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Rotaviruses and Rotavirus Vaccines
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Rotaviruses and Rotavirus Vaccines

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Viral Pathogens".

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 48060

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editors

Prof. Julie Bines

E-Mail Website
Guest Editor
1. Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, 3052, Australia
2. Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia
3. Department of Gastroenterology and Clinical Nutrition, Royal Children’s Hospital, Parkville, 3052, Australia
Interests: rotavirus; vaccine development; international child health; intussusception
Dr. Celeste Donato

E-Mail Website
Guest Editor
1. Enteric Diseases Group, Murdoch Children’s Research Institute, Parkville, 3052, Australia
2. Department of Paediatrics, The University of Melbourne, Parkville, 3052, Australia
3. Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, 3800, Australia
Interests: rotavirus; molecular epidemiology; virus evolution; viral dynamics

Special Issue Information

Dear colleagues,

The Rotavirus genus within the Reoviridae virus family encompasses a large and diverse population of viruses capable of causing disease in a variety of animal species. Group A Rotavirus remains a leading cause of morbidity and mortality due to gastroenteritis in young children worldwide; estimated to have caused 128,500 deaths and 258,173,300 episodes of diarrhea among children under 5 years of age in 2016 [1]. However, the burden of disease has decreased substantially over the last decade, largely due to the inclusion of rotavirus vaccines into the national immunisation programs of over 100 countries worldwide.

Rotavirus is classified into G and P genotypes based on the two outer capsid proteins VP7 and VP4 respectively. To date, 36 G types and 51 P types have been described in humans and various animal species. The most common genotypes in humans are G1, G2, G3, G4, G9, and G12, in combination with P[4], P[6], and P[8]. The growing utilization of Next Generation Sequencing is expanding our knowledge of rotavirus genetic diversity through an increase in whole genome sequencing. Rotavirus strains are able to evolve rapidly employing numerous mechanisms including genetic drift and reassortment. Whilst rotavirus strains exhibit a degree of host species restriction; zoonotic transmission substantially increases the genetic diversity of strains causing human infection. Understanding changes to rotavirus epidemiology and genetic diversity in the vaccine era is critical to ensure the continued success of the global vaccination efforts.

For this Special Issue of Pathogens, we invite authors to submit original research or review articles representing recent advances in our knowledge of rotavirus epidemiology, genotypic diversity and genomic characterisation. We look forward to your contribution.

Prof. Julie Bines
Dr. Celeste Donato
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • epidemiology
  • rotavirus vaccines
  • molecular phylogeny
  • virus evolution
  • zoonosis
  • vaccines
  • virology

Published Papers (15 papers)

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Editorial

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6 pages, 215 KiB  
Editorial
Rotaviruses and Rotavirus Vaccines
by Celeste M. Donato and Julie E. Bines
Pathogens 2021, 10(8), 959; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10080959 - 29 Jul 2021
Cited by 5 | Viewed by 2536
Abstract
Group A rotaviruses belong to the Reoviridae virus family and are classified into G and P genotypes based on the outer capsid proteins VP7 and VP4, respectively [...] Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)

Research

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9 pages, 1759 KiB  
Article
Rotavirus Strain Distribution before and after Introducing Rotavirus Vaccine in India
by Tintu Varghese, Shainey Alokit Khakha, Sidhartha Giri, Nayana P. Nair, Manohar Badur, Geeta Gathwala, Sanjeev Chaudhury, Shayam Kaushik, Mrutunjay Dash, Nirmal K. Mohakud, Rajib K. Ray, Prasantajyoti Mohanty, Chethrapilly Purushothaman Girish Kumar, Seshadri Venkatasubramanian, Rashmi Arora, Venkata Raghava Mohan, Jacqueline E. Tate, Umesh D. Parashar and Gagandeep Kang
Pathogens 2021, 10(4), 416; https://doi.org/10.3390/pathogens10040416 - 01 Apr 2021
Cited by 15 | Viewed by 3460
Abstract
In April 2016, an indigenous monovalent rotavirus vaccine (Rotavac) was introduced to the National Immunization Program in India. Hospital-based surveillance for acute gastroenteritis was conducted in five sentinel sites from 2012 to 2020 to monitor the vaccine impact on various genotypes and the [...] Read more.
In April 2016, an indigenous monovalent rotavirus vaccine (Rotavac) was introduced to the National Immunization Program in India. Hospital-based surveillance for acute gastroenteritis was conducted in five sentinel sites from 2012 to 2020 to monitor the vaccine impact on various genotypes and the reduction in rotavirus positivity at each site. Stool samples collected from children under 5 years of age hospitalized with diarrhea were tested for group A rotavirus using a commercial enzyme immunoassay, and rotavirus strains were characterized by RT-PCR. The proportion of diarrhea hospitalizations attributable to rotavirus at the five sites declined from a range of 56–29.4% in pre-vaccine years to 34–12% in post-vaccine years. G1P[8] was the predominant strain in the pre-vaccination period, and G3P[8] was the most common in the post-vaccination period. Circulating patterns varied throughout the study period, and increased proportions of mixed genotypes were detected in the post-vaccination phase. Continuous long-term surveillance is essential to understand the diversity and immuno-epidemiological effects of rotavirus vaccination. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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11 pages, 618 KiB  
Article
Genotype Diversity before and after the Introduction of a Rotavirus Vaccine into the National Immunisation Program in Fiji
by Sarah Thomas, Celeste M. Donato, Sokoveti Covea, Felisita T. Ratu, Adam W. J. Jenney, Rita Reyburn, Aalisha Sahu Khan, Eric Rafai, Varja Grabovac, Fatima Serhan, Julie E. Bines and Fiona M. Russell
Pathogens 2021, 10(3), 358; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10030358 - 17 Mar 2021
Cited by 6 | Viewed by 2455
Abstract
The introduction of the rotavirus vaccine, Rotarix, into the Fiji National Immunisation Program in 2012 has reduced the burden of rotavirus disease and hospitalisations in children less than 5 years of age. The aim of this study was to describe the pattern of [...] Read more.
The introduction of the rotavirus vaccine, Rotarix, into the Fiji National Immunisation Program in 2012 has reduced the burden of rotavirus disease and hospitalisations in children less than 5 years of age. The aim of this study was to describe the pattern of rotavirus genotype diversity from 2005 to 2018; to investigate changes following the introduction of the rotavirus vaccine in Fiji. Faecal samples from children less than 5 years with acute diarrhoea between 2005 to 2018 were analysed at the WHO Rotavirus Regional Reference Laboratory at the Murdoch Children’s Research Institute, Melbourne, Australia, and positive samples were serotyped by EIA (2005–2006) or genotyped by heminested RT-PCR (2007 onwards). We observed a transient increase in the zoonotic strain equine-like G3P[8] in the initial period following vaccine introduction. G1P[8] and G2P[4], dominant genotypes prior to vaccine introduction, have not been detected since 2015 and 2014, respectively. A decrease in rotavirus genotypes G2P[8], G3P[6], G8P[8] and G9P[8] was also observed following vaccine introduction. Monitoring the rotavirus genotypes that cause diarrhoeal disease in children in Fiji is important to ensure that the rotavirus vaccine will continue to be protective and to enable early detection of new vaccine escape strains if this occurs. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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19 pages, 7712 KiB  
Article
Characterisation of a G2P[4] Rotavirus Outbreak in Western Australia, Predominantly Impacting Aboriginal Children
by Celeste M. Donato, Nevada Pingault, Elena Demosthenous, Susie Roczo-Farkas and Julie E. Bines
Pathogens 2021, 10(3), 350; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens10030350 - 16 Mar 2021
Cited by 3 | Viewed by 2156
Abstract
In May, 2017, an outbreak of rotavirus gastroenteritis was reported that predominantly impacted Aboriginal children ≤4 years of age in the Kimberley region of Western Australia. G2P[4] was identified as the dominant genotype circulating during this period and polyacrylamide gel electrophoresis revealed the [...] Read more.
In May, 2017, an outbreak of rotavirus gastroenteritis was reported that predominantly impacted Aboriginal children ≤4 years of age in the Kimberley region of Western Australia. G2P[4] was identified as the dominant genotype circulating during this period and polyacrylamide gel electrophoresis revealed the majority of samples exhibited a conserved electropherotype. Full genome sequencing was performed on representative samples that exhibited the archetypal DS-1-like genome constellation: G2-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2 and phylogenetic analysis revealed all genes of the outbreak samples were closely related to contemporary Japanese G2P[4] samples. The outbreak samples consistently fell within conserved sub-clades comprised of Hungarian and Australian G2P[4] samples from 2010. The 2017 outbreak variant was not closely related to G2P[4] variants associated with prior outbreaks in Aboriginal communities in the Northern Territory. When compared to the G2 component of the RotaTeq vaccine, the outbreak variant exhibited mutations in known antigenic regions; however, these mutations are frequently observed in contemporary G2P[4] strains. Despite the level of vaccine coverage achieved in Australia, outbreaks continue to occur in vaccinated populations, which pose challenges to regional areas and remote communities. Continued surveillance and characterisation of emerging variants are imperative to ensure the ongoing success of the rotavirus vaccination program in Australia. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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19 pages, 6366 KiB  
Article
Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012–2017)
by Benilde Munlela, Eva D. João, Celeste M. Donato, Amy Strydom, Simone S. Boene, Assucênio Chissaque, Adilson F. L. Bauhofer, Jerónimo Langa, Marta Cassocera, Idalécia Cossa-Moiane, Jorfélia J. Chilaúle, Hester G. O’Neill and Nilsa de Deus
Pathogens 2020, 9(12), 1026; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9121026 - 06 Dec 2020
Cited by 4 | Viewed by 2557
Abstract
Mozambique introduced the Rotarix® vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we [...] Read more.
Mozambique introduced the Rotarix® vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we report whole genome sequence analysis for 36 G1P[8] strains using an Illumina MiSeq platform. All strains exhibited a Wa-like genetic backbone (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis showed that most of the Mozambican strains clustered closely together in a conserved clade for the entire genome. No distinct clustering for pre- and post-vaccine strains were observed. These findings may suggest no selective pressure by the introduction of the Rotarix® vaccine in 2015. Two strains (HJM1646 and HGM0544) showed varied clustering for the entire genome, suggesting reassortment, whereas a further strain obtained from a rural area (MAN0033) clustered separately for all gene segments. Bayesian analysis for the VP7 and VP4 encoding gene segments supported the phylogenetic analysis and indicated a possible introduction from India around 2011.7 and 2013.0 for the main Mozambican clade. Continued monitoring of rotavirus strains in the post-vaccine period is required to fully understand the impact of vaccine introduction on the diversity and evolution of rotavirus strains. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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16 pages, 1195 KiB  
Article
Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction
by Mike J. Mwanga, Jennifer R. Verani, Richard Omore, Jacqueline E. Tate, Umesh D. Parashar, Nickson Murunga, Elijah Gicheru, Robert F. Breiman, D. James Nokes and Charles N. Agoti
Pathogens 2020, 9(12), 981; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9120981 - 24 Nov 2020
Cited by 8 | Viewed by 3064
Abstract
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 [...] Read more.
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use of vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less than 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected RVA in 55 samples (22.2%). Of these, VP7 (G) and VP4 (P) segments were successfully sequenced in 48 (87.3%) and phylogenetic analysis based on the VP7 sequences identified seven genetic clusters with six different GP combinations: G3P[8], G1P[8], G2P[4], G2P[8], G9P[8] and G12P[8]. The G3P[8] strains predominated the season (n = 37, 67.2%) and comprised three distinct G3 genetic clusters that fell within Lineage I and IX (the latter also known as equine-like G3 Lineage). Both the two G3 lineages have been recently detected in several countries. Our study is the first to document African children infected with G3 Lineage IX. These data highlight the global nature of RVA transmission and the importance of increasing global rotavirus vaccine coverage. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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9 pages, 584 KiB  
Article
FUT2 Secretor Status Influences Susceptibility to VP4 Strain-Specific Rotavirus Infections in South African Children
by Jaime MacDonald, Michelle J. Groome, Janet Mans and Nicola Page
Pathogens 2020, 9(10), 795; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9100795 - 27 Sep 2020
Cited by 12 | Viewed by 2335
Abstract
Gastroenteritis is a preventable cause of morbidity and mortality worldwide. Rotavirus vaccination has significantly reduced the disease burden, but the sub-optimal vaccine efficacy observed in low-income regions needs improvement. Rotavirus VP4 ‘spike’ proteins interact with FUT2-defined, human histo-blood group antigens on mucosal surfaces, [...] Read more.
Gastroenteritis is a preventable cause of morbidity and mortality worldwide. Rotavirus vaccination has significantly reduced the disease burden, but the sub-optimal vaccine efficacy observed in low-income regions needs improvement. Rotavirus VP4 ‘spike’ proteins interact with FUT2-defined, human histo-blood group antigens on mucosal surfaces, potentially influencing strain circulation and the efficacy of P[8]-based rotavirus vaccines. Secretor status was investigated in 500 children <5 years-old hospitalised with diarrhoea, including 250 previously genotyped rotavirus-positive cases (P[8] = 124, P[4] = 86, and P[6] = 40), and 250 rotavirus-negative controls. Secretor status genotyping detected the globally prevalent G428A single nucleotide polymorphism (SNP) and was confirmed by Sanger sequencing in 10% of participants. The proportions of secretors in rotavirus-positive cases (74%) were significantly higher than in the rotavirus-negative controls (58%; p < 0.001). The rotavirus genotypes P[8] and P[4] were observed at significantly higher proportions in secretors (78%) than in non-secretors (22%), contrasting with P[6] genotypes with similar proportions amongst secretors (53%) and non-secretors (47%; p = 0.001). This suggests that rotavirus interacts with secretors and non-secretors in a VP4 strain-specific manner; thus, secretor status may partially influence rotavirus VP4 wild-type circulation and P[8] rotavirus vaccine efficacy. The study detected a mutation (rs1800025) ~50 bp downstream of the G428A SNP that would overestimate non-secretors in African populations when using the TaqMan® SNP Genotyping Assay. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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12 pages, 911 KiB  
Article
Retrospective Case-Control Study of 2017 G2P[4] Rotavirus Epidemic in Rural and Remote Australia
by Bianca F. Middleton, Margie Danchin, Helen Quinn, Anna P. Ralph, Nevada Pingault, Mark Jones, Marie Estcourt and Tom Snelling
Pathogens 2020, 9(10), 790; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9100790 - 26 Sep 2020
Cited by 8 | Viewed by 2928
Abstract
Background: A widespread G2P[4] rotavirus epidemic in rural and remote Australia provided an opportunity to evaluate the performance of Rotarix and RotaTeq rotavirus vaccines, ten years after their incorporation into Australia’s National Immunisation Program. Methods: We conducted a retrospective case-control analysis. Vaccine-eligible children [...] Read more.
Background: A widespread G2P[4] rotavirus epidemic in rural and remote Australia provided an opportunity to evaluate the performance of Rotarix and RotaTeq rotavirus vaccines, ten years after their incorporation into Australia’s National Immunisation Program. Methods: We conducted a retrospective case-control analysis. Vaccine-eligible children with laboratory-confirmed rotavirus infection were identified from jurisdictional notifiable infectious disease databases and individually matched to controls from the national immunisation register, based on date of birth, Aboriginal status and location of residence. Results: 171 cases met the inclusion criteria; most were Aboriginal and/or Torres Strait Islander (80%) and the median age was 19 months. Of these cases, 65% and 25% were fully or partially vaccinated, compared to 71% and 21% of controls. Evidence that cases were less likely than controls to have received a rotavirus vaccine dose was weak, OR 0.79 (95% CI, 0.46–1.34). On pre-specified subgroup analysis, there was some evidence of protection among children <12 months (OR 0.48 [95% CI, 0.22–1.02]), and among fully vs. partially vaccinated children (OR 0.65 [95% CI, 0.42–1.01]). Conclusion: Despite the known effectiveness of rotavirus vaccination, a protective effect of either rotavirus vaccine during a G2P[4] outbreak in these settings among predominantly Aboriginal children was weak, highlighting the ongoing need for a more effective rotavirus vaccine and public health strategies to better protect Aboriginal children. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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16 pages, 615 KiB  
Article
Molecular Epidemiology of Rotavirus A Strains Pre- and Post-Vaccine (Rotarix®) Introduction in Mozambique, 2012–2019: Emergence of Genotypes G3P[4] and G3P[8]
by Eva D. João, Benilde Munlela, Assucênio Chissaque, Jorfélia Chilaúle, Jerónimo Langa, Orvalho Augusto, Simone S. Boene, Elda Anapakala, Júlia Sambo, Esperança Guimarães, Diocreciano Bero, Marta Cassocera, Idalécia Cossa-Moiane, Jason M. Mwenda, Isabel Maurício, Hester G. O’Neill and Nilsa de Deus
Pathogens 2020, 9(9), 671; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9090671 - 19 Aug 2020
Cited by 20 | Viewed by 5267
Abstract
Group A rotavirus (RVA) remains the most important etiological agent associated with severe acute diarrhea in children. Rotarix® monovalent vaccine was introduced into Mozambique’s Expanded Program on Immunization in September 2015. In the present study, we report the diversity and prevalence of [...] Read more.
Group A rotavirus (RVA) remains the most important etiological agent associated with severe acute diarrhea in children. Rotarix® monovalent vaccine was introduced into Mozambique’s Expanded Program on Immunization in September 2015. In the present study, we report the diversity and prevalence of rotavirus genotypes, pre- (2012–2015) and post-vaccine (2016–2019) introduction in Mozambique, among diarrheic children less than five years of age. Genotyping data were analyzed for five sentinel sites for the periods indicated. The primary sentinel site, Mavalane General Hospital (HGM), was analyzed for the period 2012–2019, and for all five sites (country-wide analyses), 2015–2019. During the pre-vaccine period, G9P[8] was the most predominant genotype for both HGM (28.5%) and the country-wide analysis (46.0%). However, in the post-vaccine period, G9P[8] was significantly reduced. Instead, G3P[8] was the most common genotype at HGM, while G1P[8] predominated country-wide. Genotypes G9P[4] and G9P[6] were detected for the first time, and the emergence of G3P[8] and G3P[4] genotypes were observed during the post-vaccine period. The distribution and prevalence of rotavirus genotypes were distinct in pre- and post-vaccination periods, while uncommon genotypes were also detected in the post-vaccine period. These observations support the need for continued country-wide surveillance to monitor changes in strain diversity, due to possible vaccine pressure, and consequently, the effect on vaccine effectiveness. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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22 pages, 1268 KiB  
Article
Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia
by Wairimu M. Maringa, Peter N. Mwangi, Julia Simwaka, Evans M. Mpabalwani, Jason M. Mwenda, Ina Peenze, Mathew D. Esona, M. Jeffrey Mphahlele, Mapaseka L. Seheri and Martin M. Nyaga
Pathogens 2020, 9(8), 663; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9080663 - 17 Aug 2020
Cited by 15 | Viewed by 4040
Abstract
A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 [...] Read more.
A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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14 pages, 3856 KiB  
Article
Epidemiological Trends of Five Common Diarrhea-Associated Enteric Viruses Pre- and Post-Rotavirus Vaccine Introduction in Coastal Kenya
by Arnold W. Lambisia, Sylvia Onchaga, Nickson Murunga, Clement S. Lewa, Steven Ger Nyanjom and Charles N. Agoti
Pathogens 2020, 9(8), 660; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9080660 - 15 Aug 2020
Cited by 15 | Viewed by 3761
Abstract
Using real-time RT-PCR, we screened stool samples from children aged <5 years presenting with diarrhea and admitted to Kilifi County Hospital, coastal Kenya, pre- (2003 and 2013) and post-rotavirus vaccine introduction (2016 and 2019) for five viruses, namely rotavirus group A (RVA), norovirus [...] Read more.
Using real-time RT-PCR, we screened stool samples from children aged <5 years presenting with diarrhea and admitted to Kilifi County Hospital, coastal Kenya, pre- (2003 and 2013) and post-rotavirus vaccine introduction (2016 and 2019) for five viruses, namely rotavirus group A (RVA), norovirus GII, adenovirus, astrovirus and sapovirus. Of the 984 samples analyzed, at least one virus was detected in 401 (40.8%) patients. Post rotavirus vaccine introduction, the prevalence of RVA decreased (23.3% vs. 13.8%, p < 0.001) while that of norovirus GII increased (6.6% vs. 10.9%, p = 0.023). The prevalence of adenovirus, astrovirus and sapovirus remained statistically unchanged between the two periods: 9.9% vs. 14.2%, 2.4% vs. 3.2 %, 4.6% vs. 2.6%, (p = 0.053, 0.585 and 0.133), respectively. The median age of diarrhea cases was higher post vaccine introduction (12.5 months, interquartile range (IQR): 7.9–21 vs. 11.2 months pre-introduction, IQR: 6.8–16.5, p < 0.001). In this setting, RVA and adenovirus cases peaked in the dry months while norovirus GII and sapovirus peaked in the rainy season. Astrovirus did not display clear seasonality. In conclusion, following rotavirus vaccine introduction, we found a significant reduction in the prevalence of RVA in coastal Kenya but an increase in norovirus GII prevalence in hospitalized children. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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17 pages, 42573 KiB  
Article
Phylogenetic Analyses of Rotavirus A from Cattle in Uruguay Reveal the Circulation of Common and Uncommon Genotypes and Suggest Interspecies Transmission
by Matías Castells, Rubén Darío Caffarena, María Laura Casaux, Carlos Schild, Samuel Miño, Felipe Castells, Daniel Castells, Matías Victoria, Franklin Riet-Correa, Federico Giannitti, Viviana Parreño and Rodney Colina
Pathogens 2020, 9(7), 570; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9070570 - 14 Jul 2020
Cited by 15 | Viewed by 3001
Abstract
Uruguay is one of the main exporters of beef and dairy products, and cattle production is one of the main economic sectors in this country. Rotavirus A (RVA) is the main pathogen associated with neonatal calf diarrhea (NCD), a syndrome that leads to [...] Read more.
Uruguay is one of the main exporters of beef and dairy products, and cattle production is one of the main economic sectors in this country. Rotavirus A (RVA) is the main pathogen associated with neonatal calf diarrhea (NCD), a syndrome that leads to significant economic losses to the livestock industry. The aims of this study are to determine the frequency of RVA infections, and to analyze the genetic diversity of RVA strains in calves in Uruguay. A total of 833 samples from dairy and beef calves were analyzed through RT-qPCR and sequencing. RVA was detected in 57.0% of the samples. The frequency of detection was significantly higher in dairy (59.5%) than beef (28.4%) calves (p < 0.001), while it did not differ significantly among calves born in herds that were vaccinated (64.0%) or not vaccinated (66.7%) against NCD. The frequency of RVA detection and the viral load were significantly higher in samples from diarrheic (72.1%, 7.99 log10 genome copies/mL of feces) than non-diarrheic (59.9%, 7.35 log10 genome copies/mL of feces) calves (p < 0.005 and p = 0.007, respectively). The observed G-types (VP7) were G6 (77.6%), G10 (20.7%), and G24 (1.7%), while the P-types were P[5] (28.4%), P[11] (70.7%), and P[33] (0.9%). The G-type and P-type combinations were G6P[11] (40.4%), G6P[5] (38.6%), G10P[11] (19.3%), and the uncommon genotype G24P[33] (1.8%). VP6 and NSP1-5 genotyping were performed to better characterize some strains. The phylogenetic analyses suggested interspecies transmission, including transmission between animals and humans. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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15 pages, 2312 KiB  
Article
Rotavirus A in Brazil: Molecular Epidemiology and Surveillance during 2018–2019
by Meylin Bautista Gutierrez, Alexandre Madi Fialho, Adriana Gonçalves Maranhão, Fábio Correia Malta, Juliana da Silva Ribeiro de Andrade, Rosane Maria Santos de Assis, Sérgio da Silva e Mouta, Marize Pereira Miagostovich, José Paulo Gagliardi Leite and Tulio Machado Fumian
Pathogens 2020, 9(7), 515; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9070515 - 27 Jun 2020
Cited by 21 | Viewed by 2727
Abstract
Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use [...] Read more.
Rotavirus A (RVA) vaccines succeeded in lowering the burden of acute gastroenteritis (AGE) worldwide, especially preventing severe disease and mortality. In 2019, Brazil completed 13 years of RVA vaccine implementation (Rotarix™) within the National Immunization Program (NIP), and as reported elsewhere, the use of Rotarix™ in the country has reduced childhood mortality and morbidity due to AGE. Even though both marketed vaccines are widely distributed, the surveillance of RVA causing AGE and the monitoring of circulating genotypes are important tools to keep tracking the epidemiological scenario and vaccines impact. Thus, our study investigated RVA epidemiological features, viral load and G and P genotypes circulation in children and adults presenting AGE symptoms in eleven states from three out of five regions in Brazil. By using TaqMan®-based one-step RT-qPCR, we investigated a total of 1536 stool samples collected from symptomatic inpatients, emergency department visits and outpatients from January 2018 to December 2019. G and P genotypes of RVA-positive samples were genetically characterized by multiplex RT-PCR or by nearly complete fragment sequencing. We detected RVA in 12% of samples, 10.5% in 2018 and 13.7% in 2019. A marked winter/spring seasonality was observed, especially in Southern Brazil. The most affected age group was children aged >24–60 months, with a positivity rate of 18.8% (p < 0.05). Evaluating shedding, we found a statistically lower RVA viral load in stool samples collected from children aged up to six months compared to the other age groups (p < 0.05). The genotype G3P[8] was the most prevalent during the two years (83.7% in 2018 and 65.5% in 2019), and nucleotide sequencing of some strains demonstrated that they belonged to the emergent equine-like G3P[8] genotype. The dominance of an emergent genotype causing AGE reinforces the need for continuous epidemiological surveillance to assess the impact of mass RVA immunization as well as to monitor the emergence of novel genotypes. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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15 pages, 605 KiB  
Article
Group A Rotavirus Detection and Genotype Distribution before and after Introduction of a National Immunisation Programme in Ireland: 2015–2019
by Zoe Yandle, Suzie Coughlan, Jonathan Dean, Gráinne Tuite, Anne Conroy and Cillian F. De Gascun
Pathogens 2020, 9(6), 449; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9060449 - 07 Jun 2020
Cited by 14 | Viewed by 3040
Abstract
Immunisation against rotavirus infection was introduced into Ireland in December 2016. We report on the viruses causing gastroenteritis before (2015–2016) and after (2017–2019) implementation of the Rotarix vaccine, as well as changes in the diversity of circulating rotavirus genotypes. Samples from patients aged [...] Read more.
Immunisation against rotavirus infection was introduced into Ireland in December 2016. We report on the viruses causing gastroenteritis before (2015–2016) and after (2017–2019) implementation of the Rotarix vaccine, as well as changes in the diversity of circulating rotavirus genotypes. Samples from patients aged ≤ 5 years (n = 11,800) were received at the National Virus Reference Laboratory, Dublin, and tested by real-time RT-PCR for rotavirus, Rotarix, norovirus, sapovirus, astrovirus, and enteric adenovirus. Rotavirus genotyping was performed either by multiplex or hemi-nested RT-PCR, and a subset was characterised by sequence analysis. Rotavirus detection decreased by 91% in children aged 0–12 months between 2015/16 and 2018/19. Rotarix was detected in 10% of those eligible for the vaccine and was not found in those aged >7 months. Rotavirus typically peaks in March–May, but following vaccination, the seasonality became less defined. In 2015–16, G1P[8] was the most common genotype circulating; however, in 2019 G2P[4] was detected more often. Following the introduction of Rotarix, a reduction in numbers of rotavirus infections occurred, coinciding with an increase in genotype diversity, along with the first recorded detection of an equine-like G3 strain in Ireland. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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17 pages, 1519 KiB  
Article
Uncovering the First Atypical DS-1-like G1P[8] Rotavirus Strains That Circulated during Pre-Rotavirus Vaccine Introduction Era in South Africa
by Peter N. Mwangi, Milton T. Mogotsi, Sebotsana P. Rasebotsa, Mapaseka L. Seheri, M. Jeffrey Mphahlele, Valantine N. Ndze, Francis E. Dennis, Khuzwayo C. Jere and Martin M. Nyaga
Pathogens 2020, 9(5), 391; https://0-doi-org.brum.beds.ac.uk/10.3390/pathogens9050391 - 20 May 2020
Cited by 17 | Viewed by 3319
Abstract
Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. [...] Read more.
Emergence of DS-1-like G1P[8] group A rotavirus (RVA) strains during post-rotavirus vaccination period has recently been reported in several countries. This study demonstrates, for the first time, rare atypical DS-1-like G1P[8] RVA strains that circulated in 2008 during pre-vaccine era in South Africa. Rotavirus positive samples were subjected to whole-genome sequencing. Two G1P[8] strains (RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1971/2008/G1P[8] and RVA/Human-wt/ZAF/UFS-NGS-MRC-DPRU1973/2008/G1P[8]) possessed a DS-1-like genome constellation background (I2-R2-C2-M2-A2-N2-T2-E2-H2). The outer VP4 and VP7 capsid genes of the two South African G1P[8] strains had the highest nucleotide (amino acid) nt (aa) identities of 99.6–99.9% (99.1–100%) with the VP4 and the VP7 genes of a locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU1039/2008/G1P[8]. All the internal backbone genes (VP1–VP3, VP6, and NSP1-NSP5) had the highest nt (aa) identities with cognate internal genes of another locally circulating South African strain, RVA/Human-wt/ZAF/MRC-DPRU2344/2008/G2P[6]. The two study strains emerged through reassortment mechanism involving locally circulating South African strains, as they were distinctly unrelated to other reported atypical G1P[8] strains. The identification of these G1P[8] double-gene reassortants during the pre-vaccination period strongly supports natural RVA evolutionary mechanisms of the RVA genome. There is a need to maintain long-term whole-genome surveillance to monitor such atypical strains. Full article
(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)
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