Distribution and Genetic Variability of Sapoviruses in Africa

Makhaola, Kgomotso; Moyo, Sikhulile; Kebaabetswe, Lemme P.

doi:10.3390/v12050490

Cited by 17 publications

(14 citation statements)

References 71 publications

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“…(Xue et al 2019). In keeping with previous studies (Makhaola et al 2020), GI was the most prevalent genogroup, detected in 32 out of 33 samples, and GI.2 was the most prevalent genotype, reflecting its high activity in local population during the study period.…”

Section: Discussionsupporting

confidence: 89%

Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing

et al. 2021

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Human sapovirus (SaV) is an important causative agent of nonbacterial gastroenteritis in humans. However, little is known about its circulation in China. To study the prevalence and diversity of human SaV genotypes circulating in eastern China, a 3-year environmental surveillance combined with next generation sequencing (NGS) technology was conducted. A total of 36 raw sewage samples were collected from January 2017 to December 2019 in Jinan and processed. Thirty-five (97.22%) samples were positive for human SaV genome in quantitative RT-PCR assay; 33 (91.67%) samples were positive in nested RT-PCR assay on partial capsid VP1 sequence and all amplicons were further analyzed separately by NGS. Among those, ten genotypes belonging to the genogroups of GI, GII, GIV, and GV were identified by NGS, including 4 major genotypes (GI.2, GI.1, GV.1 and GI.3) and 6 uncommon genotypes (GII.5, GII.1, GII.NA1, GII.3, GI.6 and GIV.1). A temporal switch of predominant genotype was observed from GI.2 to GI.1 around June 2019. Local and foreign sequences clustered together in some branches according to phylogenetic analysis, indicating frequent transmission of various lineages in different regions of the world. Environmental surveillance provides a comprehensive picture of human SaV in China. NGS-based environmental surveillance improves our knowledge on human SaV circulating in communities greatly and should be encouraged as a sensitive surveillance tool.

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Section: Discussionsupporting

confidence: 89%

Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing

et al. 2021

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“…The SaV genome usually contains two ORFs. The first (ORF1) encodes a single non-structural polyprotein and a major capsid protein (VP1), while a smaller capsid protein (VP2) is encoded by ORF2 (Makhaola et al 2020 ). SaVs are routinely detected by RT-PCR of the VP1 or polymerase encoding regions, and genotyping is based on differences within the VP1-coding sequence (Hansman et al 2007 ; Oka et al 2015 ).…”

Section: Classification Structure and Biology Of Enteric Virusesmentioning

confidence: 99%

“…SaVs are routinely detected by RT-PCR of the VP1 or polymerase encoding regions, and genotyping is based on differences within the VP1-coding sequence (Hansman et al 2007 ; Oka et al 2015 ). SaVs are phylogenetically clustered into 19 genogroups, of which GI, GII, GIV and GV contain human SaVs and are further subdivided into genotypes GI.1-GI.7, GII.1-GII.8, GIV.1 and GV.1-GV.2 (Oka et al 2015 ; Diez-Valcarce et al 2018 ; Makhaola et al 2020 ). Globally, strains belonging to genogroups GI and GII are more prevalent than SaVs belonging to genogroups GIV and GV (Fioretti et al 2016 ; Yoneda et al 2017 ; Mann et al 2019 ; Supadej et al 2019 ; Varela et al 2019 ).…”

Section: Classification Structure and Biology Of Enteric Virusesmentioning

confidence: 99%

“…Globally, strains belonging to genogroups GI and GII are more prevalent than SaVs belonging to genogroups GIV and GV (Fioretti et al 2016 ; Yoneda et al 2017 ; Mann et al 2019 ; Supadej et al 2019 ; Varela et al 2019 ). Recently, GI was confirmed as the most prevalent genogroup detected in people and the environment within African countries (Makhaola et al 2020 ).…”

Section: Classification Structure and Biology Of Enteric Virusesmentioning

confidence: 99%

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Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa

2021

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Enteric viruses are a diverse group of human pathogens which are primarily transmitted by the faecal-oral route and are a major cause of non-bacterial diarrhoeal disease in both developed and developing countries. Because they are shed in high numbers by infected individuals and can persist for a long time in the environment, they pose a serious threat to human health globally. Enteric viruses end up in the environment mainly through discharge or leakage of raw or inadequately treated sewage into water sources such as springs, rivers, dams, or marine estuaries. Human exposure then follows when contaminated water is used for drinking, cooking, or recreation and, importantly, when filter-feeding bivalve shellfish are consumed. The human health hazard posed by enteric viruses is particularly serious in Africa where rapid urbanisation in a relatively short period of time has led to the expansion of informal settlements with poor sanitation and failing or non-existent wastewater treatment infrastructure, and where rural communities with limited or no access to municipal water are dependent on nearby open water sources for their subsistence. The role of sewage-contaminated water and bivalve shellfish as vehicles for transmission of enteric viruses is well documented but, to our knowledge, has not been comprehensively reviewed in the African context. Here we provide an overview of enteric viruses and then review the growing body of research where these viruses have been detected in association with sewage-contaminated water or food in several African countries. These studies highlight the need for more research into the prevalence, molecular epidemiology and circulation of these viruses in Africa, as well as for development and application of innovative wastewater treatment approaches to reduce environmental pollution and its impact on human health on the continent.

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“…Sapovirus is a single strand non enveloped RNA virus that belongs to the Caliciviridae family [1][2][3][4] . The length of its genome is 7.1 to 7.7 kb, and its polyadenylated 3' terminal is responsible for viral replication, while its 5' terminal is associated with viral translation through production of VPg 5,6 .…”

Section: Introductionmentioning

confidence: 99%

Molecular study of sapovirus in acute gastroenteritis in children: a cross-sectional study

2021

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Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there are insufficient data about the presence of this virus among children with acute gastroenteritis. The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis by reverse transcriptase-polymerase chain reaction (RT-PCR). Methods: A cross-sectional study enrolled 100 children patients with acute gastroenteritis from outpatient clinics with excluded bacterial pathogens and parasitic infestation. A stool sample was collected from each child for laboratory examination. Each stool sample was subjected to study by direct microscopic examination, study for rotavirus by enzyme-linked immunoassay (ELISA) and the remaining sample was subjected to RNA extraction and RT- PCR for sapovirus. Results: The most frequently detected virus was rotavirus by ELISA (25%). RT-PCR detected sapovirus in 7% of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt (42.9%). The main presenting symptoms were fever (71.4%) and vomiting (57.1%). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in 5 patients (71.4%, P=0.01). There was an insignificant difference between symptoms of gastroenteritis in children with sapovirus and children with gastroenteritis without sapovirus as regards vomiting (P=0.7), fever (P=0.46), and abdominal pain (P=0.69). 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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Distribution and Genetic Variability of Sapoviruses in Africa

Cited by 17 publications

References 71 publications

Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing

Detection of Human Sapoviruses in Sewage in China by Next Generation Sequencing

Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa

Molecular study of sapovirus in acute gastroenteritis in children: a cross-sectional study

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