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Mogotsi MT, Ogunbayo AE, Bester PA, O'Neill HG, Nyaga MM. Longitudinal analysis of the enteric virome in paediatric subjects from the Free State Province, South Africa, reveals early gut colonisation and temporal dynamics. Virus Res 2024; 346:199403. [PMID: 38776984 PMCID: PMC11169482 DOI: 10.1016/j.virusres.2024.199403] [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: 01/31/2024] [Revised: 04/23/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
The gut of healthy neonates is devoid of viruses at birth, but rapidly becomes colonised by normal viral commensals that aid in important physiological functions like metabolism but can, in some instances, result in gastrointestinal illnesses. However, little is known about how this colonisation begins, its variability and factors shaping the gut virome composition. Thus, understanding the development, assembly, and progression of enteric viral communities over time is key. To explore early-life virome development, metagenomic sequencing was employed in faecal samples collected longitudinally from a cohort of 17 infants during their first six months of life. The gut virome analysis revealed a diverse and dynamic viral community, formed by a richness of different viruses infecting humans, non-human mammals, bacteria, and plants. Eukaryotic viruses were detected as early as one week of life, increasing in abundance and diversity over time. Most of the viruses detected are commonly associated with gastroenteritis and include members of the Caliciviridae, Picornaviridae, Astroviridae, Adenoviridae, and Sedoreoviridae families. The most common co-occurrences involved asymptomatic norovirus-parechovirus, norovirus-sapovirus, sapovirus-parechovirus, observed in at least 40 % of the samples. Majority of the plant-derived viruses detected in the infants' gut were from the Virgaviridae family. This study demonstrates the first longitudinal characterisation of the gastrointestinal virome in infants, from birth up to 6 months of age, in sub-Saharan Africa. Overall, the findings from this study delineate the composition and variability of the healthy infants' gut virome over time, which is a significant step towards understanding the dynamics and biogeography of viral communities in the infant gut.
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Affiliation(s)
- Milton Tshidiso Mogotsi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Ayodeji Emmanuel Ogunbayo
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Phillip Armand Bester
- Division of Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Hester Gertruida O'Neill
- Department of Microbiology and Biochemistry, Faculty of Natural and Agricultural Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
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Yokoyama M, Doan YH, Motomura K, Sato H, Oka T. Strong evolutionary constraints against amino acid changes in the P2 subdomain of sapovirus GI.1 capsid protein VP1. Biochem Biophys Res Commun 2024; 710:149878. [PMID: 38608492 DOI: 10.1016/j.bbrc.2024.149878] [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: 03/02/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024]
Abstract
Sapovirus (SaV) is a nonenveloped RNA virus that causes acute gastroenteritis in humans. Although SaV is a clinically important pathogen in children, an effective vaccine is currently unavailable. The capsid protein VP1 of SaVs forms the outer shell of the virion and is highly diverse, as often seen in the virion-surface proteins of RNA viruses, creating an obstacle for vaccine development. We here report a unique phenomenon pertaining to the variation of SaV VP1. Phylogenetic and information entropy analyses using full-length VP1 sequences from a public database consistently showed that the amino acid sequences of the VP1 protein have been highly conserved over more than 40 years in the major epidemic genotype GI.1 but not in GI.2. Structural modeling showed that even the VP1 P2 subdomain, which is arranged on the outermost shell of the virion and presumably exposed to anti-SaV antibodies, remained highly homogeneous in GI.1 but not in GI.2. These results suggest strong evolutionary constraints against amino acid changes in the P2 subdomain of the SaV GI.1 capsid and illustrate a hitherto unappreciated mechanism, i.e., preservation of the VP1 P2 subdomain, involved in SaV survival. Our findings could have important implications for the development of an anti-SaV vaccine.
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Affiliation(s)
- Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yen Hai Doan
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazushi Motomura
- Osaka Institute of Public Health, Osaka, Japan; Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Thailand; Research Institute of Microbial Diseases, Osaka University, Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama-shi, Tokyo 208-0011, Japan.
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Pajuelo MJ, Noazin S, Cabrera L, Toledo A, Velagic M, Arias L, Ochoa M, Moulton LH, Saito M, Gilman RH, Chakraborty S. Epidemiology of enterotoxigenic Escherichia coli and impact on the growth of children in the first two years of life in Lima, Peru. Front Public Health 2024; 12:1332319. [PMID: 38584932 PMCID: PMC10995271 DOI: 10.3389/fpubh.2024.1332319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024] Open
Abstract
Background Enterotoxigenic E. coli (ETEC) is a leading cause of diarrheal morbidity and mortality in children, although the data on disease burden, epidemiology, and impact on health at the community level are limited. Methods In a longitudinal birth cohort study of 345 children followed until 24 months of age in Lima, Peru, we measured ETEC burden in diarrheal and non-diarrheal samples using quantitative PCR (LT, STh, and STp toxin genes), studied epidemiology and measured anthropometry in children. Results About 70% of children suffered from one or more ETEC diarrhea episodes. Overall, the ETEC incidence rate (IR) was 73 per 100 child-years. ETEC infections began early after birth causing 10% (8.9-11.1) ETEC-attributable diarrheal burden at the population level (PAF) in neonates and most of the infections (58%) were attributed to ST-ETEC [PAF 7.9% (1.9-13.5)] and LT + ST-ETEC (29%) of which all the episodes were associated with diarrhea. ETEC infections increased with age, peaking at 17% PAF (4.6-27.7%; p = 0.026) at 21 to 24 months. ST-ETEC was the most prevalent type (IR 32.1) with frequent serial infections in a child. The common colonization factors in ETEC diarrhea cases were CFA/I, CS12, CS21, CS3, and CS6, while in asymptomatic ETEC cases were CS12, CS6 and CS21. Only few (5.7%) children had repeated infections with the same combination of ETEC toxin(s) and CFs, suggested genotype-specific immunity from each infection. For an average ETEC diarrhea episode of 5 days, reductions of 0.060 weight-for-length z-score (0.007 to 0.114; p = 0.027) and 0.061 weight-for-age z-score (0.015 to 0.108; p = 0.009) were noted in the following 30 days. Conclusion This study showed that ETEC is a significant pathogen in Peruvian children who experience serial infections with multiple age-specific pathotypes, resulting in transitory growth impairment.
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Affiliation(s)
- Monica J. Pajuelo
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Sassan Noazin
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | | | - Angie Toledo
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirza Velagic
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Lucero Arias
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayra Ochoa
- Laboratorio Microbiología Molecular – Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Lawrence H. Moulton
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Subhra Chakraborty
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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Kumazaki M, Usuku S. Influence of herd immunity on norovirus: a long-term field study of repeated viral gastroenteritis outbreaks at the same facilities. BMC Infect Dis 2023; 23:265. [PMID: 37101126 PMCID: PMC10132420 DOI: 10.1186/s12879-023-08251-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 04/13/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND Viral acute gastroenteritis (AG) is detected worldwide annually. Outbreaks caused by viruses associated with gastroenteritis have been reported repeatedly at the same facilities in Yokohama, Japan over several years. We investigated the statuses of these repeated outbreaks to consider herd immunity at the facility level. METHODS Between September 2007 and August 2017, 1459 AG outbreaks were reported at 1099 facilities. Stool samples were collected for virological testing, and the norovirus gene was amplified and sequenced to determine the genotype using the N-terminal region of the capsid. RESULTS The outbreaks were caused by norovirus, sapovirus, rotavirus A, and rotavirus C. Norovirus was consistently predominant over the 10-year period. Of 1099 facilities, 227 reported multiple outbreaks, of which norovirus-only combinations accounted for 76.2%. More outbreaks were due to different genotype combinations than the same genotype combinations. For facilities that experienced two norovirus outbreaks, the average interval between outbreaks was longer for groups with the same combinations than for groups with different genogroup or genotype combinations, although no statistically significant differences were observed. At 44 facilities, outbreaks occurred repeatedly during the same AG season, and most exhibited combinations of different norovirus genotypes or viruses. Among 49 combinations with the same norovirus genotype at the same facilities over 10 years, the most prevalent genotypes were combinations of genogroup II genotype 4 (GII.4), followed by GII.2, GII.6, GII.3, GII.14, and GI.3. The mean interval between outbreaks was 31.2 ± 26.8 months for all combinations, and the mean intervals were longer for non-GII.4 genotype cases than for GII.4 cases, and statistically significant differences were observed (t-test, P < 0.05). Additionally, these average intervals were longer for kindergarten/nursery schools and primary schools than for nursing homes for older adults (t-test, P < 0.05). CONCLUSIONS Repeated AG outbreaks at the same facilities in Yokohama during the 10-year study period included mainly norovirus combinations. Herd immunity at the facility level was maintained for at least the same AG season. Norovirus genotype-specific herd immunity was maintained for an average of 31.2 months during the study period, and these intervals differed depending on genotype.
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Affiliation(s)
- Makoto Kumazaki
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan.
| | - Shuzo Usuku
- Microbiological Testing and Research Division, Yokohama City Institute of Public Health, 2-7-1 Tomiokahigashi, Kanazawa-Ku, Yokohama, Kanagawa, 236-0051, Japan
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González F, Diez-Valcarce M, Reyes Y, Vielot NA, Toval-Ruíz C, Gutiérrez L, Zepeda O, Cuadra EC, Blandón P, Browne H, Bowman NM, Vílchez S, Vinjé J, Becker-Dreps S, Bucardo F. Timing and genotype distribution of symptomatic and asymptomatic sapovirus infections and re-infections in a Nicaraguan birth cohort. Clin Microbiol Infect 2023; 29:540.e9-540.e15. [PMID: 36423864 PMCID: PMC10077563 DOI: 10.1016/j.cmi.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022]
Abstract
OBJECTIVES To characterize the timing and genotype distribution of symptomatic and asymptomatic sapovirus infections and re-infections in a Nicaraguan birth cohort. METHODS Infants (N = 444) were enrolled at 10-14 days of life and observed weekly until 2 years of age. Stool samples were collected for each acute gastroenteritis (AGE) episode, and routine stool samples were collected monthly. Stool samples were tested for sapovirus using RT-qPCR, and positive samples were genotyped. RESULTS A total of 348 children completed 2 years of AGE weekly surveillance; 93 (26.7%) of them experienced sapovirus AGE. Most infections occurred after 5 months of age and mainly during the second year of life (62.4%, 58/93) and early in the rainy season. Sapovirus screening in all stools from a subset of 67 children who consistently provided samples showed sapovirus infections in 91 of 330 (27.6%) AGE episodes and in 39 of 1350 (2.9%) routine stools. In this subset, the median age at the first sapovirus AGE was 11.2 months (95% CI, 9.3-15.9 months); 38 of 67 (57%) children experienced re-infections, 19 symptomatic and 19 asymptomatic. On average, sapovirus re-infections were reported 7.2 months after symptomatic and 5.3 months after asymptomatic infections. Genogroup GI (64%, 69/108) was the most common detected. Sapovirus GI.1 was more frequently detected in AGE stool samples than in routine stool samples (47.2%, 43/91 vs. 25.6%, 10/39; p 0.005), and re-infection with the same genotype was uncommon. DISCUSSION The first sapovirus infections occurred at approximately 11 months of age, whereas the median time to symptomatic re-infection was 7.2 months. Re-infections with the same sapovirus genotype were rare during 2 years of life suggesting genotype-specific protection after natural infection.
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Affiliation(s)
- Fredman González
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Marta Diez-Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Yaoska Reyes
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Nadja A Vielot
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christian Toval-Ruíz
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Lester Gutiérrez
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Omar Zepeda
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Edwing Centeno Cuadra
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Patricia Blandón
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Hannah Browne
- National Foundation for the Centers for Disease Control and Prevention Inc., Atlanta, GA, USA
| | - Natalie M Bowman
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Samuel Vílchez
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua
| | - Jan Vinjé
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Sylvia Becker-Dreps
- Department of Family Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Filemón Bucardo
- Department of Microbiology, National Autonomous University of Nicaragua - León, León, Nicaragua.
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El-Heneidy A, Ware RS, Lambert SB, Grimwood K. Sapovirus Infections in an Australian Community-Based Healthy Birth Cohort During the First 2 Years of Life. Clin Infect Dis 2023; 76:1043-1049. [PMID: 36310530 PMCID: PMC10029984 DOI: 10.1093/cid/ciac861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/17/2022] [Accepted: 10/27/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Sapovirus is an important cause of acute gastroenteritis (AGE) in young children. However, knowledge gaps remain in community settings. We investigated the epidemiology, disease characteristics, and healthcare use associated with sapovirus infections in Australian children during their first 2 years of life. METHODS Children in the Brisbane-based Observational Research in Childhood Infectious Diseases birth cohort provided daily gastrointestinal symptoms (vomiting/loose stools), weekly stool swabs, and healthcare data until age 2 years. Swabs were batch-tested for sapovirus using real-time polymerase chain reaction assays. Incidence rates and estimates of associations were calculated. RESULTS Overall, 158 children returned 11 124 swabs. There were 192 sapovirus infection episodes. The incidence rate in the first 2 years of life was 0.89 infections per child-year (95% confidence interval [CI], .76-1.05), and the symptomatic incidence rate was 0.26 episodes per child-year (95% CI, .17-.37). Age ≥6 months, the fall season, and childcare attendance increased disease incidence significantly. Fifty-four of the 180 (30%) infections with linked symptom diaries were symptomatic, with 72% recording vomiting and 48% diarrhea. Prior infection reduced risk of further infections (adjusted hazard ratio, 0.70 [95% CI, .54-.81]) in the study period. Viral loads were higher and viral shedding duration was longer in symptomatic than asymptomatic children. Twenty-three (43%) symptomatic episodes required healthcare, including 6 emergency department presentations and 2 hospitalizations. CONCLUSIONS Sapovirus infections are common in Australian children aged 6-23 months. Efforts to reduce childhood AGE after the global rollout of rotavirus vaccines should include sapovirus where estimates of its incidence in communities will be crucial.
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Affiliation(s)
- Asmaa El-Heneidy
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Robert S Ware
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
| | - Stephen B Lambert
- UQ Centre for Clinical Research, The University of Queensland, Herston, Australia
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, Westmead, New South Wales, Australia
| | - Keith Grimwood
- School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Queensland, Australia
- Departments of Paediatrics and Infectious Diseases, Gold Coast Health, Gold Coast, Queensland, Australia
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Rouhani S, Peñataro Yori P, Paredes Olortegui M, Lima AA, Ahmed T, Mduma ER, George A, Samie A, Svensen E, Lima I, Mondal D, Mason CJ, Kalam A, Guerrant RL, Lang D, Zaidi A, Kang G, Houpt E, Kosek MN. The Epidemiology of Sapovirus in the Etiology, Risk Factors, and Interactions of Enteric Infection and Malnutrition and the Consequences for Child Health and Development (MAL-ED) Study: Evidence of Protection Following Natural Infection. Clin Infect Dis 2022; 75:1334-1341. [PMID: 36094137 PMCID: PMC9555839 DOI: 10.1093/cid/ciac165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Sapovirus is one of the principal agents of acute viral enteritis in children. Because it has not been routinely included in diagnostic evaluations, the epidemiology and natural history remain poorly described. METHODS A birth cohort of 1715 children from 8 countries contributed surveillance samples (n = 35 620) and diarrheal specimens (n = 6868) from 0 to 24 months of age. Sapovirus was detected by quantitative polymerase chain reaction concurrently to other enteropathogens using multiarray cards. Logistic regression was used to identify risk factors, and longitudinal models were employed to estimate incidence rates and evaluate evidence of protective immunity. RESULTS Sapovirus was detected in 24.7% (n = 1665) of diarrheal stools and 12.8% (n = 4429) of monthly surveillance samples. More than 90% of children were infected and 60% experienced sapovirus diarrhea in the first 2 years of life. Breastfeeding and higher socioeconomic status were associated with reduced incidence of infection and illness. Specimens with sapovirus detected had an increased odds of coinfection with rotavirus (odds ratio [OR], 1.6 [95% confidence interval {CI}, 1.3-2.0]), astrovirus (OR, 1.5 [95% CI, 1.3-1.7]), adenovirus (OR, 1.3 [95% CI, 1.1-1.5]), and Shigella (OR, 1.4 [95% CI, 1.3-1.6]). Prior infection with sapovirus conferred a risk reduction of 22% for subsequent infection (hazard ratio [HR], 0.78 [95% CI, .74-.85]) and 24% for subsequent diarrhea (95% CI, 11.0%-35.0%; HR, 0.76). CONCLUSIONS Sapovirus is a common cause of early childhood diarrhea. Further research on coinfections is warranted. Evidence of acquired immunity was observed even in the absence of genotype-specific analysis for this pathogen of known genetic diversity.
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Affiliation(s)
- Saba Rouhani
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA.,Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - Aldo A Lima
- Federal University of Ceará, Fortaleza, Brazil
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | | | | | | | - Ila Lima
- Federal University of Ceará, Fortaleza, Brazil
| | - Dinesh Mondal
- Nutrition Infection Interaction Research Group, Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Carl J Mason
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | | | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Dennis Lang
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USAand
| | - Anita Zaidi
- Enteric and Diarrheal Diseases Programme, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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Pitkänen O, Markkula J, Hemming-Harlo M. Sapovirus, Norovirus and Rotavirus Detections in Stool Samples of Hospitalized Finnish Children With and Without Acute Gastroenteritis. Pediatr Infect Dis J 2022; 41:e203-e207. [PMID: 35185141 PMCID: PMC8997665 DOI: 10.1097/inf.0000000000003493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/24/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Sapovirus, norovirus and rotavirus are major causes of childhood acute gastroenteritis (AGE) globally. Asymptomatic infections of these viruses have not been extensively studied. AIM To examine the prevalence and the genetic variations of sapovirus, norovirus and rotavirus in children with and without symptoms of AGE. METHODS We collected 999 stool samples from children under 16 years old from September 2009 to August 2011 at Tampere University Hospital, Finland. In total 442 children (44%) had symptoms of AGE and 557 patients (56%) had acute respiratory tract infection (ARTI) only. Samples were examined for sapovirus, norovirus and rotavirus using reverse transcription-polymerase chain reaction and the positive amplicons were sequenced. RESULTS Totally 54% and 14% of the patients in AGE and ARTI groups, respectively, tested positive. All viruses were more frequently detected in AGE patients than in ARTI patients (norovirus, 25% vs. 7.2%, respectively; rotavirus, 24% vs. 6.1%; sapovirus, 5.2% vs. 1.4%). In ARTI patients, the cases were seen most frequently during the first two years of life. Norovirus was the most detected pathogen in both groups with genogroup GII covering ≥97% of norovirus strains. Sapovirus was mostly detected in children under 18 months old without predominating genotype. Rotavirus was often detected after recent rotavirus vaccination and 18% and 88% of the strains were rotavirus vaccine-derived in AGE and ARTI groups, respectively. CONCLUSIONS We showed that the most common viruses causing gastroenteritis in children may be found in the stools of an asymptomatic carrier which may function as a potential reservoir for AGE.
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Affiliation(s)
| | - Jukka Markkula
- From the Vaccine Research Center
- Tampere Center for Child Health Research, Arvo Ylpön katu 34, University of Tampere, Finland
| | - Maria Hemming-Harlo
- Tampere Center for Child Health Research, Arvo Ylpön katu 34, University of Tampere, Finland
- The Pediatric Research Center, Biomedicum Haartmaninkatu 8, University of Helsinki, Finland
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9
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Li W, Li W, Li L, Guo Y, Chen J, Shang S, Mao J. Multiplex detection of eight different viral enteropathogens in clinical samples, combining RT-PCR technology with melting curve analysis. Virol J 2022; 19:61. [PMID: 35392937 PMCID: PMC8991609 DOI: 10.1186/s12985-022-01789-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 03/24/2022] [Indexed: 11/22/2022] Open
Abstract
Background Early and accurate identification of infection viruses among children can benefit the personalized medical treatment and management, and reduce the future occurrence of serious symptoms. Thus, it is critical to develop a high-throughput multiplex real-time RT-PCR method to improve the accuracy and efficiency in routine clinical lab tests. Methods We developed a real time RT-PCR combined with melting curve analysis (RRCMC) method for simultaneous detection of rotavirus A, B, C, norovirus GI and GII, adenovirus, astrovirus and sapovirus. Results Stool samples were collected from 160 children with acute diarrhea and tested by RRCMC assay. A total of 71 patients were tested positive with norovirus, adenovirus or rotavirus. The RRCMC assay has high specificity. There is no internal cross-reaction among the 8 diarrhea viruses and no cross-reaction of other commonly intestinal pathogens and human genome. The limit detection was ranged from 1 × 102 to 1 × 105 nucleic acid copies/ml for each diarrhea virus. Conclusion The RRCMC method is a suitable rapid clinical test for infectious viruses, with the advantages of high-throughput, low cost, high sensitivity and specificity.
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Affiliation(s)
- Wei Li
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, People's Republic of China
| | - Weiwei Li
- Jiangsu Bioperfectus Biotechnology Technologies Co, LTD, Taizhou, People's Republic of China
| | - Lin Li
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, People's Republic of China
| | - Yajun Guo
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, People's Republic of China
| | - Jie Chen
- Department of Gastroenterology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, People's Republic of China
| | - Shiqiang Shang
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, People's Republic of China.
| | - Jianhua Mao
- Department of Nephrology, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 3333 Binsheng road, Hangzhou, 310052, People's Republic of China.
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10
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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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11
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High Prevalence and Diversity of Caliciviruses in a Community Setting Determined by a Metagenomic Approach. Microbiol Spectr 2022; 10:e0185321. [PMID: 35196791 PMCID: PMC8865552 DOI: 10.1128/spectrum.01853-21] [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] [Indexed: 11/20/2022] Open
Abstract
We recently carried out a metagenomic study to determine the fecal virome of infants during their first year of life in a semirural community in Mexico. A total of 97 stool samples from nine children were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In this work, we describe the prevalence and incidence of caliciviruses in this birth cohort. We found that 54 (56%) and 24 (25%) of the samples were positive for norovirus and sapovirus sequence reads detected by next-generation sequencing, respectively. Potential infections were arbitrarily considered when at least 20% of the complete virus genome was determined. Considering only these samples, there were 3 cases per child/year for norovirus and 0.33 cases per child/year for sapovirus. All nine children had sequence reads related to norovirus in at least 2 and up to 10 samples, and 8 children excreted sapovirus sequence reads in 1 and up to 5 samples during the study. The virus in 35 samples could be genotyped. The results showed a high diversity of both norovirus (GI.3[P13], GI.5, GII.4, GII.4[P16], GII.7[P7], and GII.17[P17]) and sapovirus (GI.1, GI.7, and GII.4) in the community. Of interest, despite the frequent detection of caliciviruses in the stools, all children remained asymptomatic during the study. Our results clearly show that metagenomic studies in stools may reveal a detailed picture of the prevalence and diversity of gastrointestinal viruses in the human gut during the first year of life. IMPORTANCE Human caliciviruses are important etiological agents of acute gastroenteritis in children under 5 years of age. Several studies have characterized their association with childhood diarrhea and their presence in nondiarrheal stool samples. In this work, we used a next-generation sequencing approach to determine, in a longitudinal study, the fecal virome of infants during their first year of life. Using this method, we found that caliciviruses can be detected significantly more frequently than previously reported, providing a more detailed picture of the prevalence and genetic diversity of these viruses in the human gut during early life.
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Ballard SB, Requena D, Mayta H, Sanchez GJ, Oyola-Lozada MG, Colquechagua Aliaga FD, Cabrera L, Vittet Mondonedo MD, Taquiri C, Tilley CAPTDH, Simons CDRMP, Meza RA, Bern C, Saito M, Figueroa-Quintanilla DA, Gilman RH. Enteropathogen Changes After Rotavirus Vaccine Scale-up. Pediatrics 2022; 149:183843. [PMID: 34918158 PMCID: PMC9647525 DOI: 10.1542/peds.2020-049884] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES To inform next steps in pediatric diarrhea burden reduction by understanding the shifting enteropathogen landscape after rotavirus vaccine implementation. METHODS We conducted a case-control study of 1788 medically attended children younger than 5 years, with and without gastroenteritis, after universal rotavirus vaccine implementation in Peru. We tested case and control stools for 5 viruses, 19 bacteria, and parasites; calculated coinfection-adjusted attributable fractions (AFs) to determine pathogen-specific burdens; and evaluated pathogen-specific gastroenteritis severity using Clark and Vesikari scales. RESULTS Six pathogens were independently positively associated with gastroenteritis: norovirus genogroup II (GII) (AF 29.1, 95% confidence interval [CI]: 28.0-32.3), rotavirus (AF 8.9, 95% CI: 6.8-9.7), sapovirus (AF 6.3, 95% CI: 4.3-7.4), astrovirus (AF 2.8, 95% CI: 0.0-4.0); enterotoxigenic Escherichia coli heat stable and/or heat labile and heat stable (AF 2.4, 95% CI: 0.6-3.1), and Shigella spp. (AF 2.0, 95% CI: 0.4-2.2). Among typeable rotavirus cases, we most frequently identified partially heterotypic strain G12P[8] (54 of 81, 67%). Mean severity was significantly higher for norovirus GII-positive cases relative to norovirus GII-negative cases (Vesikari [12.7 vs 11.8; P < .001] and Clark [11.7 vs 11.4; P = .016]), and cases in the 6- to 12-month age range relative to cases in other age groups (Vesikari [12.7 vs 12.0; P = .0002] and Clark [12.0 vs 11.4; P = .0016]). CONCLUSIONS Norovirus is well recognized as the leading cause of pediatric gastroenteritis in settings with universal rotavirus vaccination. However, sapovirus is often overlooked. Both norovirus and sapovirus contribute significantly to the severe pediatric disease burden in this setting. Decision-makers should consider multivalent vaccine acquisition strategies to target multiple caliciviruses in similar countries after successful rotavirus vaccine implementation.
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Affiliation(s)
- Sarah-Blythe Ballard
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland,Naval Medical Research Unit No. 6, Callao, Peru,Address correspondence to Sarah-Blythe Ballard, MD, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, 615 N Wolfe St, Room W5515, Baltimore, MD 21205. E-mail:
| | - David Requena
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Holger Mayta
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru,Asociación Benéfica PRISMA, Lima, Peru
| | - Gerardo J. Sanchez
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria G. Oyola-Lozada
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Macarena D. Vittet Mondonedo
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Carmen Taquiri
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - CAPT Drake H. Tilley
- Naval Medical Research Unit No. 6, Callao, Peru,Fleet Surgical Team SEVEN, Okinawa, Japan
| | | | | | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Mayuko Saito
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru,Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Robert H. Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland,Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru,Asociación Benéfica PRISMA, Lima, Peru
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13
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Zaki MES, Shrief R, Hassan RH. Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020. F1000Res 2021; 10:123. [PMID: 34900224 PMCID: PMC8630562 DOI: 10.12688/f1000research.29991.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there is limited data on sapovirus in Egypt. . The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis <5 years in Mansoura, Egypt from January 2019 to February 2020 by reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: The cross-sectional study enrolled a 100 children <5 years who presented with acute gastroenteritis at an outpatient clinic in Mansoura, Egypt between January 2019 and February 2020. Clinical data, demographic data and a stool sample was collected from each child. Stools were screened by microscopy for parasites and culture methods for bacteria and excluded from the study if positive for either. Specimens were also screened for rotavirus by enzyme immune assays (EIA) and sapovirus by reverse transcription PCR. Results: The most frequently detected virus was rotavirus by ELISA 25% (25/100). RT-PCR detected sapovirus in 7% (7/100) of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt 42.9% (3/7). The main presenting symptoms were fever 71.4% (5/7) and vomiting 57.1% (4/7). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in five samples (5/7) , 71.4%, P=0.01. Conclusion: The present study highlights the emergence of sapovirus as a frequent pathogen associated with acute gastroenteritis in children. There is a need for a national survey program for the study of sapovirus among other pathogens associated with acute gastroenteritis for better management of such infection.
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Affiliation(s)
- Maysaa El Sayed Zaki
- Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
| | - Raghdaa Shrief
- Medical Microbioogy and Immunology Department, Faculty of Medicine, Damietta University, New Damietta, 34511, Egypt
| | - Rasha H Hassan
- Pediatrics Department, Faculty of Medicine, Mansoura University, Mansoura, 35516, Egypt
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14
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Pitkänen O, Markkula J, Hemming-Harlo M. A major decrease of viral acute gastroenteritis in hospitalized Finnish children as rotavirus returns as the most detected pathogen. Int J Infect Dis 2021; 114:273-278. [PMID: 34775115 DOI: 10.1016/j.ijid.2021.11.016] [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: 08/17/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 11/30/2022] Open
Abstract
INTRODUCTION We assessed the prevalence and circulating genotypes of rotavirus, norovirus and sapovirus in children. The results were compared to previous surveillance studies from 2006-2008, 2009-2011 and 2012-2014 with similar methodology and setting, covering the start of universal vaccination with RotaTeq® in 2009. METHODS Stool samples were collected from children aged <16 years with acute gastroenteritis at Tampere University Hospital, Finland, from January 1st, 2017 to December 31st, 2018. The samples were analyzed using reverse transcription PCR and positive amplicons were sequenced. RESULTS A total of 178 stool samples were collected from 214 children. Rotavirus was detected in 56 (32 %), norovirus in 48 (27 %) and sapovirus in 11 (6.3 %) stool samples. Rotavirus G9P[8] and G12P[8] were the most detected genotypes in vaccinated and unvaccinated children. GII.4 comprised 96 % of the norovirus detections. CONCLUSIONS The prevalence of all-cause acute gastroenteritis in a hospital-setting has decreased by 51 % from 2012-2014, and by 88 % from 2006-2008. Rotavirus returns as the most common cause of viral acute gastroenteritis in children, but the prevalence remains at a low level. No considerable changes were seen in the genotyping results of norovirus and sapovirus.
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Affiliation(s)
- Oskari Pitkänen
- Vaccine Research Center, Arvo Ylpön katu 34, 33014 Tampere University, Finland.
| | - Jukka Markkula
- Vaccine Research Center, Arvo Ylpön katu 34, 33014 Tampere University, Finland.
| | - Maria Hemming-Harlo
- Tampere Center for Child Health Research, Arvo Ylpön katu 34, 33014 Tampere University, Finland; Children's Hospital, 00014 University of Helsinki, Finland.
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15
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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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16
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Razizadeh MH, Khatami A, Zarei M. Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis. Rev Med Virol 2021; 32:e2302. [PMID: 34626019 DOI: 10.1002/rmv.2302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/11/2023]
Abstract
Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.
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Affiliation(s)
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Zarei
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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17
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Diez Valcarce M, Kambhampati AK, Calderwood LE, Hall AJ, Mirza SA, Vinjé J. Global distribution of sporadic sapovirus infections: A systematic review and meta-analysis. PLoS One 2021; 16:e0255436. [PMID: 34411109 PMCID: PMC8376006 DOI: 10.1371/journal.pone.0255436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/15/2021] [Indexed: 02/04/2023] Open
Abstract
Acute gastroenteritis (AGE), characterized by diarrhea and vomiting, is an important cause of global mortality, accounting for 9% of all deaths in children under five years of age. Since the reduction of rotavirus in countries that have included rotavirus vaccines in their national immunization programs, other viruses such as norovirus and sapovirus have emerged as more common causes of AGE. Due to widespread use of real-time RT-PCR testing, sapovirus has been increasingly reported as the etiologic agent in both AGE outbreaks and sporadic AGE cases. We aimed to assess the role of sapovirus as a cause of endemic AGE worldwide by conducting a systematic review of published studies that used molecular diagnostics to assess the prevalence of sapovirus among individuals with AGE symptoms. Of 106 articles included, the pooled sapovirus prevalence was 3.4%, with highest prevalence among children <5 years of age (4.4%) and among individuals in community settings (7.1%). Compared to studies that used conventional RT-PCR, RT-qPCR assays had a higher pooled prevalence (5.6%). Among individuals without AGE symptoms, the pooled sapovirus prevalence was 2.7%. These results highlight the relative contribution of sapovirus to cases of AGE, especially in community settings and among children <5 years of age.
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Affiliation(s)
- Marta Diez Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Emory University Rollins School of Public Health, Atlanta, GA, United States of America
| | - Anita K. Kambhampati
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Laura E. Calderwood
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Cherokee Nation Assurance, Arlington, VA, United States of America
| | - Aron J. Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sara A. Mirza
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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18
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de Moraes MTB, Leitão GAA, Olivares AIO, Xavier MDPTP, Bispo RDS, Sharma S, Leite JPG, Svensson L, Nordgren J. Molecular Epidemiology of Sapovirus in Children Living in the Northwest Amazon Region. Pathogens 2021; 10:965. [PMID: 34451429 PMCID: PMC8400878 DOI: 10.3390/pathogens10080965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Sapovirus is an important etiological agent of acute gastroenteritis (AGE), mainly in children under 5 years old living in lower-income communities. Eighteen identified sapovirus genotypes have been observed to infect humans. The aim of this study was to identify sapovirus genotypes circulating in the Amazon region. Twenty-eight samples were successfully genotyped using partial sequencing of the capsid gene. The genotypes identified were GI.1 (n = 3), GI.2 (n = 7), GII.1 (n = 1), GII.2 (n = 1), GII.3 (n = 5), GII.5 (n = 1), and GIV.1 (n = 10). The GIV genotype was the most detected genotype (35.7%, 10/28). The phylogenetic analysis identified sapovirus genotypes that had no similarity with other strains reported from Brazil, indicating that these genotypes may have entered the Amazon region via intense tourism in the Amazon rainforest. No association between histo-blood group antigen expression and sapovirus infection was observed.
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Affiliation(s)
- Marcia Terezinha Baroni de Moraes
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, RJ, Brazil; (G.A.A.L.); (M.d.P.T.P.X.); (J.P.G.L.)
| | - Gabriel Azevedo Alves Leitão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, RJ, Brazil; (G.A.A.L.); (M.d.P.T.P.X.); (J.P.G.L.)
| | | | - Maria da Penha Trindade Pinheiro Xavier
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, RJ, Brazil; (G.A.A.L.); (M.d.P.T.P.X.); (J.P.G.L.)
| | - Romanul de Souza Bispo
- Research Center Roraima Health Observatory (ObservaRR), Federal University of Roraima, Boa Vista 69310-000, RR, Brazil;
| | - Sumit Sharma
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, 581 85 Linköping, Sweden; (S.S.); (L.S.); (J.N.)
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro 21040-360, RJ, Brazil; (G.A.A.L.); (M.d.P.T.P.X.); (J.P.G.L.)
| | - Lennart Svensson
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, 581 85 Linköping, Sweden; (S.S.); (L.S.); (J.N.)
- Department of Medicine, Division of Infectious Diseases, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Johan Nordgren
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Linköping University, 581 85 Linköping, Sweden; (S.S.); (L.S.); (J.N.)
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McMurry TL, McQuade ETR, Liu J, Kang G, Kosek MN, Lima AAM, Bessong PO, Samie A, Haque R, Mduma ER, Leite JP, Bodhidatta L, Iqbal NT, Page N, Kiwelu I, Bhutta ZA, Ahmed T, Houpt ER, Platts-Mills JA. Duration of Postdiarrheal Enteric Pathogen Carriage in Young Children in Low-resource Settings. Clin Infect Dis 2021; 72:e806-e814. [PMID: 33033835 PMCID: PMC8315229 DOI: 10.1093/cid/ciaa1528] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 02/07/2023] Open
Abstract
Background Prolonged enteropathogen shedding after diarrhea complicates the identification of etiology in subsequent episodes and is an important driver of pathogen transmission. A standardized approach has not been applied to estimate the duration of shedding for a wide range of pathogens. Methods We used a multisite birth cohort of children 0–24 months of age from whom diarrheal and monthly nondiarrheal stools were previously tested by quantitative polymerase chain reaction for 29 enteropathogens. We modeled the probability of detection of the etiologic pathogen before and after diarrhea using a log-normal accelerated failure time survival model and estimated the median duration of pathogen carriage as well as differences in subclinical pathogen carriage 60 days after diarrhea onset in comparison to a prediarrhea baseline. Results We analyzed 3247 etiologic episodes of diarrhea for the 9 pathogens with the highest attributable burdens of diarrhea. The median duration of postdiarrheal carriage varied widely by pathogen, from about 1 week for rotavirus (median, 8.1 days [95% confidence interval {CI}, 6.2–9.6]) to >1 month for Cryptosporidium (39.5 days [95% CI, 30.6–49.0]). The largest increases in subclinical pathogen carriage before and after diarrhea were seen for Cryptosporidium (prevalence difference between 30 days prior and 60 days after diarrhea onset, 0.30 [95% CI, .23–.39]) and Shigella (prevalence difference, 0.21 [95% CI, .16–.27]). Conclusions Postdiarrheal shedding was widely variable between pathogens, with strikingly prolonged shedding seen for Cryptosporidium and Shigella. Targeted antimicrobial therapy and vaccination for these pathogens may have a relatively large impact on transmission.
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Affiliation(s)
- Timothy L McMurry
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | - Elizabeth T Rogawski McQuade
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA.,Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA.,Asociación Benéfica PRISMA, Iquitos, Peru
| | | | | | | | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | | | | | | | - Nicola Page
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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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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21
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Cilli A, Luchs A, Morillo SG, Carmona RDCC, Dos Santos FCP, Maeda AY, Primo D, Pacheco GT, Souza EV, Medeiros RS, Timenetsky MDCST. Surveillance and molecular characterization of human sapovirus in patients with acute gastroenteritis in Brazil, 2010 to 2017. J Clin Virol 2021; 140:104844. [PMID: 33971579 DOI: 10.1016/j.jcv.2021.104844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/06/2021] [Accepted: 04/17/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND Human sapoviruses (HuSaV) are associated with acute gastroenteritis (AGE), causing sporadic cases and outbreaks in patients worldwide. In Brazil, however, there are few reports describing the prevalence of HuSaV in patients with AGE. OBJECTIVE Describing the diversity of HuSaV in Brazil by detecting and molecularly characterizing HuSaV among patients with AGE during an 8-year period (2010-2017). STUDY DESIGN A total of 3974 stool samples, testing negative for rotavirus (RVA), norovirus (NoV) and human adenovirus (HAdV), were selected and screened for the presence of HuSaV. Nested RT-PCR were performed for a partial region of VP1, sequenced and genetic analyzed for genotyping the positive samples. RESULTS In the current study, the HuSaV prevalence was determined to be 3.7% (149/3974). A higher prevalence, 5.7% (118/2074), was observed in children under 2 years of age. During the surveillance period, 13 outbreaks were detected: 12 outbreaks in children under 3 years old and one outbreak in adults. Among the 149 HuSaV positive cases, 106 samples (71%) were successfully sequenced. The most prevalent genotype found was GI.1 (44.3%), followed by GI.2 (21.7%), GI.3 (3.8%), GI.6 (2.8%), GII.1 (5.7%), GII.2 (8.5%), GII.3 (2.8%), GII.4 (2.8%), GII.5 (5.7%) and GIV.1 (1.9%). Two GIV.1 strains characterized in this study are, to date, the only strains of this genotype reported in Brazil. CONCLUSIONS The present study elucidated the circulation of HuSaV in Brazil and highlight that HuSaV has not assumed an epidemiological importance in the country after the introduction of the RVA vaccine.
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Affiliation(s)
- Audrey Cilli
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil.
| | - Adriana Luchs
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Simone G Morillo
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | | | | | - Adriana Y Maeda
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Dieli Primo
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Gabriela T Pacheco
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Ellen V Souza
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
| | - Roberta S Medeiros
- Adolfo Lutz Institute, Virology Centre, Av. Dr Arnaldo, no: 355, São Paulo, SP, Brazil
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22
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Okitsu S, Khamrin P, Thongprachum A, Hikita T, Kumthip K, Pham NTK, Takanashi S, Hayakawa S, Maneekarn N, Ushijima H. Diversity of human sapovirus genotypes detected in Japanese pediatric patients with acute gastroenteritis, 2014-2017. J Med Virol 2021; 93:4865-4874. [PMID: 33704833 DOI: 10.1002/jmv.26934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 11/09/2022]
Abstract
Sapovirus (SaV) is one of the pathogens related to acute gastroenteritis (AGE) in adults and children worldwide. This study reported the diversity of SaV genotypes in children with AGE in Japan from July 2014 to June 2017. Of a total of 2259 stool samples tested by using reverse transcription-PCR method and further analyzed by nucleotide sequencing, 114 (5.0%) were positive for SaV and GI.1 (83.3%) was the most predominant genotype, followed by GII.1, GIV.1, GI.2, GI.3, and GII.3 genotypes. Monthly distribution analysis demonstrated two epidemic peaks from July to December 2015 and February to May 2017. However, no detection peak was observed in 2014 and 2016. Phylogenetic analysis of the complete VP1 nucleotide sequences of these GI.1 strains revealed two major clusters of GI.1 and each of which contained GI.1 strains of both 2015 and 2017. This study suggests that the continuous surveillance of SaV is needed to monitor high genetic diversity in Japanese children with AGE.
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Affiliation(s)
- Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Pattara Khamrin
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.,Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | | | | | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Ngan Thi Kim Pham
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sayaka Takanashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Emerging and Re-emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
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23
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Rogawski McQuade ET, Liu J, Kang G, Kosek MN, Lima AAM, Bessong PO, Samie A, Haque R, Mduma ER, Shrestha S, Leite JP, Bodhidatta L, Iqbal N, Page N, Kiwelu I, Bhutta Z, Ahmed T, Houpt ER, Platts-Mills JA. Protection From Natural Immunity Against Enteric Infections and Etiology-Specific Diarrhea in a Longitudinal Birth Cohort. J Infect Dis 2021; 222:1858-1868. [PMID: 31984416 PMCID: PMC7653087 DOI: 10.1093/infdis/jiaa031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/22/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The degree of protection conferred by natural immunity is unknown for many enteropathogens, but it is important to support the development of enteric vaccines. METHODS We used the Andersen-Gill extension of the Cox model to estimate the effects of previous infections on the incidence of subsequent subclinical infections and diarrhea in children under 2 using quantitative molecular diagnostics in the MAL-ED cohort. We used cross-pathogen negative control associations to correct bias due to confounding by unmeasured heterogeneity of exposure and susceptibility. RESULTS Prior rotavirus infection was associated with a 50% lower hazard (calibrated hazard ratio [cHR], 0.50; 95% confidence interval [CI], 0.41-0.62) of subsequent rotavirus diarrhea. Strong protection was evident against Cryptosporidium diarrhea (cHR, 0.32; 95% CI, 0.20-0.51). There was also protection due to prior infections for norovirus GII (cHR against diarrhea, 0.67; 95% CI, 0.49-0.91), astrovirus (cHR, 0.62; 95% CI, 0.48-0.81), and Shigella (cHR, 0.79; 95% CI, 0.65-0.95). Minimal protection was observed for other bacteria, adenovirus 40/41, and sapovirus. CONCLUSIONS Natural immunity was generally stronger for the enteric viruses than bacteria, potentially due to less antigenic diversity. Vaccines against major causes of diarrhea may be feasible but likely need to be more immunogenic than natural infection.
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Affiliation(s)
- Elizabeth T Rogawski McQuade
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virgina, USA.,Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virgina, USA
| | - Jie Liu
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virgina, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virgina, USA.,Asociación Benéfica PRISMA, Iquitos, Peru
| | | | | | | | - Rashidul Haque
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Ladaporn Bodhidatta
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | | | - Nicola Page
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | - Tahmeed Ahmed
- International Centre for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Eric R Houpt
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virgina, USA
| | - James A Platts-Mills
- Division of Infectious Diseases & International Health, University of Virginia, Charlottesville, Virgina, USA
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24
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McCall C, Wu H, O'Brien E, Xagoraraki I. Assessment of enteric viruses during a hepatitis outbreak in Detroit MI using wastewater surveillance and metagenomic analysis. J Appl Microbiol 2021; 131:1539-1554. [PMID: 33550682 DOI: 10.1111/jam.15027] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 12/24/2022]
Abstract
AIMS This study investigates enteric viruses in wastewater during an outbreak of acute hepatitis caused by hepatitis A virus (HAV) in a large metropolitan area. Emphasis is given to caliciviruses and HAV. METHODS AND RESULTS Metagenomic analysis was performed to characterize enteric viruses excreted by the population of Detroit MI, during a hepatitis A outbreak that occurred in 2017 and 2018. Additionally, HAV, norovirus GII, and sapovirus were quantified, using qPCR, in 54 untreated wastewater samples collected over the course of 4 months. Correlation analysis was performed to identify associations between the number of disease cases and HAV concentrations in wastewater. HAV obtained the highest relative abundance among other enteric viruses detected in wastewater metagenomes. Metagenomic analysis also detected several other enteric viruses including astrovirus, enterovirus and hepatitis E virus. Average sapovirus concentrations of 1·36 × 106 gc l-1 were significantly greater than norovirus GII concentrations (2·94 × 104 gc l-1 ). Additionally, norovirus GI and GII along with sapovirus GI.1 were detected using metagenomics. HAV loads in wastewater were significantly correlated with the number of disease cases reported 1 week after wastewater sampling. CONCLUSIONS Surveying untreated wastewater is a promising method for detecting early signs of hepatitis A outbreaks and for routine environmental monitoring of enteric viruses circulating in the environment. SIGNIFICANCE AND IMPACT OF THE STUDY Authors demonstrate the usefulness of metagenomics for genogrouping and enteric viral surveillance.
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Affiliation(s)
- C McCall
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - H Wu
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - E O'Brien
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
| | - I Xagoraraki
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI, USA
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25
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Burke RM, Mattison CP, Marsh Z, Shioda K, Donald J, Salas SB, Naleway AL, Biggs C, Schmidt MA, Hall AJ. Norovirus and Other Viral Causes of Medically Attended Acute Gastroenteritis Across the Age Spectrum: Results from the Medically Attended Acute Gastroenteritis Study in the United States. Clin Infect Dis 2021; 73:e913-e920. [PMID: 34398953 DOI: 10.1093/cid/ciab033] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Acute gastroenteritis (AGE) causes a substantial burden in the United States, but its etiology frequently remains undetermined. Active surveillance within an integrated healthcare delivery system was used to estimate the prevalence and incidence of medically attended norovirus, rotavirus, sapovirus, and astrovirus. METHODS Active surveillance was conducted among all enrolled members of Kaiser Permanente Northwest during July 2014-June 2016. An age-stratified, representative sample of AGE-associated medical encounters were recruited to provide a stool specimen to be tested for norovirus, rotavirus, sapovirus, and astrovirus. Medically attended AGE (MAAGE) encounters for a patient occurring within 30 days were grouped into 1 episode, and all-cause MAAGE incidence was calculated. Pathogen- and healthcare setting-specific incidence estimates were calculated using age-stratified bootstrapping. RESULTS The overall incidence of MAAGE was 40.6 episodes per 1000 person-years (PY), with most episodes requiring no more than outpatient care. Norovirus was the most frequently detected pathogen, with an incidence of 5.5 medically attended episodes per 1000 PY. Incidence of norovirus MAAGE was highest among children aged < 5 years (20.4 episodes per 1000 PY), followed by adults aged ≥ 65 years (4.5 episodes per 1000 PY). Other study pathogens showed similar patterns by age, but lower overall incidence (sapovirus: 2.4 per 1000 PY; astrovirus: 1.3 per 1000 PY; rotavirus: 0.5 per 1000 PY). CONCLUSIONS Viral enteropathogens, particularly norovirus, are important contributors to MAAGE, especially among children < 5 years of age. The present findings underline the importance of judicious antibiotics use for pediatric AGE and suggest that an effective norovirus vaccine could substantially reduce MAAGE.
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Affiliation(s)
- Rachel M Burke
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA
| | - Claire P Mattison
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Zachary Marsh
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Kayoko Shioda
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA.,Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee,USA
| | - Judy Donald
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - S Bianca Salas
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Allison L Naleway
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Christianne Biggs
- Public Health Division of the Oregon Health Authority, Portland, Oregon,USA
| | - Mark A Schmidt
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon,USA
| | - Aron J Hall
- Viral Gastroenteritis Branch, Division of Viral Diseases, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, Georgia,USA
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26
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Li R, Zhang R, Tan P, Han Y, Chen Y, Wang Z, Han D, Zhang J, Xie J, Zhang R, Li J. Quality evaluation of molecular diagnostic tests for astrovirus, sapovirus and poliovirus: A multicenter study. Clin Chim Acta 2020; 512:172-178. [PMID: 33181150 DOI: 10.1016/j.cca.2020.11.006] [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: 07/27/2020] [Revised: 10/23/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Astrovirus (AstV), Sapovirus (SaV) and Poliovirus (PV) are important pathogens that cause infections in children under five years of age. It is a very important task to systematically monitor and evaluate the diagnostic performance of these viruses in clinical laboratories. METHODS In our study, we performed a multicenter evaluation study among 21 laboratories across China using simulated stool samples spiked with self-designed AstV, SaV and PV pseudoviral particles. RESULTS The testing capability of 80.0% (16/20, AstV), 52.6% (10/19, SaV), and 25.0% (2/8, PV) of the participating laboratories were found to be "competent" in reporting correct results for all samples. The main type of errors were false negatives. None of the laboratories identified the subtypes of AstV and SaV, and six laboratories specifically identified the subtypes of PV. Lacking of well-trained personnel and adequate funding were the main challenges. From the questionnaire results, 55.6% laboratories (10/18) believe that training personnel could improve the laboratory testing performance. CONCLUSIONS The laboratories showed a competent diagnostic performance for AstV, but inferior diagnostic performances for SaV and PV. Sensitivity of detection and the ability for virus typing should be improved clinically. Professional and standardized personnel training is urgently needed to further improve laboratory performance.
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Affiliation(s)
- Rui Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Runling Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Yuqing Chen
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Zhe Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Dongsheng Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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27
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Sakagami A, Ueki Y, Dapat C, Saito M, Oshitani H. Genetic analysis of sapoviruses detected in outbreaks and sporadic cases of acute gastroenteritis in Miyagi Prefecture, Japan. J Clin Virol 2020; 132:104648. [PMID: 33038625 DOI: 10.1016/j.jcv.2020.104648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Human sapovirus (SaV) causes sporadic and endemic acute gastroenteritis worldwide. However, little is known about the relationship between the mode of transmission and genetic characteristics of SaV. OBJECTIVE To investigate the molecular characteristics of SaV-associated acute gastroenteritis among sporadic cases, foodborne, and nonfoodborne outbreaks. STUDY DESIGN We performed a systematic review of publications and genetic analysis of SaV in fecal specimens from 98 outpatients with acute gastroenteritis, 32 stool samples from 8 foodborne outbreaks, and 63 stool samples from 23 nonfoodborne outbreaks in Miyagi Prefecture, Japan from 1993 and between 2004 and 2020. Reverse transcription polymerase chain reaction (RT-PCR) was employed for the detection of SaV, and the partial capsid gene was sequenced for genotyping and phylogenetic analysis. RESULTS The overall detection rate of SaV in sporadic cases, foodborne, and nonfoodborne outbreaks was 5.8, 1.7, and 4.3%, respectively. Genotypic analysis revealed GI.1 to be the predominant genotype in sporadic cases (31.5%) and nonfoodborne outbreaks (52.1%), whereas it was not detected in foodborne outbreaks. Some outbreaks occurred following sporadic cases with the same genotype. CONCLUSIONS The distribution of SaV genotypes was different between foodborne outbreaks and other settings. The effective SaV infection control may differ depending on the genomic characteristics.
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Affiliation(s)
- Akie Sakagami
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, 4-7-2 Saiwai-cho, Miyagino-ku, Sendai, Miyagi 983-0836, Japan
| | - Yo Ueki
- Department of Microbiology, Miyagi Prefectural Institute of Public Health and Environment, 4-7-2 Saiwai-cho, Miyagino-ku, Sendai, Miyagi 983-0836, Japan
| | - Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
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28
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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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29
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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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30
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Sapovirus: an important cause of acute gastroenteritis in children. THE LANCET CHILD & ADOLESCENT HEALTH 2019; 3:758-759. [PMID: 31439497 DOI: 10.1016/s2352-4642(19)30270-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/10/2023]
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31
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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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Pietsch C, Liebert UG. Intrahost viral evolution during chronic sapovirus infections. J Clin Virol 2019; 113:1-7. [DOI: 10.1016/j.jcv.2019.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/22/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022]
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Guerrero-Latorre L, Romero B, Bonifaz E, Timoneda N, Rusiñol M, Girones R, Rios-Touma B. Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1334-1343. [PMID: 30248857 DOI: 10.1016/j.scitotenv.2018.07.213] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban discharges, viruses play an important role on disease, being causes of gastroenteritis, hepatitis, meningitis, respiratory infections, among others. This study analyzes the presence of viruses in highly impacted surface waters of urban rivers using next-generation sequencing techniques. Three representative locations of urban rivers, receiving the main discharges from Quito sewerage system, were selected. Water samples of 500 mL were concentrated by skimmed-milk flocculation method and the viral nucleic acid was extracted and processed for high throughput sequencing using Illumina MiSeq. The results yielded very relevant data of circulating viruses in the capital of Ecuador. A total of 29 viral families were obtained, of which 26 species were associated with infections in humans. Among the 26 species identified, several were related to gastroenteritis: Human Mastadenovirus F, Bufavirus, Sapporovirus, Norwalk virus and Mamastrovirus 1. Also detected were: Gammapapillomavirus associated with skin infections, Polyomavirus 1 related to cases of kidney damage, Parechovirus A described as cause of neonatal sepsis with neurological affectations and Hepatovirus A, the etiologic agent of Hepatitis A. Other emergent viruses identified, of which its pathogenicity remains to be fully clarified, were: Bocavirus, Circovirus, Aichi Virus and Cosavirus. The wide diversity of species detected through metagenomics gives us key information about the public health risks present in the urban rivers of Quito. In addition, this study describes for the first time the presence of important infectious agents not previously reported in Ecuador and with very little reports in Latin America.
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Affiliation(s)
- Laura Guerrero-Latorre
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Brigette Romero
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Edison Bonifaz
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Natalia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Blanca Rios-Touma
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería Ambiental, Universidad de las Américas, Quito, Ecuador.
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Mancini P, Bonanno Ferraro G, Iaconelli M, Suffredini E, Valdazo-González B, Della Libera S, Divizia M, La Rosa G. Molecular characterization of human Sapovirus in untreated sewage in Italy by amplicon-based Sanger and next-generation sequencing. J Appl Microbiol 2018; 126:324-331. [DOI: 10.1111/jam.14129] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/12/2018] [Accepted: 10/01/2018] [Indexed: 12/24/2022]
Affiliation(s)
- P. Mancini
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - G. Bonanno Ferraro
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - M. Iaconelli
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - E. Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health; Istituto Superiore di Sanità; Rome Italy
| | - B. Valdazo-González
- The National Institute for Biological Standards and Control; The Medicines and Healthcare Products Regulatory Agency; Hertfordshire UK
| | - S. Della Libera
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
| | - M. Divizia
- Department of Biomedicine and Prevention; University of Rome “Tor Vergata”; Rome Italy
| | - G. La Rosa
- Department of Environment and Health; Istituto Superiore di Sanità; Rome Italy
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Oka T, Iritani N, Yamamoto SP, Mori K, Ogawa T, Tatsumi C, Shibata S, Harada S, Wu FT. Broadly reactive real-time reverse transcription-polymerase chain reaction assay for the detection of human sapovirus genotypes. J Med Virol 2018; 91:370-377. [PMID: 30320885 DOI: 10.1002/jmv.25334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/04/2018] [Indexed: 12/14/2022]
Abstract
Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe-based real-time reverse transcription-polymerase chain reaction (RT-PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader-range sapovirus real-time RT-PCR assay. The assay can detect 2.5 × 107 and 2.5 × 10 1 copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1-7, GII.1-8, GIV.1, and GV.1, 2. No cross-reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.
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Affiliation(s)
- Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Nobuhiro Iritani
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Seiji P Yamamoto
- Division of Microbiology, Osaka Institute of Public Health, Osaka, Japan
| | - Kohji Mori
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Tomoko Ogawa
- Division of Virology, Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Chika Tatsumi
- Division of Virology, Shimane Prefectural Institute of Public Health and Environmental Science, Shimane, Japan
| | - Shinichiro Shibata
- Microbiology Department, Nagoya City Public Health Research Institute, Aichi, Japan
| | - Seiya Harada
- Department of Microbiology, Kumamoto Prefectural Institute of Public Health and Environmental Science, Kumamoto, Japan
| | - Fang-Tzy Wu
- Center for Research, Diagnostics and Vaccine Development, Taiwan Centers for Disease Control, Taipei, Taiwan
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Platts-Mills JA, Liu J, Rogawski ET, Kabir F, Lertsethtakarn P, Siguas M, Khan SS, Praharaj I, Murei A, Nshama R, Mujaga B, Havt A, Maciel IA, McMurry TL, Operario DJ, Taniuchi M, Gratz J, Stroup SE, Roberts JH, Kalam A, Aziz F, Qureshi S, Islam MO, Sakpaisal P, Silapong S, Yori PP, Rajendiran R, Benny B, McGrath M, McCormick BJJ, Seidman JC, Lang D, Gottlieb M, Guerrant RL, Lima AAM, Leite JP, Samie A, Bessong PO, Page N, Bodhidatta L, Mason C, Shrestha S, Kiwelu I, Mduma ER, Iqbal NT, Bhutta ZA, Ahmed T, Haque R, Kang G, Kosek MN, Houpt ER. Use of quantitative molecular diagnostic methods to assess the aetiology, burden, and clinical characteristics of diarrhoea in children in low-resource settings: a reanalysis of the MAL-ED cohort study. LANCET GLOBAL HEALTH 2018; 6:e1309-e1318. [PMID: 30287127 PMCID: PMC6227251 DOI: 10.1016/s2214-109x(18)30349-8] [Citation(s) in RCA: 227] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
Background Optimum management of childhood diarrhoea in low-resource settings has been hampered by insufficient data on aetiology, burden, and associated clinical characteristics. We used quantitative diagnostic methods to reassess and refine estimates of diarrhoea aetiology from the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) cohort study. Methods We re-analysed stool specimens from the multisite MAL-ED cohort study of children aged 0–2 years done at eight locations (Dhaka, Bangladesh; Vellore, India; Bhaktapur, Nepal; Naushero Feroze, Pakistan; Venda, South Africa; Haydom, Tanzania; Fortaleza, Brazil; and Loreto, Peru), which included active surveillance for diarrhoea and routine non-diarrhoeal stool collection. We used quantitative PCR to test for 29 enteropathogens, calculated population-level pathogen-specific attributable burdens, derived stringent quantitative cutoffs to identify aetiology for individual episodes, and created aetiology prediction scores using clinical characteristics. Findings We analysed 6625 diarrhoeal and 30 968 non-diarrhoeal surveillance stools from 1715 children. Overall, 64·9% of diarrhoea episodes (95% CI 62·6–71·2) could be attributed to an aetiology by quantitative PCR compared with 32·8% (30·8–38·7) using the original study microbiology. Viral diarrhoea (36·4% of overall incidence, 95% CI 33·6–39·5) was more common than bacterial (25·0%, 23·4–28·4) and parasitic diarrhoea (3·5%, 3·0–5·2). Ten pathogens accounted for 95·7% of attributable diarrhoea: Shigella (26·1 attributable episodes per 100 child-years, 95% CI 23·8–29·9), sapovirus (22·8, 18·9–27·5), rotavirus (20·7, 18·8–23·0), adenovirus 40/41 (19·0, 16·8–23·0), enterotoxigenic Escherichia coli (18·8, 16·5–23·8), norovirus (15·4, 13·5–20·1), astrovirus (15·0, 12·0–19·5), Campylobacter jejuni or C coli (12·1, 8·5–17·2), Cryptosporidium (5·8, 4·3–8·3), and typical enteropathogenic E coli (5·4, 2·8–9·3). 86·2% of the attributable incidence for Shigella was non-dysenteric. A prediction score for shigellosis was more accurate (sensitivity 50·4% [95% CI 46·7–54·1], specificity 84·0% [83·0–84·9]) than current guidelines, which recommend treatment only of bloody diarrhoea to cover Shigella (sensitivity 14·5% [95% CI 12·1–17·3], specificity 96·5% [96·0–97·0]). Interpretation Quantitative molecular diagnostics improved estimates of pathogen-specific burdens of childhood diarrhoea in the community setting. Viral causes predominated, including a substantial burden of sapovirus; however, Shigella had the highest overall burden with a high incidence in the second year of life. These data could improve the management of diarrhoea in these low-resource settings. Funding Bill & Melinda Gates Foundation.
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Affiliation(s)
- James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Elizabeth T Rogawski
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA; Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - Shaila S Khan
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | | | | | - Buliga Mujaga
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | - Timothy L McMurry
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James H Roberts
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | | | | | - M Ohedul Islam
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Pimmada Sakpaisal
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sasikorn Silapong
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Pablo P Yori
- Asociación Benéfica PRISMA, Iquitos, Peru; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Monica McGrath
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Jessica C Seidman
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Dennis Lang
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Michael Gottlieb
- Foundation for the National Institutes of Health, Bethesda, MD, USA
| | - Richard L Guerrant
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | - Nicola Page
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Ladaporn Bodhidatta
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Carl Mason
- Armed Forces Research Institute of Medical Sciences (AFRIMS), Bangkok, Thailand
| | - Sanjaya Shrestha
- Walter Reed/AFRIMS Research Unit, Nepal, Kathmandu, Nepal; University of Bergen, Bergen, Norway
| | - Ireen Kiwelu
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania
| | | | | | | | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | | | - Margaret N Kosek
- Asociación Benéfica PRISMA, Iquitos, Peru; Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
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First Complete Genome Sequences of Human Sapovirus Strains Classified as GI.3, GI.4, GI.6, GI.7, and GII.7. GENOME ANNOUNCEMENTS 2018; 6:6/12/e00168-18. [PMID: 29567738 PMCID: PMC5864949 DOI: 10.1128/genomea.00168-18] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the first complete genome sequences of genotype GI.3, GI.4, GI.6, GI.7, and GII.7 sapovirus strains, detected from fecal samples of acute gastroenteritis patients. Complete or nearly complete genome sequences of all 18 genotypes of human sapoviruses are now available for phylogenetic analysis and primer design.
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