GII.10 (10%), GII.2 (6.7%), GII.16 (5%), GII.7 (3.3%), GII.9, GII.13, GII.20 and GI.3 (1.7% each) strains. For sapoviruses, GI.1, GII.1 (20.0% each), GII.6 (13.3%), GI.2 (8.9%), GII.2 (11.1%), GV.1 (8.9%), GIV.1 (6.7%), GI.3 and GII.4 (2.2% each) genotypes were detected. This study demonstrates a high genetic diversity of noroviruses and sapoviruses in Northwest Ethiopia. The positivity rate in stool samples from young children with diarrhoea was high for both caliciviruses. Continued monitoring is recommended to identify trends in genetic diversity and seasonal variations.
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Mann P, Pietsch C, Liebert UG. Genetic Diversity of Sapoviruses among Inpatients in Germany, 2008-2018. Viruses 2019; 11:v11080726. [PMID: 31394867 PMCID: PMC6723979 DOI: 10.3390/v11080726] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/28/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022] Open
Abstract
Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: (1) a selection of 342 diarrheal stools collected from inpatient children during 2008−2009, and (2) 5555 stool samples collected during 2010–2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.
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Affiliation(s)
- Pia Mann
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany.
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
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