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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] [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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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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Tang X, Hu Y, Zhong X, Xu H. Molecular Epidemiology of Human Adenovirus, Astrovirus, and Sapovirus Among Outpatient Children With Acute Diarrhea in Chongqing, China, 2017-2019. Front Pediatr 2022; 10:826600. [PMID: 35311045 PMCID: PMC8929441 DOI: 10.3389/fped.2022.826600] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE To investigate the epidemiology of human adenovirus (HAdV), human astrovirus (HAstV), and sapovirus (SaV), children with acute diarrhea in Chongqing, China from 2017 to 2019 were enrolled. Improved surveillance could provide better guidance for diarrhea prevention. METHODS Between 2017 and 2019, fecal specimens were collected from children <14 years of age presenting with acute diarrhea for treatment at the outpatient department of the Children's Hospital, Chongqing Medical University. Human HAdV in the fecal specimens was detected by PCR, while RT-PCR was adopted for the detection of HAstV and SaV. RESULTS A total of 1,352 fecal specimens were screened in this study. The detection rate of HAdV was 4.44% (60/1352), HAstV was 2.81% (38/1352), and SaV was 1.04% (14/1352). The prevalence of enteric viruses in males was not significantly different to females (p > 0.05). We found 96.67% (58/60) of the HAdV-positive cases, 92.11% (35/38) of the HAstV-positive cases, and 100% (14/14) of the SaV-positive cases among the children under 4 years old. HAdV cases were identified throughout the year, while the infection of HAstV peaked from March to May every year. By contrast, SaV was detected in May, July, and from September to December. In total, 41 strains of HAdV-F were identified, including F41 (39/60) and F40 (2/60). Furthermore, A31, B3, B7, C1, C2, C5, and C6 were also detected in the study. In addition, we detected two genotypes of HAstV, HAstV-1 (34/38) and HAstV-5 (4/38), and two genotypes of SaV, GI0.1 (13/14), GI0.2 (1/14). CONCLUSION The enteric viruses HAdV, HAstV, and SaV contribute to the overall burden of diarrhea in Chongqing, especially in children <4 years of age. Two genotypes were identified for HAstV (HAstV-1 and HAstV-5) and SaV (GI.1 and GI.2) with an additional nine genotypes detected in HAdV cases. While the F41 HAdV strain was predominant, HAdV-A31 was also detected in 10% of cases. The study results along with continuous surveillance of enteric viruses will aid in the design and implementation of future enteric vaccines and diarrhea mitigation strategies.
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Affiliation(s)
- Xiang Tang
- Children's Hosptital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Yue Hu
- Children's Hosptital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
| | - Xiaoni Zhong
- School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Hongmei Xu
- Children's Hosptital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing, China
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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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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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Diez-Valcarce M, Castro CJ, Marine RL, Halasa N, Mayta H, Saito M, Tsaknaridis L, Pan CY, Bucardo F, Becker-Dreps S, Lopez MR, Magaña LC, Ng TFF, Vinjé J. Genetic diversity of human sapovirus across the Americas. J Clin Virol 2018; 104:65-72. [PMID: 29753103 DOI: 10.1016/j.jcv.2018.05.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/24/2018] [Accepted: 05/04/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Sapoviruses are responsible for sporadic and epidemic acute gastroenteritis worldwide. Sapovirus typing protocols have a success rate as low as 43% and relatively few complete sapovirus genome sequences are available to improve current typing protocols. OBJECTIVE/STUDY DESIGN To increase the number of complete sapovirus genomes to better understand the molecular epidemiology of human sapovirus and to improve the success rate of current sapovirus typing methods, we used deep metagenomics shotgun sequencing to obtain the complete genomes of 68 sapovirus samples from four different countries across the Americas (Guatemala, Nicaragua, Peru and the US). RESULTS VP1 genotyping showed that all sapovirus sequences could be grouped in the four established genogroups (GI (n = 13), GII (n = 30), GIV (n = 23), GV (n = 2)) that infect humans. They include the near-complete genome of a GI.6 virus and a recently reported novel GII.8 virus. Sequences of the complete RNA-dependent RNA polymerase gene could be grouped into three major genetic clusters or polymerase (P) types (GI.P, GII.P and GV.P) with all GIV viruses harboring a GII polymerase. One (GII.P-GII.4) of the new 68 sequences was a recombinant virus with the hotspot between the NS7 and VP1 regions. CONCLUSIONS Analyses of this expanded database of near-complete sapovirus sequences showed several mismatches in the genotyping primers, suggesting opportunities to revisit and update current sapovirus typing methods.
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Affiliation(s)
| | | | - Rachel L Marine
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Holger Mayta
- Department of Cellular and Molecular Sciences, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Cellular and Molecular Sciences, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Department of Virology, Tohoku University, Graduate School of Medicine, Sendai, Japan
| | | | - Chao-Yang Pan
- California Department of Public Health, Richmond, CA, USA
| | - Filemon Bucardo
- Department of Microbiology, University of Leon, Leon, Nicaragua
| | - Sylvia Becker-Dreps
- Department of Family Medicine and Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | | | - Terry Fei Fan Ng
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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Lu CY, Huang LM, Fan TY, Cheng AL, Chang LY. Incidence of respiratory viral infections and associated factors among children attending a public kindergarten in Taipei City. J Formos Med Assoc 2017; 117:132-140. [PMID: 28420553 DOI: 10.1016/j.jfma.2017.02.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/04/2017] [Accepted: 02/07/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Kindergarteners frequently encounter various infectious diseases, so surveillance of viral infectious diseases would provide information for their health promotion. METHODS We enrolled kindergarten attendees, age 2-5 years, during the academic years of 2006 and 2007 in a Taipei City kindergarten. Daily monitoring of illness and regular biweekly physical examinations were undertaken. Multiple infections were defined as one child having two or more laboratory-confirmed viral infections with different viruses or different serotypes during one academic year. RESULTS The overall laboratory-confirmed incidence rate of respiratory viral infection was 239 per 100 person-years in the 2006 academic year and 136 per 100 person-years in the 2007 academic year. The attack rate for seasonal influenza was 17% in the 2006 academic year and 27% in the 2007 academic year. Boys and children with allergies had significantly higher risks to get multiple viral infections [odds ratio (OR) 1.81, 95% confidence interval (CI) 1.20-2.75; OR 1.56, 95% CI 1.00-2.39, respectively]. Boys also tended to get enterovirus infections (OR 1.56, 95% CI 1.02-2.38) while children with allergies tended to acquire adenovirus infections (OR 1.71, 95% CI 1.12-2.66). CONCLUSION Boys and children with allergies were more susceptible to multiple viral infections, so they should be more cautious about viral infections.
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Affiliation(s)
- Chun-Yi Lu
- Departments of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Li-Min Huang
- Departments of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tsui-Yien Fan
- Departments of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - A-Ling Cheng
- Departments of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Luan-Yin Chang
- Departments of Pediatrics, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan.
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Murray TY, Nadan S, Page NA, Taylor MB. Diverse sapovirus genotypes identified in children hospitalised with gastroenteritis in selected regions of South Africa. J Clin Virol 2016; 76:24-9. [PMID: 26803285 DOI: 10.1016/j.jcv.2016.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/15/2015] [Accepted: 01/05/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Sapoviruses (SaVs) are recognised as causative agents of gastroenteritis worldwide. However, data on the genetic diversity of this virus in Africa are lacking, particularly in the form of current long-term studies. OBJECTIVE To determine the genetic diversity of SaVs in children hospitalised with gastroenteritis in South Africa (SA). STUDY DESIGN From April 2009 to December 2013, SaVs were characterised from stool specimens from children hospitalised with gastroenteritis in four provinces of SA. RESULTS Fourteen different SaV genotypes were identified from the 221 strains that were characterised. Genogroup (G) IV predominated overall and was detected in 24% (53/221) of specimens. The other identified genotypes included six belonging to GI (GI.1-GI.3, GI.5, GI.6, and GI.7) and seven belonging to GII (GII.1-GII.7). CONCLUSION This study has provided the first comprehensive data on the genetic diversity of SaVs in a clinical setting in SA, contributing to the global knowledge of this virus.
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Affiliation(s)
- Tanya Y Murray
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007 Pretoria, South Africa.
| | - Sandrama Nadan
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007 Pretoria, South Africa; Centre for Enteric Diseases, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131 Johannesburg, South Africa.
| | - Nicola A Page
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Private Bag X4, Sandringham, 2131 Johannesburg, South Africa.
| | - Maureen B Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, 0007 Pretoria, South Africa.
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Marques Mendanha de Oliveira D, Souza M, Souza Fiaccadori F, César Pereira Santos H, das Dôres de Paula Cardoso D. Monitoring of Calicivirus among day-care children: evidence of asymptomatic viral excretion and first report of GI.7 Norovirus and GI.3 Sapovirus in Brazil. J Med Virol 2013; 86:1569-75. [PMID: 24123103 DOI: 10.1002/jmv.23791] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/16/2022]
Abstract
Caliciviruses (Norovirus and Sapovirus) are important causes of acute gastroenteritis, with Norovirus (NoV) considered the leading cause of epidemic non-bacterial acute gastroenteritis; however, molecular and epidemiological data of the circulating Calicivirus (CV) strains among day-care children are still considered scarce. The role of asymptomatic CV excretion on viral transmission also remains poorly understood. The aim of the present study was to monitor the occurrence of NoV and Sapovirus (SaV) in a day-care center and to describe the molecular epidemiology of the circulating strains. Genomic sequencing and phylogenetic analysis of the capsid region were carried out in CV positive samples obtained from children younger than 5 years, with or without diarrhea, between October 2009 and October 2011. A total of 539 fecal samples were screened for CV. Forty-three (8%) were positive for NoV and 25 (4.6%) for SaV. Surprisingly, positivity rates for CV were significant in asymptomatic children, and virus circulation was detected in every month of the study. Great genomic diversity of CV was observed, and the circulating NoV strains were: GII.6, GII.2, GII.1, GI.7, GII.4, and GI.1. The SaV genotypes GI.1 and GI.3 were also detected. Five CV outbreaks caused by distinct viral strains were documented. This study provides an insight on the genetic diversity of CV in a day-care in Central West Brazil, highlighting the probable role of asymptomatic viral excretion and the significance of semi-closed settings in the dissemination of these agents.
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