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Yamani LN, Utsumi T, Doan YH, Fujii Y, Dinana Z, Wahyuni RM, Gunawan E, Soegijanto S, Athiyyah AF, Sudarmo SM, Ranuh RG, Darma A, Soetjipto, Juniastuti, Bawono RG, Matsui C, Deng L, Abe T, Shimizu H, Ishii K, Katayama K, Lusida MI, Shoji I. Complete genome analyses of G12P[8] rotavirus strains from hospitalized children in Surabaya, Indonesia, 2017-2018. J Med Virol 2023; 95:e28485. [PMID: 36625390 DOI: 10.1002/jmv.28485] [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: 09/26/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Rotavirus A (RVA) is a major viral cause of acute gastroenteritis (AGE) worldwide. G12 RVA strains have emerged globally since 2007. There has been no report of the whole genome sequences of G12 RVAs in Indonesia. We performed the complete genome analysis by the next-generation sequencing of five G12 strains from hospitalized children with AGE in Surabaya from 2017 to 2018. All five G12 strains were Wa-like strains (G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1) and were clustered into lineage-III of VP7 gene phylogenetic tree. STM430 sample was observed as a mixed-infection between G12 and G1 strains: G12/G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. A phylogenetic tree analysis revealed that all five Indonesian G12 strains (SOEP379, STM371, STM413, STM430, and STM433) were genetically close to each other in all 11 genome segments with 98.0%-100% nucleotide identities, except VP3 and NSP4 of STM430, suggesting that these strains have originated from a similar ancestral G12 RVA. The VP3 and NSP4 genome segments of STM430-G12P[8] were separated phylogenetically from those of the other four G12 strains, probably due to intra-genotype reassortment between the G12 and G1 Wa-like strains. The change from G12P[6] lineage-II in 2007 to G12P[8] lineage-III 2017-2018 suggests the evolution and diversity of G12 RVAs in Indonesia over the past approximately 10 years.
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Affiliation(s)
- Laura Navika Yamani
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Epidemiology, Biostatistics, Population Studies and Health Promotion, Faculty of Public Health, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Viral Diarrhea, Research Center on Global Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Takako Utsumi
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Yen Hai Doan
- Laboratory VIII, Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Zayyin Dinana
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Viral Diarrhea, Research Center on Global Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Rury Mega Wahyuni
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Emily Gunawan
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Soegeng Soegijanto
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Alpha Fardah Athiyyah
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Child Health, Soetomo Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Subijanto Marto Sudarmo
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Child Health, Soetomo Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Reza Gunadi Ranuh
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Child Health, Soetomo Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Andy Darma
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Child Health, Soetomo Hospital, Universitas Airlangga, Surabaya, Indonesia
| | - Soetjipto
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Viral Diarrhea, Research Center on Global Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Juniastuti
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Viral Diarrhea, Research Center on Global Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Rheza Gandi Bawono
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Chieko Matsui
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Lin Deng
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Takayuki Abe
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
| | - Hiroyuki Shimizu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Ishii
- Department of Quality Assurance and Radiological Protection, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Maria Inge Lusida
- Laboratory of Viral Diarrhea, Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Laboratory of Viral Diarrhea, Research Center on Global Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Ikuo Shoji
- Division of Infectious Disease Control, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
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2
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Rotavirus Strain Trends in United States, 2009–2016: Results from the National Rotavirus Strain Surveillance System (NRSSS). Viruses 2022; 14:v14081775. [PMID: 36016397 PMCID: PMC9414880 DOI: 10.3390/v14081775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Before the introduction of vaccines, group A rotaviruses (RVA) were the leading cause of acute gastroenteritis in children worldwide. The National Rotavirus Strain Surveillance System (NRSSS) was established in 1996 by the Centers for Disease Control and Prevention (CDC) to perform passive RVA surveillance in the USA. We report the distribution of RVA genotypes collected through NRSSS during the 2009–2016 RVA seasons and retrospectively examine the genotypes detected through the NRSSS since 1996. During the 2009–2016 RVA seasons, 2134 RVA-positive fecal specimens were sent to the CDC for analysis of the VP7 and VP4 genes by RT-PCR genotyping assays and sequencing. During 2009–2011, RVA genotype G3P[8] dominated, while G12P[8] was the dominant genotype during 2012–2016. Vaccine strains were detected in 1.7% of specimens and uncommon/unusual strains, including equine-like G3P[8] strains, were found in 1.9%. Phylogenetic analyses showed limited VP7 and VP4 sequence variation within the common genotypes with 1–3 alleles/lineages identified per genotype. A review of 20 years of NRSSS surveillance showed two changes in genotype dominance, from G1P[8] to G3P[8] and then G3P[8] to G12P[8]. A better understanding of the long-term effects of vaccine use on epidemiological and evolutionary dynamics of circulating RVA strains requires continued surveillance.
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3
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Omatola CA, Ogunsakin RE, Olaniran AO. Prevalence, Pattern and Genetic Diversity of Rotaviruses among Children under 5 Years of Age with Acute Gastroenteritis in South Africa: A Systematic Review and Meta-Analysis. Viruses 2021; 13:1905. [PMID: 34696335 PMCID: PMC8538439 DOI: 10.3390/v13101905] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/15/2021] [Indexed: 12/26/2022] Open
Abstract
Rotavirus is the most significant cause of severe acute gastroenteritis among children under 5 years of age, worldwide. Sub-Saharan Africa particularly bears the brunt of the diarrheal deaths. A meta-analysis was conducted on 43 eligible studies published between 1982 and 2020 to estimate the pooled prevalence of rotavirus infection and changes in the main rotavirus strains circulating before and after vaccine introduction among under-five children in South Africa. The pooled national prevalence of rotavirus infection was estimated at 24% (95% CI: 21-27%) for the pre-vaccination period and decreased to 23% (95% CI: 21-25%) in the post-vaccination period. However, an increased number of cases was observed in the KwaZulu-Natal (21-28%) and Western Cape (18-24%) regions post-vaccination. The most dominant genotype combinations in the pre-vaccine era was G1P[8], followed by G2P[4], G3P[8], and G1P[6]. After vaccine introduction, a greater genotype diversity was observed, with G9P[8] emerging as the predominant genotype combination, followed by G2P[4], G12P[8], and G1P[8]. The introduction of the rotavirus vaccine was associated with a reduction in the burden of rotavirus-associated diarrhea in South Africa, although not without regional fluctuation. The observed changing patterns of genotype distribution highlights the need for ongoing surveillance to monitor the disease trend and to identify any potential effects associated with the dynamics of genotype changes on vaccine pressure/failure.
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Affiliation(s)
- Cornelius A. Omatola
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa;
| | - Ropo E. Ogunsakin
- Discipline of Public Health Medicine, School of Nursing and Public Health, College of Health Sciences, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa;
| | - Ademola O. Olaniran
- Discipline of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal (Westville Campus), Private Bag X54001, Durban 4000, South Africa;
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4
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Gupta S, Gauhar M, Bubber P, Ray P. Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013-2016. J Med Virol 2021; 93:6200-6209. [PMID: 34138482 DOI: 10.1002/jmv.27142] [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: 05/26/2021] [Accepted: 06/07/2021] [Indexed: 11/05/2022]
Abstract
G12 strains are now considered to be the sixth most prevalent human rotaviruses globally. India has introduced rotavirus vaccine Rotavac® into the national immunization program in 2016 and Himachal Pradesh (HP) is the first state to launch it. During epidemiological rotavirus surveillance in HP, predominance of G12 rotaviruses was observed. This study investigated the genetic variability and evolution of HP G12 strains (n = 15) associated with P-genotypes P[6], P[4], and P[8] identified between 2013 and 2016. Phylogenetic analysis of VP7 gene revealed that all characterized G12 strains clustered in lineage-III and diversified into three subclusters indicating that these strains may have originated from three different ancestral G12 strains. The comparative sequence analysis of HP strains with Rotavac® and Rotarix® vaccine strains revealed various amino acid substitutions in epitope regions of VP7 and VP4 proteins especially at the antibody neutralization sites. Only 12/29 VP7 epitope residues and 2/25 VP4 epitope residues were found to be conserved between HP rotavirus strains and vaccine strains. Both long and short electropherotypes were observed in G12P[4] strains, while a single long electropherotype was observed in G12P[6] strains. Children of ≤11 months were significantly infected with G12 rotaviruses. The frequency of vomiting episodes (≥5/day) was significantly higher in children infected with G12 rotavirus strains as compared to non-G12 rotaviruses (p = 0.0405). Our study provides the comprehensive data on clinical characteristics and evolutionary pattern of the G12 rotavirus, the most prevalent strain in HP and emphasizes the need to monitor these strains for inclusion in future vaccine.
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Affiliation(s)
- Shipra Gupta
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Mariyam Gauhar
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India
| | - Parvesh Bubber
- Department of Biochemistry, School of Sciences, IGNOU, New Delhi, India
| | - Pratima Ray
- Department of Biotechnology, School of Chemical & Life Sciences, Jamia Hamdard, New Delhi, India.,Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
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5
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Cárcamo-Calvo R, Muñoz C, Buesa J, Rodríguez-Díaz J, Gozalbo-Rovira R. The Rotavirus Vaccine Landscape, an Update. Pathogens 2021; 10:520. [PMID: 33925924 PMCID: PMC8145439 DOI: 10.3390/pathogens10050520] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Rotavirus is the leading cause of severe acute childhood gastroenteritis, responsible for more than 128,500 deaths per year, mainly in low-income countries. Although the mortality rate has dropped significantly since the introduction of the first vaccines around 2006, an estimated 83,158 deaths are still preventable. The two main vaccines currently deployed, Rotarix and RotaTeq, both live oral vaccines, have been shown to be less effective in developing countries. In addition, they have been associated with a slight risk of intussusception, and the need for cold chain maintenance limits the accessibility of these vaccines to certain areas, leaving 65% of children worldwide unvaccinated and therefore unprotected. Against this backdrop, here we review the main vaccines under development and the state of the art on potential alternatives.
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Affiliation(s)
- Roberto Cárcamo-Calvo
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
| | - Carlos Muñoz
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
| | - Javier Buesa
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Jesús Rodríguez-Díaz
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
| | - Roberto Gozalbo-Rovira
- Department of Microbiology, School of Medicine, University of Valencia, Av. Blasco Ibañez 17, 46010 Valencia, Spain; (R.C.-C.); (C.M.); (J.B.)
- Instituto de Investigación INCLIVA, Hospital Clínico Universitario de Valencia, 46010 Valencia, Spain
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6
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Mokoena F, Esona MD, Seheri LM, Nyaga MM, Magagula NB, Mukaratirwa A, Mulindwa A, Abebe A, Boula A, Tsolenyanu E, Simwaka J, Rakau KG, Peenze I, Mwenda JM, Mphahlele MJ, Steele AD. Whole Genome Analysis of African G12P[6] and G12P[8] Rotaviruses Provides Evidence of Porcine-Human Reassortment at NSP2, NSP3, and NSP4. Front Microbiol 2021; 11:604444. [PMID: 33510725 PMCID: PMC7835662 DOI: 10.3389/fmicb.2020.604444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/10/2020] [Indexed: 01/27/2023] Open
Abstract
Group A rotaviruses (RVA) represent the most common cause of pediatric gastroenteritis in children <5 years, worldwide. There has been an increase in global detection and reported cases of acute gastroenteritis caused by RVA genotype G12 strains, particularly in Africa. This study sought to characterize the genomic relationship between African G12 strains and determine the possible origin of these strains. Whole genome sequencing of 34 RVA G12P[6] and G12P[8] strains detected from the continent including southern (South Africa, Zambia, Zimbabwe), eastern (Ethiopia, Uganda), central (Cameroon), and western (Togo) African regions, were sequenced using the Ion Torrent PGM method. The majority of the strains possessed a Wa-like backbone with consensus genotype constellation of G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, while a single strain from Ethiopia displayed a DS-1-like genetic constellation of G12-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. In addition, three Ethiopian and one South African strains exhibited a genotype 2 reassortment of the NSP3 gene, with genetic constellation of G12-P[8]-I1-R1-C1-M1-A1-N1-T2-E1-H1. Overall, 10 gene segments (VP1–VP4, VP6, and NSP1–NSP5) of African G12 strains were determined to be genetically related to cognate gene sequences from globally circulating human Wa-like G12, G9, and G1 strains with nucleotide (amino acid) identities in the range of 94.1–99.9% (96.5–100%), 88.5–98.5% (93–99.1%), and 89.8–99.0% (88.7–100%), respectively. Phylogenetic analysis showed that the Ethiopian G12P[6] possessing a DS-1-like backbone consistently clustered with G2P[4] strains from Senegal and G3P[6] from Ethiopia with the VP1, VP2, VP6, and NSP1–NSP4 genes. Notably, the NSP2, NSP3, and NSP4 of most of the study strains exhibited the closest relationship with porcine strains suggesting the occurrence of reassortment between human and porcine strains. Our results add to the understanding of potential roles that interspecies transmission play in generating human rotavirus diversity through reassortment events and provide insights into the evolutionary dynamics of G12 strains spreading across selected sub-Saharan Africa regions.
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Affiliation(s)
- Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Science, North West University, Mmabatho, South Africa.,Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Mathew Dioh Esona
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Luyanda Mapaseka Seheri
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Martin Munene Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Nonkululelo Bonakele Magagula
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Arnold Mukaratirwa
- Department of Medical Microbiology, University of Zimbabwe-College of Health Sciences, Harare, Zimbabwe
| | | | - Almaz Abebe
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Angeline Boula
- Mother and Child Center, Chantal Biya Foundation, Yaoundé, Cameroon
| | - Enyonam Tsolenyanu
- Department of Paediatrics, Sylvanus Olympio Teaching Hospital of Lome, Lome, Togo
| | - Julia Simwaka
- Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Kebareng Giliking Rakau
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Ina Peenze
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Jason Mathiu Mwenda
- African Rotavirus Surveillance Network, Immunization, Vaccines and Development Cluster, WHO African Regional Office, Brazzaville, Congo
| | - Maphahlaganye Jeffrey Mphahlele
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Andrew Duncan Steele
- Diarrhoeal Pathogens Research Unit, Department of Virology, Sefako Makgatho Health Sciences University, Pretoria, South Africa.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, WA, United States
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7
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Camilloni B, Alunno A, Nunzi E, Sarnari L, Ianiro G, Monini M. Hospital-acquired rotavirus acute gastroenteritis in 10 consecutive seasons in Umbria (Italy). J Med Virol 2020; 92:3202-3208. [PMID: 32285951 DOI: 10.1002/jmv.25878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/02/2020] [Accepted: 04/11/2020] [Indexed: 11/11/2022]
Abstract
Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in young (aged <5 years) children. Several studies showed that RVA is one of the main cause of nosocomial gastroenteritis in hospitalized pediatric population worldwide, with an incidence ranging from 8 to 33 cases per 100 hospitalized children. Nosocomial infections, in which AGE symptoms develop at least 2 days after admission, may severely affect children already admitted to hospital for other causes. This study aimed to define the trends of the RVA genotypes through statistical analysis of the data obtained by the rotavirus surveillance in Umbria in 10 consecutive seasons, from 2007-2008 to 2016-2017, with update information on hospital-acquired RVA AGE. During RVA gastroenteritis surveillance in Umbria (Italy) in 2007 to 2017, a total of 741 RVA positive faecal samples were collected from children hospitalized with AGE, and RVA strains were genotyped following standard EuroRotaNet protocols. Of the 741 analyzed samples, 75 (10%) were reported to be hospital-acquired. Comparing the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections, we observed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community except in 2010 to 2011, 2011 to 2012, and 2012 to 2013 when G1P[8], G4P[8] and the novel strain G12P[8] caused a large community- and hospital-acquired outbreak. Of the 741 analyzed samples, 75 (10%) were reported to be hospital-acquired. Comparing the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections, we observed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community except in 2010 to 2011, 2011 to 2012, and 2012 to 2013 when G1P[8], G4P[8], and the novel strain G12P[8] caused a large community- and hospital-acquired outbreak. The information from this study will be useful to implement guidelines for preventing nosocomial RVA AGE, which should include an improved management of the hospitalized patients and an increase in vaccination coverage.
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Affiliation(s)
| | - Anna Alunno
- Department of Medicine, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Laura Sarnari
- School of Hygiene and Preventive Medicine, University of Perugia, Perugia, Italy
| | - Giovanni Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Marina Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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8
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Oishi T, Matsunaga M, Nakano T, Sudo S, Kuwajima H, Tokuriki S, Study SR. Occurrence of severe rotavirus gastroenteritis in children younger than three years of age before and after the introduction of rotavirus vaccine: a prospective observational study in four pediatric clinics in Shibata City, Niigata Prefecture, Japan. Hum Vaccin Immunother 2020; 16:2495-2501. [PMID: 32609565 PMCID: PMC7644216 DOI: 10.1080/21645515.2020.1720435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In Japan, rotavirus (RV) vaccines have already been introduced but not used for universal vaccination as of 2018. Therefore, we identified cases of severe rotavirus gastroenteritis (RVGE) in children younger than three years of age and investigated the occurrence of infection before and after the introduction of RV vaccines. An ecological study through prospective surveillance was conducted in four pediatric clinics in Shibata City, Niigata Prefecture, Japan, during the 2011 to 2018 RVGE epidemic seasons. We divided the study period into three eras: pre-vaccine introduction era (2011), low-mid coverage transitional era (2012 to 2014, RV vaccine coverage rate: 32.9–56.5%), and high coverage plateau era (2015 to 2018, 67.7–81.7%). In this study, the incidence rate of severe RVGE was significantly lower in the plateau era than in the pre-vaccine introduction and transitional eras. Furthermore, the hospitalization rate due to RVGE in Shibata City was lower in the plateau era than in the pre-vaccination introduction and transitional eras. The number of hospitalizations due to RVGE in subjects who required or did not require intravenous rehydration at the pediatric clinics significantly decreased with the increase in vaccine coverage rates by more than 70% in the plateau era.
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Affiliation(s)
- Tomohiro Oishi
- Department of Pediatrics, Kawasaki Medical School , Kurashiki, Japan
| | - Masamichi Matsunaga
- Pediatric Department, Niigata Prefectural Shibata Hospital , Shibata City, Japan
| | - Tokushi Nakano
- Pediatric Department, Nakano Children's Clinic , Shibata City, Japan
| | - Shoji Sudo
- Pediatric Department, Sudo Pediatric Clinic , Shibata City, Japan
| | | | - Shuko Tokuriki
- Pediatric Department, Twin Smile Clinic , Shibata City, Japan
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9
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Ianiro G, Micolano R, Di Bartolo I, Scavia G, Monini M. Group A rotavirus surveillance before vaccine introduction in Italy, September 2014 to August 2017. ACTA ACUST UNITED AC 2020; 24. [PMID: 30994104 PMCID: PMC6470368 DOI: 10.2807/1560-7917.es.2019.24.15.1800418] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Introduction Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in young children, causing ca 250,000 deaths worldwide, mainly in low-income countries. Two proteins, VP7 (glycoprotein, G genotype) and VP4 (protease-sensitive protein, P genotype), are the basis for the binary RVA nomenclature. Although 36 G types and 51 P types are presently known, most RVA infections in humans worldwide are related to five G/P combinations: G1P[8], G2P[4], G3P[8], G4P[8], G9P[8]. Aim This study aimed to characterise the RVA strains circulating in Italy in the pre-vaccination era, to define the trends of circulation of genotypes in the Italian paediatric population. Methods Between September 2014 and August 2017, after routine screening in hospital by commercial antigen detection kit, 2,202 rotavirus-positive samples were collected in Italy from children hospitalised with AGE; the viruses were genotyped following standard European protocols. Results This 3-year study revealed an overall predominance of the G12P[8] genotype (544 of 2,202 cases; 24.70%), followed by G9P[8] (535/2,202; 24.30%), G1P[8] (459/2,202; 20.84%) and G4P[8] (371/2,202; 16.85%). G2P[4] and G3P[8] genotypes were detected at low rates (3.32% and 3.09%, respectively). Mixed infections accounted for 6.49% of cases (143/2,202), uncommon RVA strains for 0.41% of cases (9/2,202). Conclusions The emergence of G12P[8] rotavirus in Italy, as in other countries, marks this genotype as the sixth most common human genotype. Continuous surveillance of RVA strains and monitoring of circulating genotypes are important for a better understanding of rotavirus evolution and genotype distribution, particularly regarding strains that may emerge from reassortment events.
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Affiliation(s)
- Giovanni Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Roberto Micolano
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Gaia Scavia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Marina Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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10
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Epidemiological Surveillance of Norovirus and Rotavirus in Sewage (2016-2017) in Valencia (Spain). Microorganisms 2020; 8:microorganisms8030458. [PMID: 32213877 PMCID: PMC7144017 DOI: 10.3390/microorganisms8030458] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/03/2020] [Accepted: 03/23/2020] [Indexed: 12/02/2022] Open
Abstract
The aim of the present study was to perform the molecular epidemiology of rotaviruses and noroviruses detected in sewage samples from a large wastewater facility from the city of Valencia, Spain. A total of 46 sewage samples were collected over a one-year period (September 2016 to September 2017). Norovirus and rotavirus were detected and quantified by RT-qPCR, genotyped by semi-nested RT-PCR and further characterized by sequencing and phylogenetic analyses. Noroviruses and rotaviruses were widely distributed in sewage samples (69.6% for norovirus GI, 76.0% norovirus GII, and 71.7% rotaviruses) and viral loads varied from 4.33 to 5.75 log PCRU/L for norovirus GI, 4.69 to 6.95 log PCRU/L for norovirus GII, and 4.08 to 6.92 log PCRU/L for rotavirus. Overall, 87.5% (28/32) of GI noroviruses could not be genotyped, 6.25% (2/32) of the samples contained GI.2 genotype, and another 6.25% (2/32) were positive for GI.4 genotype. The most common genotype of GII noroviruses was GII.2 (40%, 14/35), followed by GII.6 (8.6%, 3/35) and GII.17 (5.7%, 2/35) while the remaining GII strains could not be typed (45.7%, 16/35). Rotavirus VP4 genotype P[8] was the only one found in 19 out of 33 rotavirus-positive samples (57.7%). G2 was the most prevalent rotavirus VP7 genotype (15.2%, 5/33) followed by G3, G9, and G12, with two positive samples for each genotype (6.1%, 2/33). In one sample both G1 and G2 genotypes were detected simultaneously (3%). The results presented here show that the surveillance of noroviruses and rotaviruses in sewage is useful for the study of their transmission in the population and their molecular epidemiology.
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11
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Silva-Sales M, Martínez-Puchol S, Gonzales-Gustavson E, Hundesa A, Gironès R. High Prevalence of Rotavirus A in Raw Sewage Samples from Northeast Spain. Viruses 2020; 12:v12030318. [PMID: 32188099 PMCID: PMC7150846 DOI: 10.3390/v12030318] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/08/2020] [Accepted: 03/14/2020] [Indexed: 12/20/2022] Open
Abstract
Rotavirus A (RVA) is the most common virus associated with infantile gastroenteritisworldwide, being a public health threat, as it is excreted in large amounts in stool and can persist inthe environment for extended periods. In this study, we performed the detection of RVA and humanadenovirus (HAdV) by TaqMan qPCR and assessed the circulation of RVA genotypes in threewastewater treatment plants (WWTPs) between 2015 and 2016 in Catalonia, Spain. RVA wasdetected in 90% and HAdV in 100% of the WWTP samples, with viral loads ranging between 3.96 ×104 and 3.30 × 108 RT-PCR Units/L and 9.51 × 104 and 1.16 × 106 genomic copies/L, respectively. RVAVP7 and VP4 gene analysis revealed the circulation of G2, G3, G9, G12, P[4], P[8], P[9] and P[10].Nucleotide sequencing (VP6 fragment) showed the circulation of I1 and I2 genotypes, commonlyassociated with human, bovine and porcine strains. It is important to mention that the RVA strainsisolated from the WWTPs were different from those recovered from piglets and calves living in thesame area of single sampling in 2016. These data highlight the importance of monitoring watermatrices for RVA epidemiology and may be a useful tool to evaluate and predict possibleemergence/reemergence of uncommon strains in a region.
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12
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de Waure C, Sarnari L, Chiavarini M, Ianiro G, Monini M, Alunno A, Camilloni B. 10-Year Rotavirus Infection Surveillance: Epidemiological Trends in the Pediatric Population of Perugia Province. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E1008. [PMID: 32033439 PMCID: PMC7036783 DOI: 10.3390/ijerph17031008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/23/2020] [Accepted: 02/03/2020] [Indexed: 11/28/2022]
Abstract
Rotavirus (RV) infections are a leading cause of severe gastroenteritis in children, and vaccination is currently recommended in Italy, according to the National Immunization Plan 2017-2019. The objective of this study was to describe the epidemiological and molecular RV surveillance in the pediatric population of Perugia province, Umbria. Between September 2007 and August 2018, 663 RV-positive stool specimens were collected from children <15 years of age presenting with gastroenteritis to the emergency room of the Perugia province hospitals who were then hospitalized. Yearly hospitalization rates were expressed per 100,000 persons, and denominators were extrapolated from the National Institute of Statistics. During the 10-year surveillance, the epidemiological trend was fluctuating but slightly decreasing (Max: 89.7 per 100,000 in 2010/2011; Min: 34.8 per 100,000 in 2017/2018). The hospitalization rate was higher in males and in children under five years of age. Among common genotypes, G1P[8] was prevalent most of the years. The uncommon G12P [8] genotype emerged and was the most common in 2012/2013 (58.2%). Afterwards, its circulation remained high. As the Umbria Region started vaccinating from the 2018 birth cohort, our study reviewed pre-vaccination data and will help to assess the protection induced by vaccination and its effect on circulating strains.
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Affiliation(s)
- Chiara de Waure
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; (C.d.W.); (L.S.)
| | - Laura Sarnari
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; (C.d.W.); (L.S.)
| | - Manuela Chiavarini
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy; (C.d.W.); (L.S.)
| | - Giovanni Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.I.); (M.M.)
| | - Marina Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.I.); (M.M.)
| | - Anna Alunno
- Department of Medicine, University of Perugia, 06132 Perugia, Italy; (A.A.); (B.C.)
| | - Barbara Camilloni
- Department of Medicine, University of Perugia, 06132 Perugia, Italy; (A.A.); (B.C.)
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13
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Roczo-Farkas S, Kirkwood CD, Cowley D, Barnes GL, Bishop RF, Bogdanovic-Sakran N, Boniface K, Donato CM, Bines JE. The Impact of Rotavirus Vaccines on Genotype Diversity: A Comprehensive Analysis of 2 Decades of Australian Surveillance Data. J Infect Dis 2019; 218:546-554. [PMID: 29790933 DOI: 10.1093/infdis/jiy197] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/03/2018] [Indexed: 12/28/2022] Open
Abstract
Background Introduction of rotavirus vaccines into national immunization programs (NIPs) could result in strain selection due to vaccine-induced selective pressure. This study describes the distribution and diversity of rotavirus genotypes before and after rotavirus vaccine introduction into the Australian NIP. State-based vaccine selection facilitated a unique comparison of diversity in RotaTeq and Rotarix vaccine states. Methods From 1995 to 2015, the Australian Rotavirus Surveillance Program conducted genotypic analysis on 13051 rotavirus-positive samples from children <5 years of age, hospitalized with acute gastroenteritis. Rotavirus G and P genotypes were determined using serological and heminested multiplex reverse-transcription polymerase chain reaction assays. Results G1P[8] was the dominant genotype nationally in the prevaccine era (1995-2006). Following vaccine introduction (2007-2015), greater genotype diversity was observed with fluctuating genotype dominance. Genotype distribution varied based on the vaccine implemented, with G12P[8] dominant in states using RotaTeq, and equine-like G3P[8] and G2P[4] dominant in states and territories using Rotarix. Conclusions The increased diversity and differences in genotype dominance observed in states using RotaTeq (G12P[8]), and in states and territories using Rotarix (equine-like G3P[8] and G2P[4]), suggest that these vaccines exert different immunological pressures that influence the diversity of rotavirus strains circulating in Australia.
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Affiliation(s)
- Susie Roczo-Farkas
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Carl D Kirkwood
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
| | - Daniel Cowley
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Graeme L Barnes
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Department of Gastroenterology and Clinical Nutrition, Royal Children's Hospital, Parkville
| | - Ruth F Bishop
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nada Bogdanovic-Sakran
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Karen Boniface
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Celeste M Donato
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria, Australia
| | - Julie E Bines
- Enteric Virus Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.,Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington
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14
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Arana A, Jere KC, Chaguza C, Montes M, Alkorta M, Iturriza-Gomara M, Cilla G. Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018. INFECTION GENETICS AND EVOLUTION 2019; 71:67-75. [DOI: 10.1016/j.meegid.2019.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/31/2019] [Accepted: 03/20/2019] [Indexed: 12/16/2022]
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15
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Damanka SA, Agbemabiese CA, Dennis FE, Lartey BL, Adiku TK, Enweronu-Laryea CC, Armah GE. Genetic analysis of Ghanaian G1P[8] and G9P[8] rotavirus A strains reveals the impact of P[8] VP4 gene polymorphism on P-genotyping. PLoS One 2019; 14:e0218790. [PMID: 31242245 PMCID: PMC6594640 DOI: 10.1371/journal.pone.0218790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022] Open
Abstract
The World Health Organisation rotavirus surveillance networks have documented and shown eclectic geographic and temporal diversity in circulating G- and P- genotypes identified in children <5 years of age. To effectively monitor vaccine performance and effectiveness, robust molecular and phylogenetic techniques are essential to detect novel strain variants that might emerge due to vaccine pressure. This study inferred the phylogenetic history of the VP7 and VP4 genes of previously non-typeable strains and provided insight into the diversity of P[8] VP4 sequences which impacted the outcome of our routine VP4 genotyping method. Near-full-length VP7 gene and the VP8* fragment of the VP4 gene were obtained by Sanger sequencing and genotypes were determined using RotaC v2.0 web-based genotyping tool. The genotypes of the 57 rotavirus-positive samples with sufficient stool was determined. Forty-eight of the 57 (84.2%) had the P[8] specificity, of which 43 (89.6%) were characterized as P[8]a subtype and 5 (10.4%) as the rare OP354-like subtype. The VP7 gene of 27 samples were successfully sequenced and their G-genotypes confirmed as G1 (18/27) and G9 (9/27). Phylogenetic analysis of the P[8]a sequences placed them in subcluster IIIc within lineage III together with contemporary G1P[8], G3P[8], G8P[8], and G9P[8] strains detected globally from 2006-2016. The G1 VP7 sequences of the study strains formed a monophyletic cluster with African G1P[8] strains, previously detected in Ghana and Mali during the RotaTeq vaccine trial as well as Togo. The G9 VP7 sequences of the study strains formed a monophyletic cluster with contemporary African G9 sequences from neighbouring Burkina Faso within the major sub-cluster of lineage III. Mutations identified in the primer binding region of the VP8* sequence of the Ghanaian P[8]a strains may have resulted in the genotyping failure since the newly designed primer successfully genotyped the previously non-typeable P[8] strains. In summary, the G1, G9, and P[8]a sequences were highly similar to contemporary African strains at the lineage level. The study also resolved the methodological challenges of the standard genotyping techniques and highlighted the need for regular evaluation of the multiplex PCR-typing method especially in the post-vaccination era. The study further highlights the need for regions to start using sequencing data from local rotavirus strains to design and update genotyping primers.
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Affiliation(s)
- Susan Afua Damanka
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
- * E-mail:
| | - Chantal Ama Agbemabiese
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Francis Ekow Dennis
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Belinda Larteley Lartey
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
| | - Theophilus Korku Adiku
- School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | | | - George Enyimah Armah
- Department of Electron Microscopy and Histopathology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Accra, Ghana
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16
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Full-length genome analysis of the first human G8P[14] rotavirus strain from Morocco suggests evidence of zoonotic transmission. Virus Genes 2019; 55:465-478. [PMID: 31197545 DOI: 10.1007/s11262-019-01677-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/06/2019] [Indexed: 10/26/2022]
Abstract
An unusual group A rotavirus (RVA) strain MAR/ma31/2011/G8P[14] was detected for the first time in Morocco in a stool sample from hospitalized child aged 18 months suffering from acute gastroenteritis and fever in 2011. Complete genome sequencing of the ma31 strain was done using the capillary sequencing technology. The analysis revealed the G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 constellation and the backbone genes: I2-R2-C2-M2-A11-N2-T6-E2-H3 are commonly found in RVA strains from artiodactyls such as cattle. The constellation was shared with another Italian zoonotic G8P[14] strains (BA01 and BA02), two Hungarian human strains (182-02 and BP1062) and a sheep RVA strain OVR762. Phylogenetic analysis of each genome segment of ma31 revealed a mixed gene configuration originated from animals and human. Comparison of the antigenic regions of VP7 and VP4 amino acid sequences between ma31 strain and selected animal and human strains bearing G8 and or P[14], showed a high level of conservation, while many substitutions was observed in comparison with RotaTeq™ and Rotarix™ vaccine strains. In contrast, alignment analysis of the four antigenic sites of VP6 revealed a high degree of conservation. These findings reveal a typical zoonotic origin of the strain and confirm a high potential for RVA zoonotic transmission between bovine and humans, allowing the generation of novel rotavirus genotypes.
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17
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Carvalho-Costa FA, de Assis RMS, Fialho AM, Araújo IT, Silva MF, Gómez MM, Andrade JS, Rose TL, Fumian TM, Volotão EM, Miagostovich MP, Leite JPG. The evolving epidemiology of rotavirus A infection in Brazil a decade after the introduction of universal vaccination with Rotarix®. BMC Pediatr 2019; 19:42. [PMID: 30704518 PMCID: PMC6354375 DOI: 10.1186/s12887-019-1415-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/22/2019] [Indexed: 01/15/2023] Open
Abstract
Background Brazil introduced the monovalent rotavirus vaccine (Rotarix®) in 2006. This study aimed to assess the epidemiology and genotype distribution of species-A rotavirus (RVA) in Brazil, comparing the pre- and post-vaccination periods. Methods Laboratory-based RVA surveillance included 866 municipalities in 22 Brazilian states, over a 21-year period. A total of 16,185 children with diarrheal diseases (DD) aged up to 12 years between 1996 and 2005 (pre-vaccination period, n = 7030) and from 2006 to 2017 (post-vaccination period, n = 9155) were enrolled. RVA was detected using ELISA immune assay and/or polyacrylamide gel electrophoresis and genotyped using nested PCR and/or nucleotide sequencing. RVA-positivity and genotypes detection rates were compared in distinct periods and age groups and Rotarix vaccination status. Results RVA-positivity in pre- and post-vaccination periods was, respectively: 4–11 months bracket, 33.3% (668/2006) and 16.3% (415/2547) (p < 0.001); 12–24 months, 28.2% (607/2154) and 22.2% (680/3068) (p < 0.001); 25–48 months, 17.4% (215/1235) and 29.4% (505/1720) (p < 0.001). Genotypes distribution in the pre- and post-vaccination periods was, respectively: G1P [8]/G1P[Not Typed], 417/855 (48.8%) and 118/1835 (6.4%) (p < 0.001); G2P [4]/G2P[NT], 47/855 (5.5%) and 838/1835 (45.7%) (p < 0.001); G3P [8]/G3P[NT], 55/855 (6.4%) and 253/1835 (13.8%) (p < 0.001); G9P [8]/G9P[NT], 238/855 (27.8%) and 152/1835 (8.3%) (p < 0.001); G12P [8]/G129P[NT], 0/871 (0%) and 249/1835(13.6%) (p < 0.001). Concerning infants aged 4–11 months, RVA frequency in fully vaccinated and non-vaccinated individuals was 11.9% (125/1052) and 24.5% (58/237) (p < 0.001), respectively. In children aged 12–24 months, RVA detection rate was 18.1% (253/1395) and 29.6% (77/260) (p < 0.001), for the vaccinated and non-vaccinated individuals, respectively (p < 0.001). Conclusions RVA infection was significantly less frequent in children aged ≤2 years with DD after implementing vaccination, mainly among vaccinated children. It was also observed a decrease of P [8] circulation and emergence of G2P[4] in 2005, and afterwards in the post-vaccine era, with spreading of G12P[8] in 2014–2015 and of G3P[8] in 2017. Continuous RVA surveillance must be carried out in this scenario.
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Affiliation(s)
- Filipe A Carvalho-Costa
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil. .,Laboratory of Epidemiology and Molecular Systematics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Leonidas Deane, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil. .,Regional Office Fiocruz Piauí. Rua Magalhães Filho, n° 519, Centro/Norte, Teresina, Piauí, Brazil.
| | - Rosane M S de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre M Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Irene T Araújo
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelle F Silva
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariela M Gómez
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S Andrade
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana L Rose
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tulio M Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Eduardo M Volotão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marize P Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
| | - José Paulo G Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Av. Brasil 4365 Pavilhão Hélio e Peggy Pereira, Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil
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Ianiro G, Recanatini C, D'Errico MM, Monini M. Uncommon G9P[4] group A rotavirus strains causing dehydrating diarrhea in young children in Italy. INFECTION GENETICS AND EVOLUTION 2018; 64:57-64. [PMID: 29909243 DOI: 10.1016/j.meegid.2018.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 10/28/2022]
Abstract
Group A rotaviruses (RVA) are one of the major cause of acute gastroenteritis (AGE) in young children, being responsible for up to 250.000 deaths worldwide, mostly in developing countries. The two outer capsid proteins VP7 (glycoprotein, G-genotype) and VP4 (protease-sensitive protein, P-genotype) are the basis for the binary RVA nomenclature. Although at least 36 G-types and 51 P-types of rotavirus are presently known, most RVA infections in humans, worldwide as well as in Italy, are related to six major G/P combinations: G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]. In November 2016, in the framework of the Italian 2016/17 rotavirus surveillance season, a total of 22 rotavirus-positive samples from hospitalized children presenting AGE symptoms were collected in a small area of Central Italy (Ancona, Marche). After genotyping, 3 samples presented the G9P[4] genotype. In order to better understand the origin of these uncommon RVA strains causing dehydrating diarrhea in three children, the strains RVA/Human-wt/ITA/AN18/2016/G9P[4], RVA/Human-wt/ITA/AN19/2016/G9P[4] and RVA/Human-wt/ITA/AN22/2016/G9P[4] were subjected to nucleotide sequencing of all the 11 gene segments to define their genomic constellation. Nucleotide sequencing revealed that the genomic constellation of the three strains was G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2, highlighting human origin for all the gene segments investigated. The molecular characterization of RVAs and the continue monitoring of their circulation is needed to better define the epidemiology of these pathogen and to detect the emergence of viral variants presenting a high spreading potential in humans in the post-vaccination era.
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Affiliation(s)
- Giovanni Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.
| | - Claudia Recanatini
- Faculty of Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Marcello M D'Errico
- Faculty of Medicine, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Marina Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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Boni-Cisse C, Meite S, Mlan AB, Zaba F, N'Guessan R, Lepri NA, Lartey B. Genotypic characterization of rotavirus in children under 5 years circulating in Côte D'Ivoire from 2010 to 2013. Virol J 2018; 15:78. [PMID: 29699581 PMCID: PMC5922014 DOI: 10.1186/s12985-018-0973-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/26/2018] [Indexed: 12/20/2022] Open
Abstract
Background Rotavirus infection is the most common cause of severe gastroenteritis in children under five years of age in both developed and developing countries. The World Health Organisation (WHO) recommends the surveillance of rotavirus strains prior to vaccine introduction in all applicable countries. The objective of this study was to describe the epidemiological characteristics as well as to determine the circulating genotypes of rotaviruses in Côte d’Ivoire prior to vaccine introduction. Methods The study included children under five years of age who met the inclusion criteria after informed consent had been sort from their parents or guardians. Rotavirus VP6 antigens were detected for each stool sample using Enzyme Immunoassay (EIA). Genotyping of positive EIA samples was performed by reverse-transcriptase-PCR (RT-PCR) assays. Results A total of 684 children were recruited. Children aged between 6 and 11 months were the most represented with 34%. Rotavirus VP6 antigens were found in 27.1% (186/684) of samples tested. Commonly detected G genotypes included G12 (46.6% (82/176) and G1 (13.1% (23/176) whilst P[8] (49.8% (91/183) was the most predominant P genotype. Rotavirus G12P[8] was the most predominant strain circulating in Côte d’Ivoire within the period of study and constituted 26.6% of all strains detected. Conclusion The monitoring of circulating strains will help guide decision-makers in the choice of vaccine. Genotypic variability of circulating rotavirus strains over the years implies there is a need for continuous rotavirus strain surveillance even after vaccine introduction.
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Affiliation(s)
- Catherine Boni-Cisse
- UFR des Sciences Médicales, Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire. .,Laboratory of Sentinel Site Surveillance of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea CHU Yopougon, Abidjan, Côte d'Ivoire.
| | - Sindou Meite
- UFR des Sciences Médicales, Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire.,Laboratory of Sentinel Site Surveillance of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea CHU Yopougon, Abidjan, Côte d'Ivoire
| | - Alice Britoh Mlan
- UFR des Sciences Médicales, Département de Microbiologie, Université Félix Houphouët Boigny, Abidjan, Côte d'Ivoire.,Laboratory of Sentinel Site Surveillance of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea CHU Yopougon, Abidjan, Côte d'Ivoire
| | - Flore Zaba
- Laboratory of Sentinel Site Surveillance of Paediatric Bacterial Meningitis and Rotavirus Diarrhoea CHU Yopougon, Abidjan, Côte d'Ivoire
| | | | - Nicaise Aka Lepri
- Expanded Program on Immunization of Côte d'Ivoire, Abidjan, Côte d'Ivoire
| | - Bélinda Lartey
- NMIMR West African Regional Rotavirus Reference Laboratory, Accra, Ghana
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20
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Pellegrinelli L, Ianiro G, Pariani E, Monini M, Ruggeri FM, Binda S. Molecular characterization of rotavirus disclosed the first introduction of G12P[8] strain in northern Italy. Future Virol 2018. [DOI: 10.2217/fvl-2017-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: This paper discusses the unexpected findings from the RotaNet-Italy hospital-based surveillance study carried out in northern Italy. Materials & methods: From September 2015 to August 2016, 51 rotavirus-A (RVA) positive fecal samples were collected from children aged less than 15 years, who were hospitalized for acute gastroenteritis in Lombardy, northern Italy. Results: Molecular characterization revealed the predominance of the uncommon G12P[8] RVA strain, which was detected in 49% of cases. Phylogenetic analysis showed that these G12 strains clustered into lineage 3. Conclusion: To our knowledge, this is the first study on the G12P[8] genotype’s introduction in northern Italy. Our findings emphasize the importance of the surveillance of RVA gastroenteritis with the aim of obtaining new insight into the unusual newly emerging RVA strains.
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Affiliation(s)
- Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Giovanni Ianiro
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Marina Monini
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Franco Maria Ruggeri
- Department of Veterinary Public Health & Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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21
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Role of rotavirus vaccination on an emerging G8P[8] rotavirus strain causing an outbreak in central Japan. Vaccine 2017; 36:43-49. [PMID: 29183732 DOI: 10.1016/j.vaccine.2017.11.056] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/11/2017] [Accepted: 11/14/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND In this study, we examined the effectiveness of RV1 and RV5 vaccines during an outbreak of G8P[8] rotavirus group A strain (G8P[8]-RVA). These vaccines were originally designed to provide protection against severe diseases caused by common circulating strains, whereas G8P[8]-RVA remains emerging strain and partially heterotypic to the vaccines. It is imperative to investigate vaccine effectiveness (VE) against G8P[8]-RVA because this strain appears to be predominant in recent years, particularly, in post-vaccine era. METHODS RVA infection and genotypes were confirmed by polymerase chain reaction (PCR) followed by sequence-based genotyping. VE was determined during an outbreak of G8P[8]-RVA in Shizuoka Prefecture, Japan, in February-July 2017, retrospectively, by comparing vaccination status of children suffering from acute gastroenteritis (AGE) between 'PCR-positive' and 'PCR-negative' cases using conditional logistic regression adjusted for age. RESULTS Among 80 AGE children, RVA was detected in 58 (73%), of which 53 (66%) was G8P[8]-RVA. The clinical characteristics of G8P[8]-RVA and other RVA strains were identically severe. Notably, the attack rates of G8P[8]-RVA in vaccinated (61.1%) and unvaccinated (65.5%) children were almost similar. Indeed, no substantial effectiveness were found against G8P[8]-RVA (VE, 14% [95% CI: -140% to 70%]) or other RVA strains (VE, 58% [95% CI: -20% to 90%]) for mild infections. However, these vaccines remained strongly effective against moderate (VE, 75% [95% CI: 1% to 40%]) and severe (VE, 92% [95% CI: 60% to 98%]) RVA infections. The disease severity including Vesikari score, duration and frequency of diarrhea, and body temperature were significantly lower in vaccinated children. CONCLUSIONS This study demonstrates the effectiveness of current RV vaccines against moderate and severe, but not against the mild infections during an outbreak caused by unusual G8P[8]-RVA, which was virtually not targeted in the vaccines.
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22
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Almeida TNV, de Sousa TT, da Silva RA, Fiaccadori FS, Souza M, Badr KR, de Paula Cardoso DDD. Phylogenetic analysis of G1P[8] and G12P[8] rotavirus A samples obtained in the pre- and post-vaccine periods, and molecular modeling of VP4 and VP7 proteins. Acta Trop 2017; 173:153-159. [PMID: 28606817 DOI: 10.1016/j.actatropica.2017.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 05/31/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022]
Abstract
Reduction in morbimortality rates for acute gastroenteritis (AGE) by Rotavirus A (RVA) has been observed after the introduction of vaccines, however the agent continues to circulate. The present study described the genomic characterization of the 11 dsRNA segments of two RVA samples G1P[8] obtained in the pre- and post-vaccination periods and one of G12P[8] sample (post-vaccine), compared to Rotarix™ vaccine. Analysis by molecular sequencing of the samples showed that the three samples belonged to genogroup I. In addition, the analysis of VP7 gene revealed that the samples G1 (pre-vaccine), G1 (post-vaccine) and G12 were characterized as lineages II, I and III, respectively. Regarding to VP4 and NSP4 gene it was observed that all samples belonged to lineage III, whereas for VP6 gene, the sample of the pre- and post-vaccine belonged to the lineage IV and I, respectively. Considering the VP7 gene, it was observed high nucleotide and amino acid identity for the two G1 samples when compared to Rotarix™ vaccine and lesser identity for the G12 sample. In relation to antigenic epitope of VP7 greater modifications were observed for the G12 sample in the 7-2 epitope that was confirmed by molecular modeling. On the other hand, for VP4, some changes in the 8-1 and 8-3 antigenic epitopes was observed for the three samples. This data could be interpreted as a low selective pressure exerted by vaccination in relation to G1P[8] samples and lesser protection in relation to G12P[8]. Thus, the continuous monitoring of RVA circulating samples remains important.
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23
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Ianiro G, Delogu R, Fiore L, Monini M, Ruggeri FM. Group A rotavirus genotypes in hospital-acquired gastroenteritis in Italy, 2012-14. J Hosp Infect 2017; 96:262-267. [PMID: 28446379 DOI: 10.1016/j.jhin.2017.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Group A rotaviruses (RVA) are the leading cause of acute gastroenteritis (AGE) in young (aged <5 years) children, causing ∼250,000 deaths worldwide, mostly in developing countries. Differences on nucleotide sequences of VP7 (G-type) and VP4 (P-type) genes are the basis for the binary RVA nomenclature. Although at least 32 G-types and 47 P-types of rotavirus are presently known, most RVA infections in humans worldwide are related to five major G/P combinations: G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]. AIM To provide the hospitals of the Italian surveillance network with update information on RVA AGE. METHODS During RVA gastroenteritis surveillance in Italy in 2012-14, a total of 2341 RVA-positive faecal samples were collected from children hospitalized with AGE, and RVA strains were genotyped following standard EuroRotaNet protocols. FINDINGS Most strains analysed belonged to the five major human genotypes and 118 out of 2341 (5.0%) were reported to be hospital-acquired. Comparison of the distributions of the RVA genotypes circulating in the community or associated with nosocomial infections showed a different distribution of genotypes circulating inside the hospital wards, with respect to those observed in the community. G1P[8] and G9P[8] RVA strains were detected frequently, whereas G12P[8] caused a single large nosocomial outbreak. CONCLUSION The information from this study will be useful to implement guidelines for preventing RVA AGE and optimizing the management of patients in hospital wards.
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Affiliation(s)
- G Ianiro
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.
| | - R Delogu
- National Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - L Fiore
- National Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - M Monini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - F M Ruggeri
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
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24
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Nakagomi T, Do LP, Agbemabiese CA, Kaneko M, Gauchan P, Doan YH, Jere KC, Steele AD, Iturriza-Gomara M, Nakagomi O, Cunliffe NA. Whole-genome characterisation of G12P[6] rotavirus strains possessing two distinct genotype constellations co-circulating in Blantyre, Malawi, 2008. Arch Virol 2016; 162:213-226. [PMID: 27718073 DOI: 10.1007/s00705-016-3103-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022]
Abstract
Rotavirus A strains detected in diarrhoeal children commonly possess any one of the genotypes G1, G2, G3, G4, and G9, with a recent increase in G12 detection globally. G12P[6] strains possessing short RNA (DS-1-like) and long RNA (Wa-like) migration patterns accounted for 27 % of the strains circulating in Blantyre, Malawi, between 2007 and 2008. To understand how the G12P[6] strains with two distinct genetic backgrounds emerged in Malawi, we conducted whole-genome analysis of two long-RNA and two short-RNA strains. While the former had a typical Wa-like genotype constellation of G12-P[6]-I1-R1-C1-M1-A1-N1-T1-E1-H1, the latter was found to have G12-P[6]-I2-R2-C2-M1-A2-N2-T2-E2-H2: a VP3 gene mono-reassortant on the DS-1-like backbone. Phylogenetic and Bayesian Markov chain Monte Carlo analyses showed that the short-RNA G12P[6] strains were generated around 2006 by reassortment between an African Wa-like G12P[6] strain donating three genes (the VP7, VP4, and VP3 genes) and a G2P[4] strain similar to the one circulating in Thailand or the United States of America that donated the remaining eight genes. On the other hand, the long-RNA strains were generated as a result of reassortment events within Wa-like G12 and non-G12 strains commonly circulating in Africa; only the VP4 gene was from a Malawian G8P[6] strain. In conclusion, this study uncovered the evolutionary pathways through which two distinct G12P[6] strains emerged in Malawi.
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Affiliation(s)
- T Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan. .,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - L P Do
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Department of Virology, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - C A Agbemabiese
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - M Kaneko
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - P Gauchan
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan
| | - Y H Doan
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Department of Virology 2, National Institute of Infectious Diseases, Tokyo, Japan
| | - K C Jere
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - A D Steele
- Vaccines and Immunization, PATH, Seattle, WA, 98121, USA.,MRC Diarrhoeal Pathogens Research Unit, MEDUNSA, University of Limpopo, Pretoria, South Africa
| | - M Iturriza-Gomara
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - O Nakagomi
- Department of Hygiene and Molecular Epidemiology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523, Japan.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - N A Cunliffe
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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25
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Delogu R, Ianiro G, Morea A, Chironna M, Fiore L, Ruggeri FM. Molecular characterization of two rare human G8P[14] rotavirus strains, detected in Italy in 2012. INFECTION GENETICS AND EVOLUTION 2016; 44:303-312. [PMID: 27449953 DOI: 10.1016/j.meegid.2016.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/30/2016] [Accepted: 07/18/2016] [Indexed: 10/21/2022]
Abstract
Since 2007, the Italian Rotavirus Surveillance Program (RotaNet-Italy) has monitored the diversity and distribution of genotypes identified in children hospitalized with rotavirus acute gastroenteritis. We report the genomic characterization of two rare human G8P[14] rotavirus strains, identified in two children hospitalized with acute gastroenteritis in the southern Italian region of Apulia during rotavirus strain surveillance in 2012. Both strains showed a G8-P[14]-I2-R2-C2-M2-A11-N2-T6-E2-H3 genomic constellation (DS-1-like genomic background). Phylogenetic analysis of each genome segment revealed a mixed configuration of genes of animal and zoonotic human origin, indicating that genetic reassortment events generated these unusual human strains. Eight out of 11 genes (VP1, VP2, VP3, VP6, VP7, NSP3, NSP4 and NSP5) of the Italian G8P[14] strains exhibited close identity with a Spanish sheep strain, whereas the remaining genes (VP4, NSP1 and NSP2) were more closely related to human strains. The amino acid sequences of the antigenic regions of outer capsid proteins VP4 and VP7 were compared with vaccine and field strains, showing high conservation between the amino acid sequences of Apulia G8P[14] strains and human and animal strains bearing G8 and/or P[14] proteins, and revealing many substitutions with respect to the RotaTeq™ and Rotarix™ vaccine strains. Conversely, the amino acid analysis of the four antigenic sites of VP6 revealed a high degree of conservation between the two Apulia strains and the human and animal strains analyzed. These results reinforce the potential role of interspecies transmission and reassortment in generating novel rotavirus strains that might not be fully contrasted by current vaccines.
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Affiliation(s)
- Roberto Delogu
- National Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Giovanni Ianiro
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Lucia Fiore
- National Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Franco M Ruggeri
- Department of Veterinary Public Health and Food Safety, Istituto Superiore di Sanità, Rome, Italy.
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26
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da Silva MFM, Fumian TM, de Assis RMS, Fialho AM, Carvalho-Costa FA, da Silva Ribeiro de Andrade J, Leite JPG. VP7 and VP8* genetic characterization of group A rotavirus genotype G12P[8]: Emergence and spreading in the Eastern Brazilian coast in 2014. J Med Virol 2016; 89:64-70. [PMID: 27322509 DOI: 10.1002/jmv.24605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2016] [Indexed: 11/07/2022]
Abstract
Group A rotavirus (RVA) genotype G12 is habitually associated with diarrhea disease (DD) in African children and recently its detection has increased worldwide. A total of 970 stool samples collected from individuals with DD in the Northeastern, Southeastern, and Southern Brazilian regions, Eastern coast, were analyzed and 321 (33%) were positive for RVA and of these, 241 (75%) genotyped as G12P[8]. The rate of RVA positivity was higher among children aged 5-10 years old (60%). All RVA infections observed in adults aged >21 years were G12P[8] (n = 27) showing that this genotype affected older age groups during the year of 2014 in Brazil. Phylogenetic analysis of VP7 and VP8* G12P[8] strains demonstrated an elevated similarity among Brazilian and G12-III prototypes strains circulating worldwide recently, suggesting that this lineage is associated with the global spread of the G12 genotype, considered as the 6th most prevalent human RVA genotype nowadays; while other G12 lineages remain sporadically detected and usually detected in association with other P genotypes. VP8* analysis revealed that Brazilian strains belong to P[8]-3 lineage, the single P[8] lineage presently detected in the country. No major nucleotide/amino acid disparities were observed among strains recovered from children and adults for VP7 and VP8* genes. These data are essential to support the surveillance studies, particularly in countries where the RVA vaccine was introduced in their National Immunization Program enabling identification of potential alterations in the epidemiological profile that can impact its efficacy in vaccination programs. J. Med. Virol. 89:64-70, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marcelle Figueira Marques da Silva
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil.
| | - Tulio Machado Fumian
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Rosane Maria Santos de Assis
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Filipe Anibal Carvalho-Costa
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - Juliana da Silva Ribeiro de Andrade
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Ministry of Health, Rio de Janeiro, RJ, Brazil
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27
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Genetic variability of VP7, VP4, VP6 and NSP4 genes of common human G1P[8] rotavirus strains circulating in Italy between 2010 and 2014. Virus Res 2016; 220:117-28. [DOI: 10.1016/j.virusres.2016.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/20/2016] [Accepted: 04/20/2016] [Indexed: 12/12/2022]
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28
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De Grazia S, Dóró R, Bonura F, Marton S, Cascio A, Martella V, Bányai K, Giammanco GM. Complete genome analysis of contemporary G12P[8] rotaviruses reveals heterogeneity within Wa-like genomic constellation. INFECTION GENETICS AND EVOLUTION 2016; 44:85-93. [PMID: 27353490 DOI: 10.1016/j.meegid.2016.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/16/2016] [Accepted: 06/19/2016] [Indexed: 11/25/2022]
Abstract
G12 rotaviruses are globally emergent rotaviruses causing severe childhood gastroenteritis. Little is known about the evolution and diversity of G12P[8] rotaviruses and the possible role that widespread vaccine use, globally, has had on their emergence. In Sicily, Italy, surveillance activity for rotaviruses has been conducted uninterruptedly since 1985, thus representing a unique observatory for the study of human rotaviruses in the pre- and post-vaccine era. G12 rotaviruses were first detected only in 2012 and between 2012 and 2014 they accounted for 8.7% of all rotavirus-associated infections among children, with peaks of 27.8% in 2012/2013 and 21% in 2014. We determined and analyzed the full-genome of 22 G12P[8] rotaviruses collected during the 2012-2014. Although all G12P[8] rotaviruses exhibited a typical Wa-like genotype constellation (G12P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), phylogenetic analysis allowed distinguishing either two or three (sub)lineages in each genome segment. On the basis of the segregation patterns into lineages/sublineages, 20 G12P[8] rotaviruses could be grouped into three stable major genomic sub-constellations, whilst two strains displayed unique genome architectures, likely due to ressortment with co-circulating strains. Altogether, these findings indicate that the onset and prolonged circulation of G12 rotaviruses was due to repeated introductions of different G12 rotaviruses circulating globally. Importantly, as regional rotavirus vaccination was initiated in 2012 reaching a 45% coverage in newborns in 2014, a correlation between the appearance and spread of G12 rotaviruses and the enacted vaccination program could not be drawn. Constant epidemiologic surveillance remains important to monitor the epidemiological dynamics of human rotaviruses.
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Affiliation(s)
- Simona De Grazia
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Renáta Dóró
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Floriana Bonura
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Szilvia Marton
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Antonio Cascio
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Giovanni M Giammanco
- Department of Health Promotion Sciences and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
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29
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Langa JS, Thompson R, Arnaldo P, Resque HR, Rose T, Enosse SM, Fialho A, de Assis RMS, da Silva MFM, Leite JPG. Epidemiology of rotavirus A diarrhea in Chókwè, Southern Mozambique, from February to September, 2011. J Med Virol 2016; 88:1751-8. [PMID: 27003797 DOI: 10.1002/jmv.24531] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2016] [Indexed: 11/12/2022]
Abstract
Acute diarrhea disease caused by Rotaviruses A (RVA) is still the leading cause of morbidity and mortality in children ≤5 years old in developing countries. An exploratory cross-sectional study was conducted between February and September, 2011 to determine the proportion of acute diarrhea caused by RVA. A total of 254 stool specimens were collected from children ≤5 years old with acute diarrhea, including outpatients (222 children) and inpatients (32 children), in three local health centers in Chókwè District, Gaza Province, South of Mozambique. RVA antigens were detected using enzyme immunoassay (EIA); the RVA G (VP7) and P (VP4) genotypes were determined by RT-PCR or analysis sequencing. Sixty (24%) out of 254 fecal specimens were positive for RVA by EIA; being 58 (97%) from children ≤2 years of age. RVA prevalence peaks in June and July (coldest and drier months) and the G[P] binary combination observed were G12P[8] (57%); G1P[8] (9%); G12P[6] (6%); and 2% for each of the following genotypes: G1P[6], G2P[6] G4P[6], and G9P[8]. Non-Typeable (NT) G and/or P genotypes were observed as follows: G12P [NT] (6%); G1P [NT], G3P[NT] and GNTP[NT] (4%). Considering the different GP combinations, G12 represented 67% of the genotypes. This is the first data showing the diversity of RVA genotypes in Mozambique highlighting the epidemiological importance of these viruses in acute diarrhea cases in children ≤2 years old. In addition, these findings will provide a baseline data before the introduction of the RVA monovalent (Rotarix(®) ) vaccine in the National Immunization Program in September 2015. J. Med. Virol. 88:1751-1758, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jerónimo S Langa
- Chokwe Health Research and Training Centre (CITSC), National Institute of Health, Maputo, Mozambique.,Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Ricardo Thompson
- Chokwe Health Research and Training Centre (CITSC), National Institute of Health, Maputo, Mozambique
| | - Paulo Arnaldo
- Chokwe Health Research and Training Centre (CITSC), National Institute of Health, Maputo, Mozambique
| | - Hugo Reis Resque
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.,Virology Section, Evandro Chagas Institute, Ananindeua, Pará, Brazil
| | - Tatiana Rose
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Sonia M Enosse
- Chokwe Health Research and Training Centre (CITSC), National Institute of Health, Maputo, Mozambique
| | - Alexandre Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | | | - Marcelle Figueira Marques da Silva
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.,Faculty of Biology, Laboratory of Virus Contaminants of Water and Food, University of Barcelona, Barcelona, Spain
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
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Abstract
SUMMARYGenotype G12 strains are now considered to be the sixth most prevalent human rotaviruses worldwide. In two Sicilian cities, Palermo and Messina, surveillance of rotavirus circulation performed since 1985 and 2009, respectively, did not detect G12 strains until 2012. From 2012 to 2014 rotavirus infection was detected in 29·7% of 1647 stool samples collected from children admitted for acute gastroenteritis to three Sicilian hospitals in Palermo, Messina and Ragusa. In 2012, G12P[8] was first detected in Palermo and then in Messina where it represented the second most frequent genotype (20% prevalence) after G1P[8]. Thereafter, G12 strains continued to circulate in Sicily, showing a marked prevalence in Ragusa (27·8%) in 2013 and in Palermo (21%) and Messina (16·6%) in 2014. All but one of the Sicilian G12 strains carried a P[8] VP4 genotype, whereas the single non-P[8] rotavirus strain was genotyped as G12P[9]. Phylogenetic analysis of the VP7 and VP4 sequences allowed distinction of several genetic lineages and separation of the G12P[8] strains into three cluster combinations. These findings indicate independent introductions of G12 rotavirus strains in Sicily in recent years.
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