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França Y, Medeiros RS, Viana E, de Azevedo LS, Guiducci R, da Costa AC, Luchs A. Genetic diversity and evolution of G12P[6] DS-1-like and G12P[9] AU-1-like Rotavirus strains in Brazil. Funct Integr Genomics 2024; 24:92. [PMID: 38733534 DOI: 10.1007/s10142-024-01360-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
In the early 2000s, the global emergence of rotavirus (RVA) G12P[8] genotype was noted, while G12P[6] and G12P[9] combinations remained rare in humans. This study aimed to characterize and phylogenetically analyze three Brazilian G12P[9] and four G12P[6] RVA strains from 2011 to 2020, through RT-PCR and sequencing, in order to enhance our understanding of the genetic relationship between human and animal-origin RVA strains. G12P[6] strains displayed a DS-1-like backbone, showing a distinct genetic clustering. G12P[6] IAL-R52/2020, IAL-R95/2020 and IAL-R465/2019 strains clustered with 2019 Northeastern G12P[6] Brazilian strains and a 2018 Benin strain, whereas IAL-R86/2011 strain grouped with 2010 Northern G12P[6] Brazilian strains and G2P[4] strains from the United States and Belgium. These findings suggest an African genetic ancestry and reassortments with co-circulating American strains sharing the same DS-1-like constellation. No recent zoonotic reassortment was observed, and the DS-1-like constellation detected in Brazilian G12P[6] strains does not seem to be genetically linked to globally reported intergenogroup G1/G3/G9/G8P[8] DS-1-like human strains. G12P[9] strains exhibited an AU-1-like backbone with two different genotype-lineage constellations: IAL-R566/2011 and IAL-R1151/2012 belonged to a VP3/M3.V Lineage, and IAL-R870/2013 to a VP3/M3.II Lineage, suggesting two co-circulating strains in Brazil. This genetic diversity is not observed elsewhere, and the VP3/M3.II Lineage in G12P[9] strains seems to be exclusive to Brazil, indicating its evolution within the country. All three G12P[9] AU-1-like strains were closely relate to G12P[9] strains from Paraguay (2006-2007) and Brazil (2010). Phylogenetic analysis also highlighted that all South American G12P[9] AU-1-like strains had a common origin and supports the hypothesis of their importation from Asia, with no recent introduction from globally circulating G12P[9] strains or reassortments with local G12 strains P[8] or P[6]. Notably, certain genes in the Brazilian G12P[9] AU-1-like strains share ancestry with feline/canine RVAs (VP3/M3.II, NSP4/E3.IV and NSP2/N3.II), whereas NSP1/A3.VI likely originated from artiodactyls, suggesting a history of zoonotic transmission with human strains. This genomic data adds understanding to the molecular epidemiology of G12P[6] and G12P[9] RVA strains in Brazil, offering insights into their genetic diversity and evolution.
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Affiliation(s)
- Yasmin França
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Ellen Viana
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | | | - Raquel Guiducci
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil
| | - Antonio Charlys da Costa
- Medical Parasitology Laboratory (LIM/46), São Paulo Tropical Medicine Institute, University of Sao Paulo, Sao Paulo, Brazil
| | - Adriana Luchs
- Enteric Diseases Laboratory, Virology Center, Adolfo Lutz Institute, Sao Paulo, Brazil.
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Parida VK, Saidulu D, Bhatnagar A, Gupta AK, Afzal MS. A critical assessment of SARS-CoV-2 in aqueous environment: Existence, detection, survival, wastewater-based surveillance, inactivation methods, and effective management of COVID-19. CHEMOSPHERE 2023; 327:138503. [PMID: 36965534 PMCID: PMC10035368 DOI: 10.1016/j.chemosphere.2023.138503] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/08/2023] [Accepted: 03/22/2023] [Indexed: 06/01/2023]
Abstract
In early January 2020, the causal agent of unspecified pneumonia cases detected in China and elsewhere was identified as a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and was the major cause of the COVID-19 outbreak. Later, the World Health Organization (WHO) proclaimed the COVID-19 pandemic a worldwide public health emergency on January 30, 2020. Since then, many studies have been published on this topic. In the present study, bibliometric analysis has been performed to analyze the research hotspots of the coronavirus. Coronavirus transmission, detection methods, potential risks of infection, and effective management practices have been discussed in the present review. Identification and quantification of SARS-CoV-2 viral loads in various water matrices have been reviewed. It was observed that the viral shedding through urine and feces of COVID-19-infected patients might be a primary mode of SARS-CoV-2 transmission in water and wastewater. In this context, the present review highlights wastewater-based epidemiology (WBE)/sewage surveillance, which can be utilized as an effective tool for tracking the transmission of COVID-19. This review also emphasizes the role of different disinfection techniques, such as chlorination, ultraviolet irradiation, and ozonation, for the inactivation of coronavirus. In addition, the application of computational modeling methods has been discussed for the effective management of COVID-19.
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Affiliation(s)
- Vishal Kumar Parida
- School of Environmental Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Duduku Saidulu
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Amit Bhatnagar
- Department of Separation Science, LUT School of Engineering Science, LUT University, Sammonkatu 12, Mikkeli FI-50130, Finland.
| | - Ashok Kumar Gupta
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
| | - Mohammad Saud Afzal
- Department of Civil Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
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Asare EO, Al-Mamun MA, Sarmin M, Faruque ASG, Ahmed T, Pitzer VE. The influence of demographic and meteorological factors on temporal patterns of rotavirus infection in Dhaka, Bangladesh. Proc Biol Sci 2022; 289:20212727. [PMID: 35673869 PMCID: PMC9174722 DOI: 10.1098/rspb.2021.2727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
To quantify the potential impact of rotavirus vaccines and identify strategies to improve vaccine performance in Bangladesh, a better understanding of the drivers of pre-vaccination rotavirus patterns is required. We developed and fitted mathematical models to 23 years (1990-2012) of weekly rotavirus surveillance data from Dhaka with and without incorporating long-term and seasonal variation in the birth rate and meteorological factors. We performed external model validation using data between 2013 and 2019 from the regions of Dhaka and Matlab. The models showed good agreement with the observed age distribution of rotavirus cases and captured the observed shift in seasonal patterns of rotavirus hospitalizations from biannual to annual peaks. The declining long-term trend in the birth rate in Bangladesh was the key driver of the observed shift from biannual to annual winter rotavirus patterns. Meteorological indices were also important: a 1°C, 1% and 1 mm increase in diurnal temperature range, surface water presence and degree of wetness were associated with a 19%, 3.9% and 0.6% increase in the transmission rate, respectively. The model demonstrated reasonable predictions for both Dhaka and Matlab, and can be used to evaluate the impact of rotavirus vaccination in Bangladesh against changing patterns of disease incidence.
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Affiliation(s)
- Ernest O. Asare
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Mohammad A. Al-Mamun
- Department of Pharmaceutical Systems and Policy, School of Pharmacy, West Virginia University, USA
| | - Monira Sarmin
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - A. S. G. Faruque
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division (NCSD), International Centre for Diarrheal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Virginia E. Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, CT, USA
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Ballard SB, Requena D, Mayta H, Sanchez GJ, Oyola-Lozada MG, Colquechagua Aliaga FD, Cabrera L, Vittet Mondonedo MD, Taquiri C, Tilley CAPTDH, Simons CDRMP, Meza RA, Bern C, Saito M, Figueroa-Quintanilla DA, Gilman RH. Enteropathogen Changes After Rotavirus Vaccine Scale-up. Pediatrics 2022; 149:e2020049884. [PMID: 34918158 PMCID: PMC9647525 DOI: 10.1542/peds.2020-049884] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES To inform next steps in pediatric diarrhea burden reduction by understanding the shifting enteropathogen landscape after rotavirus vaccine implementation. METHODS We conducted a case-control study of 1788 medically attended children younger than 5 years, with and without gastroenteritis, after universal rotavirus vaccine implementation in Peru. We tested case and control stools for 5 viruses, 19 bacteria, and parasites; calculated coinfection-adjusted attributable fractions (AFs) to determine pathogen-specific burdens; and evaluated pathogen-specific gastroenteritis severity using Clark and Vesikari scales. RESULTS Six pathogens were independently positively associated with gastroenteritis: norovirus genogroup II (GII) (AF 29.1, 95% confidence interval [CI]: 28.0-32.3), rotavirus (AF 8.9, 95% CI: 6.8-9.7), sapovirus (AF 6.3, 95% CI: 4.3-7.4), astrovirus (AF 2.8, 95% CI: 0.0-4.0); enterotoxigenic Escherichia coli heat stable and/or heat labile and heat stable (AF 2.4, 95% CI: 0.6-3.1), and Shigella spp. (AF 2.0, 95% CI: 0.4-2.2). Among typeable rotavirus cases, we most frequently identified partially heterotypic strain G12P[8] (54 of 81, 67%). Mean severity was significantly higher for norovirus GII-positive cases relative to norovirus GII-negative cases (Vesikari [12.7 vs 11.8; P < .001] and Clark [11.7 vs 11.4; P = .016]), and cases in the 6- to 12-month age range relative to cases in other age groups (Vesikari [12.7 vs 12.0; P = .0002] and Clark [12.0 vs 11.4; P = .0016]). CONCLUSIONS Norovirus is well recognized as the leading cause of pediatric gastroenteritis in settings with universal rotavirus vaccination. However, sapovirus is often overlooked. Both norovirus and sapovirus contribute significantly to the severe pediatric disease burden in this setting. Decision-makers should consider multivalent vaccine acquisition strategies to target multiple caliciviruses in similar countries after successful rotavirus vaccine implementation.
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Affiliation(s)
- Sarah-Blythe Ballard
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
- Naval Medical Research Unit No. 6, Callao, Peru
| | - David Requena
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Holger Mayta
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociación Benéfica PRISMA, Lima, Peru
| | - Gerardo J. Sanchez
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria G. Oyola-Lozada
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Macarena D. Vittet Mondonedo
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Carmen Taquiri
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - CAPT Drake H. Tilley
- Naval Medical Research Unit No. 6, Callao, Peru
- Fleet Surgical Team SEVEN, Okinawa, Japan
| | | | | | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Mayuko Saito
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Robert H. Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Infectious Disease Research Laboratory, Department of Cellular and Molcular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociación Benéfica PRISMA, Lima, Peru
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Achak M, Alaoui Bakri S, Chhiti Y, M'hamdi Alaoui FE, Barka N, Boumya W. SARS-CoV-2 in hospital wastewater during outbreak of COVID-19: A review on detection, survival and disinfection technologies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 761:143192. [PMID: 33153744 PMCID: PMC7585361 DOI: 10.1016/j.scitotenv.2020.143192] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 10/18/2020] [Indexed: 05/17/2023]
Abstract
Currently, the apparition of new SARS-CoV, known as SARS-CoV-2, affected more than 34 million people and causing high death rates worldwide. Recently, several studies reported SARS-CoV-2 ribonucleic acid (RNA) in hospital wastewater. SARS-CoV-2 can be transmitted between humans via respiratory droplets, close contact and fomites. Fecal-oral transmission is considered also as a potential route of transmission since several scientists confirmed the presence of SARS-CoV-2 RNA in feces of infected patients, therefore its transmission via feces in aquatic environment, particularly hospital wastewater. Hospitals are one of the important classes of polluting sectors around the world. It was identified that hospital wastewater contains hazardous elements and a wide variety of microbial pathogens and viruses. Therefore, this may potentially pose a significant risk of public health and environment infection. This study reported an introduction about the Physical-chemical and microbiological characterization of hospital wastewater, which can be a route to identify potential technology to reduce the impact of hospital contaminants before evacuation. The presence of SARS-CoV-2 in aqueous environment was reviewed. The knowledge of the detection and survival of SARS-CoV-2 in wastewater and hospital wastewater were described to understand the different routes of SARS-CoV-2 transmission, which is also useful to avoid the outbreak of CoV-19. In addition, disinfection technologies used commonly for deactivation of SARS-CoV-2 were highlighted. It was revealed that, chlorine-containing disinfectants are the most commonly used disinfectants in this field of research. Meanwhile, other efficient technologies must be developed and improved to avoid another wave of the pandemic of COVID-19 infections.
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Affiliation(s)
- Mounia Achak
- Science Engineer Laboratory for Energy, National School of Applied Sciences, Chouaïb Doukkali University, El Jadida, Morocco; Chemical & Biochemical Sciences, Green Process Engineering, CBS, Mohammed VI Polytechnic University, Ben Guerir, Morocco.
| | - Soufiane Alaoui Bakri
- Science Engineer Laboratory for Energy, National School of Applied Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - Younes Chhiti
- Advanced Materials and Process Engineering Laboratory, National School of Chemistry, Ibn Tofail University, Kenitra, Morocco; Mohamed VI Polytechnic University, Ben Guerir, Morocco
| | - Fatima Ezzahrae M'hamdi Alaoui
- Science Engineer Laboratory for Energy, National School of Applied Sciences, Chouaïb Doukkali University, El Jadida, Morocco
| | - Noureddine Barka
- Sultan Moulay Slimane University of Beni Mellal, Research Group in Environmental Sciences and Applied Materials (SEMA), FP Khouribga, Khouribga, Morocco
| | - Wafaa Boumya
- Science Engineer Laboratory for Energy, National School of Applied Sciences, Chouaïb Doukkali University, El Jadida, Morocco; Sultan Moulay Slimane University of Beni Mellal, Research Group in Environmental Sciences and Applied Materials (SEMA), FP Khouribga, Khouribga, Morocco
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Corpuz MVA, Buonerba A, Vigliotta G, Zarra T, Ballesteros F, Campiglia P, Belgiorno V, Korshin G, Naddeo V. Viruses in wastewater: occurrence, abundance and detection methods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140910. [PMID: 32758747 PMCID: PMC7368910 DOI: 10.1016/j.scitotenv.2020.140910] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 04/14/2023]
Abstract
This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.
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Affiliation(s)
- Mary Vermi Aizza Corpuz
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Antonio Buonerba
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Giovanni Vigliotta
- Laboratory of Microbiology, University of Salerno, 84084 Fisciano, Italy.
| | - Tiziano Zarra
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Florencio Ballesteros
- Environmental Engineering Program, National Graduate School of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines; Department of Chemical Engineering, College of Engineering, University of the Philippines, 1101 Diliman, Quezon City, Philippines.
| | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.
| | - Vincenzo Belgiorno
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
| | - Gregory Korshin
- Department of Civil and Environmental Engineering, University of Washington, Box 352700, Seattle, WA 98105-2700, United States.
| | - Vincenzo Naddeo
- Sanitary Environmental Engineering Division (SEED), Department of Civil Engineering, University of Salerno, 84084, Fisciano (SA), Italy; Inter-University Centre for Prediction and Prevention of Major Hazards (C.U.G.RI.), Via Giovanni Paolo II, 84084, Fisciano (SA), Italy.
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Emergence of G12P[6] rotavirus strains among hospitalised children with acute gastroenteritis in Belém, Northern Brazil, following introduction of a rotavirus vaccine. Arch Virol 2019; 164:2107-2117. [PMID: 31144039 DOI: 10.1007/s00705-019-04295-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
Abstract
Species A rotavirus still remains a major cause of acute gastroenteritis in infants and young children. Globally, six genotypes (G1P[8], G2P[4], G3P[8], G4P[8], G9P[8] and G12P[8]) account for >90% of circulating strains; however, genotype G12 in combination with P[6] or P[9] has been detected at increasing rates. We sought to broaden our knowledge about the rotavirus strains circulating during the early post-vaccine-introduction period. Stool samples were obtained from children hospitalised for acute gastroenteritis in Belém, Northern Brazil, from May 2008 to May 2011 and examined by reverse transcription polymerase chain reaction and nucleotide sequencing. A total of 122 out of the original 1076 rotavirus strains were judged to be non-typeable in the first analysis and were therefore re-examined. G2P[4] was the most prevalent genotype (58.0%), followed by G1P[8] (16.9%), and G12P[6] (7.5%). G12P[6] strains were identified at similar rates during the first (2.5%) and second (3.9%) years, and the rate jumped to 15.6% in the third year. Analysis of VP7 sequences of the G12P[6] strains showed that they belonged to lineage III. In addition, co-circulating G12P[6] strains displaying long and short RNA patterns were found to belong to the Wa-like and DS-1-like constellation, respectively. Additional unusual circulating strains G12P[9] and G3P[9] were also identified. This hospital-based study showed a high prevalence of G12P[6] strains in the third year of surveillance. Our results highlight the need for continuous longitudinal monitoring of circulating rotavirus strains after introduction of rotavirus vaccines in Brazil and elsewhere.
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Azaran A, Makvandi M, Teimoori A, Ebrahimi S, Heydari F, Nikfar R. Distribution of Rotavirus Genotypes Ccirculating
in Ahvaz, Iran in 2016. IRANIAN BIOMEDICAL JOURNAL 2018; 22:107-16. [PMID: 28915725 PMCID: PMC5786656 DOI: 10.22034/ibj.22.2.107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/06/2017] [Accepted: 05/08/2017] [Indexed: 02/06/2023]
Abstract
Background Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines. Methods A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016. All samples were screened by latex agglutination for the presence of rotavirus antigen. Rotavirus-positive samples were further analyzed by the semi-multiplex RT-PCR, and the sequencing was performed for G/P genotyping. Results Findings showed that 32% of the specimens were RVA-positive. Among the 32 VP7 genotyped strains, the predominant G genotype was G9 (37.5%), followed by G2 (21.9%), G1 (12.5%), G12 (9.4%), G4 (9.4%), G2G9 (6.3%), and G3 (3.1%). Among the 31 VP4 genotyped strains, P[8] genotype was the dominant (62.5%), followed by P[4] (31.3%) and P[4] P[8] (3.1%). The genotypes for G and P were identified for 31 rotaviruses (96.87%), but only one strain, G9, remained non-typeable for the P genotype. The most prevalent G/P combination was G9P[8] (28.5%), followed by G2P[4] (18.8%), G1P[8] (9.4%), G12P[8] (9.4%), G4P[8] (9.4%), G2G9P[4] (6.3%), G9P[4] P[8] (3.1%), G3P[8] (3.1%), G9P[4] (3.1%), G2P[8] (3.1%), and G9P[non-typeable] (3.1%). Conclusion A novel rotavirus strain, G12, was detected, for the first time, in patients from the southwest of Iran. Comprehensive investigations are required to evaluate the emergence of this strain.
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Affiliation(s)
- Azarakhsh Azaran
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Manoochehr Makvandi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Teimoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Saeedeh Ebrahimi
- Virology Department, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farzad Heydari
- Cukurova University, Medicine Faculty, Medical Microbiology Department, Adana, Turkey
| | - Roya Nikfar
- Department of Infectious Diseases, Aboozar Children’s Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Nayak MK, De P, Manna B, Dutta S, Bhadra UK, Chawla-Sarkar M. Species A rotaviruses isolated from hospitalized patients over 5 years of age in Kolkata, India, in 2012/13. Arch Virol 2017; 163:745-750. [PMID: 29248967 DOI: 10.1007/s00705-017-3670-0] [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: 07/04/2017] [Accepted: 11/20/2017] [Indexed: 01/16/2023]
Abstract
In hospital-based diarrhoeal disease surveillance at Infectious Diseases & Beliaghata-General Hospital (May-2012 to April-2013), Kolkata, India, stool samples were collected from patients < 5 years (n = 830) and > 5 years of age (n = 728) hospitalized with diarrhea. Group-A rotavirus (GARV) was identified by ELISA followed by multiplex RT-PCR. In children < 5 years of age, 53.4% of the samples were positive for GARV. In patients > 5 years to 90 years old, only 6.04% (n = 44) tested positive for GARV. G2P[4] strains (n = 16 [36.36%]) were the most prevalent, followed by G9P[4] strains (n = 13 [29.54%]), while P[4]-(n = 30 [68.18%]) was most prevalent among the P genotypes. The GARV strains G2, G9 and P[4] detected in adults clustered together in the phylogenetic tree with the GARV strains identified in children (< 5 years) during the same period. Rotavirus positivity was high among female patients (75%), suggesting that caregivers (mother/grandmother/older-siblings) may get infected through young children or may act as carriers for transmission.
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Affiliation(s)
- Mukti Kant Nayak
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India. .,Department of Zoology, B. B. Autonomous College, Chandikhol, Jajpur, Odisha, 755044, India.
| | - Papiya De
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Byomkesh Manna
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Shanta Dutta
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Uchhal Kumar Bhadra
- Infectious Diseases and Beliaghata General Hospital, 57-Dr SC Banerjee Road, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India.
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Luchs A, Madalosso G, Cilli A, Morillo SG, Martins SR, de Souza KAF, Namiyama GM, Gonçalves CR, Carmona RDCC, Timenetsky MDCST. Outbreak of G2P[4] rotavirus gastroenteritis in a retirement community, Brazil, 2015: An important public health risk? Geriatr Nurs 2017; 38:283-290. [DOI: 10.1016/j.gerinurse.2016.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022]
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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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12
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Luchs A, Cilli A, Morillo SG, Gregório DDS, de Souza KAF, Vieira HR, Fernandes ADM, Carmona RDCC, Timenetsky MDCST. Detection of the emerging rotavirus G12P[8] genotype at high frequency in brazil in 2014: Successive replacement of predominant strains after vaccine introduction. Acta Trop 2016; 156:87-94. [PMID: 26748357 DOI: 10.1016/j.actatropica.2015.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 12/14/2015] [Accepted: 12/19/2015] [Indexed: 12/12/2022]
Abstract
The continuum characterization of rotavirus (RVA) genotypes is essential to understand how vaccine introduction could impact virus epidemiology. In the present study, an unexpected rapid changing pattern of RVA genotypes distribution in Brazilian population during three followed seasons is described. From January/2012 to December/2014, a total of 3441 fecal specimens were collected from collaborating centers across Southern, Southeastern and Midwest of Brazil. All specimens were screened for RVA using ELISA, and genotyped by RT-PCR. Differences in proportions were tested using Chi-Squares. A p-value of less than 0.05 was considered statistically significant. RVA was detected in 19.7% (677/3441). Among RVA positive cases (n=677), a total of 652 (96.3%) samples were successfully amplified by RT-PCR. G3P[8] remained prevalent in 2012 (37.6%, 69/185) and 2013 (40.1%, 74/186) (χ(2)=0.107, p=0.743), but declined markedly in 2014 (3.5%, 10/281) (χ(2)=71.770, p=0.000). G12P[8] was second highest strain in 2012 (22.7%, 42/185), decrease rapidly in 2013 (2.7%, 5/186) (χ(2)=26.224, p=0.000) and re-emerged as the predominant genotype in 2014 (86.6%, 243/281) (χ(2)=118.299, p=0.000). From July/2014, G12P[8] was the single genotype detected in all regions studied. The sudden emergence, spread and predominance of G12P[8] strain in Brazil, raised the hypothesis of a possible G12 outbreak being in progress. Nationally, the long term decline in gastroenteritis hospitalization observed in the country after RVA vaccine introduction was confirmed. Nevertheless, the sharp increase in diarrhea hospitalization prevalence from 2013 to 2014 observed in Southern and Southeastern regions is consistent with what appears to be an outbreak of G12P[8]. Continued surveillance is needed to verify the effectiveness of the RotarixTM vaccine in Brazil together with potential emergence of unusual genotypes.
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Affiliation(s)
- Adriana Luchs
- Enteric Disease Laboratory, Virology Centre, Adolfo Lutz Institute, São Paulo, Brazil.
| | - Audrey Cilli
- Enteric Disease Laboratory, Virology Centre, Adolfo Lutz Institute, São Paulo, Brazil
| | | | | | | | - Heloísa Rosa Vieira
- Enteric Disease Laboratory, Virology Centre, Adolfo Lutz Institute, São Paulo, Brazil
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Neves MAO, Pinheiro HHC, Silva RSU, Linhares AC, Silva LD, Gabbay YB, Silva MCM, Loureiro ECB, Soares LS, Mascarenhas JDP. High prevalence of G12P[8] rotavirus strains in Rio Branco, Acre, Western Amazon, in the post-rotavirus vaccine introduction period. J Med Virol 2015; 88:782-9. [PMID: 26466923 DOI: 10.1002/jmv.24404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
The present study aimed to provide a molecular characterization of circulating rotavirus (RVA) strains in Rio Branco, Acre, in the post-rotavirus vaccination period, particularly with regard to the emerging, increasingly prevalent G12P[8] genotype. A total of 488 fecal specimens from diarrheic and non-diarrheic children were obtained between January and December 2012. RVA detection was initially performed using enzyme-linked immunosorbent assay (ELISA) method, followed by reverse-transcription polymerase chain reaction (RT-PCR) using specific primers. RVA was detected in 18.3% (44/241) of the children with acute diarrhea and in 1.2% (3/247) of the non-diarrheic children (P < 0.001), with overall RVA-positivity of 9.6% (47/488). The most common genotype was G2P[4] with 43.2% (19/44) of the diarrheic cases, followed by G12P[8] (27.3%, 12/44), G3P[6] (18.2%, 8/44), G3P[8] (4.5%, 2/44), and G12P[6] (2.3%, 1/44). G12 samples belonged to lineage III and were from children aged 4-52 months. All of these children had acute diarrhea associated with fever (83.3%, 10/12) and vomiting (66.7%, 8/12). Most of the cases occurred in August (58.3%, 7/12), 75% (9/12) of which having received the full vaccination scheme with Rotarix™. For the first time G12 was reported at relative high prevalence in Brazil. Our findings warrant further monitoring studies on the molecular characterization of circulating RVA strains after rotavirus vaccine introduction in Brazil and elsewhere, since the occurrence of either unusual our emerging genotypes may pose a challenge to vaccination strategies.
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Affiliation(s)
- Mayara A O Neves
- Center for Biological and Health Sciences, University of State of Pará, Pará, Brazil
| | | | - Rita S U Silva
- Municipality Secretary of Health of Rio Branco, Acre, Brazil
| | - Alexandre C Linhares
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Luciana D Silva
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Yvone B Gabbay
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Mônica C M Silva
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Edvaldo C B Loureiro
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
| | - Luana S Soares
- Evandro Chagas Institute, Health Surveilance Secretariat, Ministry of Health, Pará, Brazil
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Bucardo F, Nordgren J. Impact of vaccination on the molecular epidemiology and evolution of group A rotaviruses in Latin America and factors affecting vaccine efficacy. INFECTION GENETICS AND EVOLUTION 2015; 34:106-13. [PMID: 26079278 DOI: 10.1016/j.meegid.2015.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 12/15/2022]
Abstract
Despite high rotavirus (RV) vaccine coverage (∼83%) and good effectiveness (∼77%) against RV-diarrhea hospitalization, RV is still contributing to the burden of diarrhea that persists in hospital settings in several Latin American countries, where RV vaccination is being implemented. Due to the extensive genomic and antigenic diversity, among co-circulating human RV, a major concern has been that the introduction of RV vaccination could exert selection pressure leading to higher prevalence of strains not included in the vaccines and/or emergence of new strains, thus, reducing the efficacy of vaccination. Here we review the molecular epidemiology of RV in Latin America and explore issues of RV evolution and selection in light of vaccination. We further explore etiologies behind the large burden of diarrhea remaining after vaccination in some countries and discuss plausible reasons for vaccine failures.
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Affiliation(s)
- Filemón Bucardo
- Department of Microbiology, National Autonomous University of León, Nicaragua (UNAN-León), Nicaragua.
| | - Johan Nordgren
- Division of Molecular Virology, Clinical and Experimental Medicine, Medical Faculty University of Linköping, 581 85 Linköping, Sweden
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15
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Large increase of rotavirus diarrhoea in the hospital setting associated with emergence of G12 genotype in a highly vaccinated population in Nicaragua. Clin Microbiol Infect 2015; 21:603.e1-7. [DOI: 10.1016/j.cmi.2015.01.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/20/2015] [Accepted: 01/25/2015] [Indexed: 02/08/2023]
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16
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Phylogenetic analysis of human group C rotavirus circulating in Brazil reveals a potential unique NSP4 genetic variant and high similarity with Asian strains. Mol Genet Genomics 2014; 290:969-86. [PMID: 25501310 DOI: 10.1007/s00438-014-0971-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/25/2014] [Indexed: 01/23/2023]
Abstract
Group C rotaviruses (RVC) cause gastroenteritis in humans and animals worldwide, and the evidence for a possible zoonotic role has been recently provided. To gain information on the genetic diversity and relationships between human and animal RVC, we sequenced the VP4, VP7, and NSP4 genes of 12, 19, and 15 human strains, respectively, detected in São Paulo state during historical (1988 and 1993) and recent (2007 and 2008) Brazilian rotavirus surveillance. All RVC strains analyzed in the present study grouped into human genotype (G4-P[2]-E2), and did not show any evidence of animal ancestry. Phylogenetic analysis showed that RVC samples detected in 1988 and 1993 clustered together with strains from distinct continents, indicating that historical RVC strains circulating in São Paulo were closely related to those strains circulating worldwide. All three genes (VP7, VP4 and NSP4) of São Paulo RVC strains isolated in 2007-2008 exhibited close phylogenetic relationship with human RVC strains isolated in China and Japan, suggesting that they are genetically linked, and that a gene flow could be occurring between this Asian countries and Brazil. We identified two distinct clusters in the NSP4 phylogenetic tree. One cluster formed exclusively by human Brazilian strains detected in 1997 and 2003-2004 in Rio de Janeiro, Bahia, and Rio Grande do Sul states (Subgroup II) previously described in a different study, that displayed low sequence identities to other human strains formerly published, and to the Brazilian RVC strains (Subgroup I) characterized in the present study. These data suggests the circulation of two genetic profiles of the NSP4 gene in Brazil. High sequence diversity in NSP4 gene was previously reported in Asia, and additional diversity in NSP4 RVC strains spreading in the world should be expected. More in-depth molecular and epidemiological analysis of human RVC throughout the world will be needed to understand their diversity and clarify their evolution, as well as to develop classifications schemes.
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Gómez MM, Resque HR, Volotão EDM, Rose TL, Figueira Marques da Silva M, Heylen E, Zeller M, Matthijnssens J, Leite JPG. Distinct evolutionary origins of G12P[8] and G12P[9] group A rotavirus strains circulating in Brazil. INFECTION GENETICS AND EVOLUTION 2014; 28:385-8. [DOI: 10.1016/j.meegid.2014.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/04/2014] [Accepted: 04/08/2014] [Indexed: 12/12/2022]
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Tatte VS, Chothe NS, Chitambar SD. Characterisation of rotavirus strains identified in adolescents and adults with acute gastroenteritis highlights circulation of non-typeable strains: 2008–2012. Vaccine 2014; 32 Suppl 1:A68-74. [DOI: 10.1016/j.vaccine.2014.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mandile MG, Esteban LE, Argüelles MH, Mistchenko A, Glikmann G, Castello AA. Surveillance of group A Rotavirus in Buenos Aires 2008-2011, long lasting circulation of G2P[4] strains possibly linked to massive monovalent vaccination in the region. J Clin Virol 2014; 60:282-9. [PMID: 24875137 DOI: 10.1016/j.jcv.2014.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/27/2014] [Accepted: 04/25/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND Group A rotaviruses (RVA) are the most frequent single etiological agents of severe diarrhea in infants. Since 2006 RVA vaccines have been introduced in national schedules of middle and high income countries with substantial declines in rotavirus associated disease burden. However, surveillance must be maintained to, eventually, detect emerging types or variants selected by the new pressure imposed by vaccination. OBJECTIVES To analyze the molecular epidemiology of group A rotavirus after vaccine introduction in the region in the context of data from more than 15 years of continuous surveillance in Buenos Aires. STUDY DESIGN RVA positive diarrhea samples collected in Buenos Aires from 2008 to 2011 were genotyped by RT-PCR. Selected samples were sequenced to gain insight on evolution of common and globally emerging human RVA strains. RESULTS Lineage III G12P[8] strain emerged in 2008 in Buenos Aires and shared co-dominancy with G3 strains during 2009. An atypical long lasting circulation of G2P[4] strains since 2004 reached rates around 80% in 2011 in Buenos Aires. Sequencing of the VP7 and VP4 genes of representative G2P[4] isolates suggests Brazil as the origin of the 2010-2011 strains. CONCLUSIONS Globally emergent G12 lineage III strains could be established as dominant strains in a very populated area in two years since emergence. In this work it was also shown that the persistence of G2P[4] strains during 8 years could be related to massive immunization with the monovalent vaccine in the region.
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Affiliation(s)
- Marcelo G Mandile
- Laboratorio de Inmunología y Virología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal 1876, Argentina.
| | - Laura E Esteban
- Laboratorio de Inmunología y Virología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal 1876, Argentina
| | - Marcelo H Argüelles
- Laboratorio de Inmunología y Virología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal 1876, Argentina
| | - Alicia Mistchenko
- Laboratorio de Virología, Hospital de Niños Ricardo Gutiérrez, Sánchez de Bustamante 1330, Buenos Aires 1425, Argentina
| | - Graciela Glikmann
- Laboratorio de Inmunología y Virología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal 1876, Argentina
| | - Alejandro A Castello
- Laboratorio de Inmunología y Virología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal 1876, Argentina
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Luchs A, Cilli A, Morillo SG, de Cassia Compagnoli Carmona R, do Carmo Sampaio Tavares Timenetsky M. Rotavirus in adults, Brazil, 2004–2011: G2P[4] dominance and potential impact on vaccination. Braz J Infect Dis 2014; 18:53-9. [PMID: 24076114 PMCID: PMC9425225 DOI: 10.1016/j.bjid.2013.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/04/2013] [Accepted: 05/09/2013] [Indexed: 11/30/2022] Open
Abstract
Objectives The aim of this study was to monitor rotavirus (RV) infections in adults >18 years with acute gastroenteritis during 2004–2011 national Brazilian RV surveillance. In addition, to characterize the RV group A (RVA) strains in order to gain insight into the supposed vaccine selective pressure imposed to Brazilian children population. Methods A total of 2102 convenient fecal specimens were investigated by ELISA, PAGE, and RT-PCR. Results RV was detected in 203 (9.6%) of 2102 specimens, and showed a marked peak of detection in September. RVA infection was detected in 9.4% (197/2102) and RV group C (RVC) in 0.3% (6/2102). The most frequent genotypes detected in 2004 and 2005 were G9P[8] (38.5%; 5/13) and G1P[8] (54.5%; 6/11), respectively. The dominant genotype identified from 2006 to 2011 was G2P[4] (64.4%; 116/180). Detection rate varied during the 8-year period of the study from 0.7% to 12.9%. Conclusion The high detection rate of G2P[4] in adults provides further evidence that its dominance reflects the seasonality of RVA strains instead of the supposed selective advantage created by vaccination program. It also can be suggested that adult infections may serve as a reservoir to maintain RVA strains in childhood gastroenteritis. Considering the detection rate, the evident reduction of RVA frequency observed in children after vaccine introduction was not present in adults.
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Affiliation(s)
- Adriana Luchs
- Adolfo Lutz Institute, Virology Center, Enteric Disease Laboratory, Av. Dr. Arnaldo, 355, São Paulo, SP, Brazil.
| | - Audrey Cilli
- Adolfo Lutz Institute, Virology Center, Enteric Disease Laboratory, Av. Dr. Arnaldo, 355, São Paulo, SP, Brazil
| | - Simone Guadagnucci Morillo
- Adolfo Lutz Institute, Virology Center, Enteric Disease Laboratory, Av. Dr. Arnaldo, 355, São Paulo, SP, Brazil
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Rotavirus infection and its genetic characterization in non-hospitalized adults with acute gastroenteritis in Shanghai, China. Arch Virol 2013; 158:1671-7. [PMID: 23483345 DOI: 10.1007/s00705-013-1663-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/04/2013] [Indexed: 10/27/2022]
Abstract
Rotavirus is a major cause of acute gastroenteritis in infants and young children, while its role as a pathogen in adults has long been underappreciated. In order to describe the epidemiological patterns and genetic characteristics of rotavirus causing sporadic acute gastroenteritis in adults, hospital-based surveillance of rotavirus infections was conducted in Shanghai, China, between June 2010 and May 2011. Stool specimens were collected from outpatients with acute gastroenteritis admitted to three local hospitals. Rotavirus was detected using a colloidal gold test device. G and P genotyping were performed by multiplex PCR assays, and the VP7 gene of G9 strains were sequenced for further genetic characterization. Of 1,479 adult diarrheal stool samples examined during the 1-year surveillance period, 138 (9.3 %) were found to be rotavirus positive. G1 appeared to be the predominant genotype (35.5 %), suggesting a shift from genotype G3 to G1 in the study population in Shanghai. Meanwhile, a high frequency of genotype G9 (27.5 %) was also observed, and G9 was also predominant (38.1 %) in the small number of children (n=123) involved in the present study. Other specificities detected in adults were G2 (12.3 %) and G3 (13.8 %). For P genotyping, only two types, P[8] and P[4], were detected. P[8] was dominant in both children and adults. Sequence and phylogenetic analysis revealed that these strains could be divided into two different groups, with clustering within G9 lineage 3 and the subcluster of Japanese and Chinese G9 strains, respectively. In comparison to the previous data, G9 strains established themselves in a short time span as an important genotype in Shanghai, China.
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Ward P, Poitras E, Leblanc D, Gagnon CA, Brassard J, Houde A. Comparison of different RT-qPCR assays for the detection of human and bovine group A rotaviruses and characterization by sequences analysis of genes encoding VP4 and VP7 capsid proteins. J Appl Microbiol 2013; 114:1435-48. [PMID: 23421708 DOI: 10.1111/jam.12165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 01/11/2013] [Accepted: 01/23/2013] [Indexed: 12/12/2022]
Abstract
AIMS The aim of this study was to compare the performance of four RT-qPCR assays for the detection of human and bovine group A rotaviruses and to characterize the positive samples by sequence analysis of VP4 and VP7 genes. METHODS AND RESULTS RNA extracted from eight human rotavirus strains, and a panel of 33 human and 25 bovine faecal samples was subjected to different RT-qPCR detection systems. Among these assays, only RT-qPCR primers and probe systems B and C were able to detect all human rotavirus strains from cell culture solutions and faecal samples. However, the results showed that the system C was generally more sensitive by one or two logs than the other RT-qPCR assays tested. With the bovine faecal samples, the most efficient RT-qPCR systems were B and A with the detection in 100 and 92% of samples tested, respectively. Human group A rotavirus G1P[8] and bovine G6P[11] were the most frequently used strains identified in this study. A G3P[9] strain, closely related to a feline rotavirus isolated in the USA, was also discovered in a human rotavirus infection. CONCLUSION The RT-qPCR system B was the only TaqMan assay evaluated in this study able to detect rotavirus RNA in all positive human and bovine faecal samples. SIGNIFICANCE AND IMPACT OF THE STUDY Utilization of only one RT-qPCR for the detection of human and bovine group A rotaviruses and the possibility of human infection by a feline rotavirus strain.
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Affiliation(s)
- P Ward
- Agriculture and Agri-Food Canada, Food Research and Development Centre, Saint-Hyacinthe, QC, Canada.
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Tatte VS, Chitambar SD. Diversity in the VP7 encoding genes of rotavirus strains isolated from adolescent and adult cases of acute gastroenteritis. J Med Virol 2012; 84:1481-8. [DOI: 10.1002/jmv.23311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Stupka JA, Degiuseppe JI, Parra GI. Increased frequency of rotavirus G3P[8] and G12P[8] in Argentina during 2008–2009: Whole-genome characterization of emerging G12P[8] strains. J Clin Virol 2012; 54:162-7. [DOI: 10.1016/j.jcv.2012.02.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 02/09/2012] [Accepted: 02/14/2012] [Indexed: 11/28/2022]
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Tayeb HT, Balkhy HH, Aljuhani SM, Elbanyan E, Alalola S, Alshaalan M. Increased prevalence of rotavirus among children associated gastroenteritis in Riyadh Saudi Arabia. Virol J 2011; 8:548. [PMID: 22176997 PMCID: PMC3273455 DOI: 10.1186/1743-422x-8-548] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 12/18/2011] [Indexed: 11/10/2022] Open
Abstract
The aim of this study is to assess the epidemiology along with the molecular structure of rotavirus causing pediatric diarrhea among Saudi patients. However, in this report we sited the epidemiological reflect coming from our project.
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Affiliation(s)
- Hamsa T Tayeb
- National Guard Health Affairs & King Abdullah International Medical Research Center, Research Genetic Laboratory, Riyadh, Saudi Arabia.
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26
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Nozawa CM, Kerntopf GF, Czernisz EDS, Albuquerque D, Romanin P, Freitas JFE, Santos N, Benati FJ, Pietruchinski E, Linhares REC. Detection and characterization of human rotavirus in hospitalized patients in the cities of Ponta Grossa, Londrina and Assai - PR, Brazil. Braz J Infect Dis 2011; 14:553-7. [PMID: 21340294 DOI: 10.1016/s1413-8670(10)70111-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 09/06/2010] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Acute diarrheal disease is still one of the major public health problems worldwide. Rotaviruses (RV) are the most important viral etiologic agents and children under five years of age are the target population. OBJECTIVE To investigate the rate of RV infection in hospitalized patients due to acute diarrhea in the cities of Ponta Grossa, Londrina and Assai - Paraná. METHODS Latex agglutination (LA); immunochromatography (ICG); polyacrylamide gel electrophoresis (PAGE) and negative staining electron microscopy (ME) tests were used to detect the virus. For the genotyping, RT-PCR and RT-PCR-ELISA were used, respectively, for NSP4 and VP4/VP7. RESULT Out of 124 samples there were 69 positive stool samples for RV, for at least one of the used tests, 67 of them being RV group A (RV-A). Overall, most of the RV positive stool samples came from children under thirteen years of age. However, 12 positive cases occurred in patients aged 13 years or above, including an 81-year old patient. CONCLUSION The data showed similar electropherotypes and genotypes G, P and NSP4 of the inland wild circulating strains of RV.
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Soares LDS, Lobo PDS, Mascarenhas JDP, Neri DL, Guerra SDFDS, de Oliveira ADSL, Maestri RP, Oliveira DDS, de Menezes EMDFC, Linhares ADC. Identification of lineage III of G12 rotavirus strains in diarrheic children in the Northern Region of Brazil between 2008 and 2010. Arch Virol 2011; 157:135-9. [PMID: 21947565 DOI: 10.1007/s00705-011-1111-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 09/09/2011] [Indexed: 01/09/2023]
Abstract
This study reports on the surveillance for rotavirus genotypes and the identification of G12 human rotavirus in the Northern Region of Brazil. Rotavirus-positive samples were collected from children <5 years of age with acute diarrhea from January 2008 to October 2010. G2P[4] was the most prevalent genotype, accounting for 45.6% (126/303) of cases. Five rotavirus strains bearing G12P[6] genotype specificity were detected. Phylogenetic analysis of the VP7 gene showed that G12 strains clustered into lineage III. This is the first detection of G12 strains from lineage III in Latin America, broadening the current evidence for the worldwide emergence of this genotype.
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Affiliation(s)
- Luana da Silva Soares
- Seção de Virologia, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Rodovia BR 316-KM 07, S/N, Levilândia, 67.030-000 Ananindeua, Pará, Brasil.
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Multiple reassortment and interspecies transmission events contribute to the diversity of feline, canine and feline/canine-like human group A rotavirus strains. INFECTION GENETICS AND EVOLUTION 2011; 11:1396-406. [DOI: 10.1016/j.meegid.2011.05.007] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/06/2011] [Accepted: 05/06/2011] [Indexed: 11/15/2022]
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Caruzo TAR. Human rotavirus genotypes circulating in Brazil before and after a nationwide rotavirus vaccination program established in 2006. Res Rep Trop Med 2011; 2:57-64. [PMID: 30881179 DOI: 10.2147/rrtm.s13650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Accounting for an estimated 600,000 deaths worldwide each year, rotaviruses are recognized as the most important etiologic agents causing severe acute gastroenteritis among children under the age of five years. In Brazil, until rotavirus vaccination was established in the public health system in 2006, acute gastroenteritis striking children under five years and caused by these viruses was clearly associated with 3.5 million episodes of diarrhea, 650,000 visits to outpatient health care facilities, 92,000 hospitalizations, and 850 deaths each year. After the introduction of the rotavirus vaccine in Brazil in March 2006, studies all over the country have been comparing rotavirus genotypes circulating in the recent pre- and postvaccination era. Most of these studies have reported a high prevalence of the G2P[4] genotype and also a decrease in rotavirus detection all over Brazil after the introduction of the vaccine. So far, these are preliminary studies, as a longer period of time is necessary to establish if this high prevalence of G2P[4] is due to selective pressure by the vaccine on the circulating viruses or to a normal genotype fluctuation, and if it will have any impact on vaccine efficacy in the future. This review describes results from the most recent studies addressing this issue and on rotavirus genotypic variability in Brazil.
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Affiliation(s)
- Thabata A R Caruzo
- Genetics, Evolution and Bioagents Department, Institute of Biology, State University of Campinas, Campinas, São Paulo, Brazil,
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Linhares AC, Stupka JA, Ciapponi A, Bardach AE, Glujovsky D, Aruj PK, Mazzoni A, Rodriguez JAB, Rearte A, Lanzieri TM, Ortega-Barria E, Colindres R. Burden and typing of rotavirus group A in Latin America and the Caribbean: systematic review and meta-analysis. Rev Med Virol 2011; 21:89-109. [PMID: 21384462 DOI: 10.1002/rmv.682] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 01/19/2011] [Accepted: 01/21/2011] [Indexed: 01/10/2023]
Abstract
The efficacy of licensed rotavirus vaccines has only been shown against certain rotavirus group A (RV-A) types. It is critical to understand the burden of rotavirus gastroenteritis (RVGE) and its prevalent types to assess the potential impact of these vaccines in Latin America and the Caribbean (LA&C). We performed a systematic review and meta-analyses of all the available evidence reported from 1990 to 2009 on the burden of rotavirus disease and strains circulating in LA&C. Eligible studies--185 country-level reports, 174 951 faecal samples--were selected from MEDLINE, Cochrane Library, EMBASE, LILACS, regional Ministries of Health, PAHO, regional proceedings, doctoral theses, reference lists of included studies and consulting experts. Arc-sine transformations and DerSimonian-Laird random-effects model were used for meta-analyses. The proportion of gastroenteritis cases due to rotavirus was 24.3% (95%CI 22.3-26.4) and the incidence of RVGE was 170 per 1000 children-years (95%CI 130-210). We estimated a global annual mortality for 22 countries of 88.2 (95%CI 79.3-97.1) deaths per 100 000 under 5 years (47 000 deaths).The most common G type detected was G1 (34.2%), followed by G9 (14.6%), and G2 (14.4%). The most common P types detected were P[8] (56.2%), P[4] (22.1%) and P[1] 5.4%, and the most prevalent P-G type associations were P[8]G1 17.9%, P[4]G2 9.1% and P[8]G9 8.8%. In the last 10 years, G9 circulation increased remarkably and G5 almost disappeared. More recently, G12 appeared and P[4]G2 re-emerged. To our knowledge, this is the first meta-analysis of rotavirus infection and burden of disease in LA&C.
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Affiliation(s)
- Alexandre C Linhares
- Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Virology Section. Belém, Brazil.
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Than VT, Le VP, Lim I, Kim W. Complete genomic characterization of cell culture adapted human G12P[6] rotaviruses isolated from South Korea. Virus Genes 2011; 42:317-22. [DOI: 10.1007/s11262-011-0576-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 01/17/2011] [Indexed: 01/24/2023]
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Molecular characterization of rare G12P[6] rotavirus isolates closely related to G12 strains from the United States, CAU 195 and CAU 214. Arch Virol 2010; 156:511-6. [PMID: 21132336 DOI: 10.1007/s00705-010-0865-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/13/2010] [Indexed: 01/28/2023]
Abstract
Two human G12 rotaviruses, CAU 195 and CAU 214, were isolated from South Korea using cell culture and characterized on the basis of sequence divergence in the VP7, VP4, and NSP4 genes. Phylogenetic analysis of the VP7 gene sequences indicated that these strains clustered into lineage III and were most closely related to G12 rotaviruses isolated in the United States. The VP4 and NSP4 gene sequences showed that two strains belonged to the P[6]-Ia lineage and genotype [B]. This finding provides information that can be used to evaluate G12 strains and aid in the development of effective vaccines in the future.
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Esteban LE, Rota RP, Gentsch JR, Jiang B, Esona M, Glass RI, Glikmann G, Castello AA. Molecular epidemiology of group A rotavirus in Buenos Aires, Argentina 2004-2007: reemergence of G2P[4] and emergence of G9P[8] strains. J Med Virol 2010; 82:1083-93. [PMID: 20419826 DOI: 10.1002/jmv.21745] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Detection and characterization of group A rotavirus in Buenos Aires, Argentina, was conducted on 710 fecal samples from children 0-15 years old collected between 2004 and 2007. Rotavirus was detected in 140 (19.7%) samples with G9P[8] (30.0%) and G2P[4] (21.4%) as the most common genotypes. Mixed (G and/or P) infections accounted for 17.9% of the samples and the emerging G12 strain was detected during 2004 (3.5%) and 2007 (2.5%). Genotype G2 was the most prevalent during 2004 (43.9%) and 2007 (57.5%) and G9 during 2005 (58.0%) and 2006 (61.5%). Analysis of genotype prevalences from studies performed since 1996 in the same area showed striking natural fluctuations in G and P genotype frequencies. In particular, G2P[4] strains disappeared after 1999 and reemerged in 2004 to become the predominant strain by 2007 with a concomitant major decrease in G1P[8] prevalence. The VP7 genes from Argentinian G9 and G2 strains were sequenced and phylogenetic analysis was conducted in order to compare with sequences from strains isolated in regional countries reported previously. Several changes in the deduced amino acid sequence in antigenic regions of the VP7 protein from Argentinian and Brazilian strains were identified compared to vaccine strains. Overall, this study revealed relationships in the circulation of rotavirus strains in South American countries and major replacements in dominant genotypes, including the virtual disappearance of G1P[8] strains in a non-vaccinated population. High numbers of mixed infections speeding up evolution, circulation of rare serotypes, and antigenic drift could, eventually, become challenges for new vaccines.
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Affiliation(s)
- Laura E Esteban
- Laboratory of Immunology and Virology, Universidad Nacional de Quilmes, Bernal, Buenos Aires, Argentina.
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Chandrahasen C, Grimwood K, Redshaw N, Rich FJ, Wood C, Stanley J, Kirman JR. Geographical differences in the proportion of human group A rotavirus strains within New Zealand during one epidemic season. J Med Virol 2010; 82:897-902. [DOI: 10.1002/jmv.21739] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Tatte VS, Gentsch JR, Chitambar SD. Characterization of group A rotavirus infections in adolescents and adults from Pune, India: 1993-1996 and 2004-2007. J Med Virol 2010; 82:519-27. [PMID: 20087938 PMCID: PMC7167167 DOI: 10.1002/jmv.21708] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A total of 1,591 fecal specimens were collected in 1993-1996 and 2004-2007 from adolescents and adults with acute gastroenteritis in Pune, India for detection and characterization of rotavirus. At the two time points, group A rotavirus was detected in 8.6% and 16.2% of the adolescents and 5.2% and 17.2% of the adults, respectively. Reverse transcription-PCR with consensus primers followed by multiplex genotyping PCR detected common strains G1P[8], G2P[4], G3P[8], and G4P[8] in a total of 53.1% of the samples from 1993 to 1996, while the only prevalent strain identified in 2004-2007 was G2P[4] (23.5% of total). Uncommon rotavirus strains (G1P[4], G2P[8] G9P[6]/P[4]) increased from 7.8% (1993-1996) to 41.2% (2004-2007), while the prevalence of mixed rotavirus infections was high (39%/35%) at both time points. Mixed infections detected by multiplex PCR were confirmed by sequencing two or more individual genotype-specific PCR products of the VP7 and VP4 genes from the same sample. Phylogenetic analysis of the sequences showed circulation of a heterogeneous rotavirus strain population comprising genotypes G1 (lineages I and IIb), G2 (lineages I and IIb), G4 (lineage Ia), P[4] (lineages P[4]-5 and P[4]-1), P[8] (lineages P[8]-II and P[8]-III), and P[6] (M37-like lineage). The VP6 gene sequences of the nontypeable strains were most homologous to animal strains. This study documents the molecular epidemiology of rotavirus strains in adolescents and adults in India, and suggests that it may be important to monitor these strains over time for the potential impact on rotavirus vaccines under development for use in the Indian population. J. Med. Virol. 82:519-527, 2010. (c) 2010 Wiley-Liss, Inc.
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Martínez M, Amarilla AA, Galeano ME, Aquino VH, Fariña N, Russomando G, Parra GI. Predominance of rotavirus G2P[4] and emergence of G12P[9] strains in Asunción, Paraguay, 2006-2007. Arch Virol 2010; 155:525-33. [PMID: 20213281 DOI: 10.1007/s00705-010-0617-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 02/04/2010] [Indexed: 02/01/2023]
Abstract
Rotavirus is the most common cause of severe diarrhea in children worldwide. Monitoring the diversity of rotavirus strains is of great importance for current and future vaccination programs. To determine the diversity of rotavirus circulating in Asuncion, Paraguay, between 2006 and 2007, we carried out a molecular characterization of rotaviruses detected in children <5 years old and adults (>18 years old). We found that the most common circulating strain was G2P[4] (69/143), followed by G9P[8] (37/143). The temporal distribution of strains showed that, in children, G2P[4] was predominant in 2006, and that G2P[4] and G9P[8] were co-predominant in 2007, whereas in adults, G2P[4] was predominant in both years. Additionally, one G9P[6] and three G12P[9] strains were found in adult samples, making this the first report of these strains circulating in Paraguay. Sequence analysis of the G12P[9] strains suggests across-border migration of this strain within the southern cone of America.
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Affiliation(s)
- Magaly Martínez
- Molecular Biology Department, IICS, National University of Asuncion, Río de Plata y Lagerenza, 2511 Asunción, Paraguay
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Aladin F, Nawaz S, Iturriza-Gómara M, Gray J. Identification of G8 rotavirus strains determined as G12 by rotavirus genotyping PCR: updating the current genotyping methods. J Clin Virol 2010; 47:340-4. [PMID: 20138804 DOI: 10.1016/j.jcv.2010.01.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 12/31/2009] [Accepted: 01/09/2010] [Indexed: 01/20/2023]
Abstract
BACKGROUND Rotaviruses are classified into G- and P-types, which are determined by the reactivity with antibodies to the outer viral proteins, VP7 and VP4, respectively, or sequence variation in the genes encoding these proteins. There are presently a number of different rotavirus strains co-circulating within the UK, with the common human strains G1P[8], G2P[4] and G9P[8] being the most prevalent. As part of strain surveillance for the European Rotavirus Network (EuroRotaNet) a cluster (n=29) of G8 strains was detected in the UK between February and May 2009. OBJECTIVES G8 strains were initially mistyped as G12 through multiplex RT-PCR, therefore further investigation was performed to ascertain the reasons behind this mistyping. STUDY DESIGN The genes encoding the VP7 of these G8 strains were sequenced and aligned with the existing G8- and G12-specific oligonucleotide primers. RESULTS Multiple alignment of sequences derived from these strains and the G8- and G12-specific oligonucleotide primers revealed a series of point mutations which resulted in mismatches at the 3' end of the G8-specific primer binding site that prevented amplification with the G8-specific primer, whilst a close homology with the G12-specific primer allowed mis-priming. Both the G8 and G12 primers were redesigned and their ability to correctly identify G8 and G12 strains was evaluated and confirmed. CONCLUSION These findings highlight the importance of monitoring the specificity and sensitivity of the genotyping methods in order to detect changes in the genotype distribution and changes associated with genetic drift of common or uncommon genotypes.
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Affiliation(s)
- Farah Aladin
- Health Protection Agency, Centre for Infections, 61 Colindale Avenue, London, NW9 5HT, United Kingdom
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Freeman M, Kerin T, Hull J, Teel E, Esona M, Parashar U, Glass R, Gentsch J. Phylogenetic analysis of novel G12 rotaviruses in the United States: A molecular search for the origin of a new strain. J Med Virol 2009; 81:736-46. [DOI: 10.1002/jmv.21446] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Wang YH, Kobayashi N, Zhou X, Nagashima S, Zhu ZR, Peng JS, Liu MQ, Hu Q, Zhou DJ, Watanabe S, Ishino M. Phylogenetic analysis of rotaviruses with predominant G3 and emerging G9 genotypes from adults and children in Wuhan, China. J Med Virol 2009; 81:382-9. [PMID: 19107964 DOI: 10.1002/jmv.21387] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prevalence and phylogenetic relatedness of rotaviruses causing diarrheal diseases in children and adults were analyzed in Wuhan, China. During a period between June 2006 and February 2008, group A rotavirus was identified in 24.9% (280/1126) and 7.6% (83/1088) of specimens taken from children and adults, respectively. G3P[8] was the most frequent genotype in both children (66.3%) and adults (62.7%), followed by G1P[8] (20.3% and 26.2%, respectively). G9 was detected in specimens from six children (2.0%) and seven adults (5.6%). The VP7 genes of G3P[8] rotaviruses from children and adults showed extremely high sequence identities to each other (98.9-100%) and also to those of G3 viruses isolated in Wuhan in 2003-2004. In the phylogenetic analysis of the VP7 gene, the G3P[8] rotaviruses in Wuhan were clustered into a single lineage with some G3 viruses, which had been referred to as "the new variant G3" rotaviruses, reported recently in East Asia and Southeast Asia. Similar to G3P[8] rotaviruses, extremely high sequence identities between children and adults were observed for VP7 genes of G1 and G9 rotaviruses. The G9 viruses were clustered in the lineage of globally spreading strains, while G1 viruses were genetically close to those reported previously in China and Japan. These findings indicated the persistence of the variant G3 rotaviruses and spread of G9 rotaviruses derived from the global G9 lineage in Wuhan, and suggested that the rotaviruses were circulating among children and adults, irrelevant to the G types.
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Affiliation(s)
- Yuan-Hong Wang
- Wuhan Centers for Disease Prevention and Control, Wuhan, Hubei Province, China
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Castello AA, Nakagomi T, Nakagomi O, Jiang B, Kang JO, Glass RI, Glikmann G, Gentsch JR. Characterization of genotype P[9]G12 rotavirus strains from argentina: High similarity with Japanese and Korean G12 strains. J Med Virol 2009; 81:371-81. [DOI: 10.1002/jmv.21384] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Leite JPG, Carvalho-Costa FA, Linhares AC. Group A rotavirus genotypes and the ongoing Brazilian experience: a review. Mem Inst Oswaldo Cruz 2008; 103:745-53. [DOI: 10.1590/s0074-02762008000800001] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 12/16/2008] [Indexed: 12/31/2022] Open
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Page N, de Beer M, Seheri L, Dewar J, Steele A. The detection and molecular characterization of human G12 genotypes in South Africa. J Med Virol 2008; 81:106-13. [DOI: 10.1002/jmv.21362] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Paul SK, Kobayashi N, Nagashima S, Ishino M, Watanabe S, Alam MM, Ahmed MU, Hossain MA, Naik TN. Phylogenetic analysis of rotaviruses with genotypes G1, G2, G9 and G12 in Bangladesh: evidence for a close relationship between rotaviruses from children and adults. Arch Virol 2008; 153:1999-2012. [DOI: 10.1007/s00705-008-0212-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Accepted: 09/08/2008] [Indexed: 10/21/2022]
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Gurgel RQ, Cunliffe NA, Nakagomi O, Cuevas LE. Rotavirus genotypes circulating in Brazil before national rotavirus vaccination: A review. J Clin Virol 2008; 43:1-8. [DOI: 10.1016/j.jcv.2008.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2007] [Revised: 03/19/2008] [Accepted: 04/22/2008] [Indexed: 11/27/2022]
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Ribeiro LR, Giuberti RSDO, Barreira DMPG, Saick KW, Leite JPG, Miagostovich MP, Spano LC. Hospitalization due to norovirus and genotypes of rotavirus in pediatric patients, state of Espírito Santo. Mem Inst Oswaldo Cruz 2008; 103:201-6. [DOI: 10.1590/s0074-02762008000200013] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2007] [Accepted: 02/18/2008] [Indexed: 11/22/2022] Open
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Abstract
The prospect that rotavirus diarrhea in children may soon be prevented by vaccines has placed a new priority on understanding the diversity of rotavirus strains and the mechanism by which these strains evolve over time. We have characterized a total of 465 rotavirus strains collected in North India from 2000 to 2007 for G and P types by reverse transcription-PCR and sequencing. The novel G12 rotavirus strains recently detected in other countries were first detected in India in 2001 and have emerged as the predominant strains in Delhi, India, during 2005 to 2007. While the VP7 sequence was highly homologous among G12 strains isolated in Delhi, suggesting recent emergence from a common ancestor, the strains had a diverse constellation of other gene segments, demonstrating substantial reassortment. For the entire period, the common rotavirus G types G1 (26%), G2 (25%), and G9 (14%) comprised 65% of the strains, and common P types, P[4] (19%), P[6] (22%), and P[8] (35%), comprised 76% of the total P types. Of note, we detected a high percentage of unusual (17%) strains and fecal specimens with mixed (12% G and 15% P) rotavirus infections having a variety of genomic constellations. For the first time, we identified two novel rotavirus strains with unusual G/P combinations, G2P[11] and G3P[11], in patients with diarrhea. The study highlights the great diversity among rotaviruses isolated from Indian children, the opportunity for genetic reassortment between strains, and the emergence of a novel G12 strain in our country. Due to the demonstrated effect of antigenic diversity on rotavirus vaccines, it will be important to continue careful monitoring of these strains as rotavirus vaccine programs are implemented in India.
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Santos N, Honma S, Timenetsky MDCST, Linhares AC, Ushijima H, Armah GE, Gentsch JR, Hoshino Y. Development of a microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay for identification of clinically relevant human group A rotavirus G and P genotypes. J Clin Microbiol 2008; 46:462-9. [PMID: 18057127 PMCID: PMC2238104 DOI: 10.1128/jcm.01361-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/31/2007] [Accepted: 11/20/2007] [Indexed: 01/03/2023] Open
Abstract
A microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay (PCR-ELISA) has been used for the detection and identification of a variety of microorganisms. Here, we report the development of a PCR-ELISA for the identification of clinically relevant human rotavirus VP7 (G1 to G6, G8 to G10, and G12) and VP4 (P[4], P[6], P[8], P[9], and P[14]) genotypes. The G and P types of reference human and animal rotavirus strains for which specific probes were available were correctly identified by the PCR-ELISA. In addition, reference strains bearing G or P genotypes for which specific probes were unavailable, such as G11, G14, P[3], P[10], and P[11], did not display any cross-reactivity to the probes. The usefulness of the assay was further evaluated by analyzing a total of 396 rotavirus-positive stool samples collected in four countries: Brazil, Ghana, Japan, and the United States. The results of this study showed that the PCR-ELISA was sensitive and easy to perform without the use of any expensive and sophisticated equipment, the reagents used are easy to obtain commercially and advantageous over multiplex PCR since more than one type-specific probe is used and the selection of probes is more flexible.
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Affiliation(s)
- Norma Santos
- Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS-Bl. I, Ilha do Fundão, Rio de Janeiro 21.941-590, Brazil.
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Bányai K, Bogdán A, Kisfali P, Molnár P, Mihály I, Melegh B, Martella V, Gentsch JR, Szücs G. Emergence of serotype G12 rotaviruses, Hungary. Emerg Infect Dis 2007; 13:916-9. [PMID: 17553236 PMCID: PMC2792842 DOI: 10.3201/eid1306.061181] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We describe the emergence of serotype G12 rotaviruses (67 [6.9%] of 971 specimens tested) among children hospitalized with rotavirus gastroenteritis in Hungary during 2005. These findings are consistent with recent reports of the possible global spread and increasing epidemiologic importance of these strains, which may have implications for current rotavirus vaccination strategies.
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Affiliation(s)
- Krisztián Bányai
- Baranya County Institute of State Public Health Service, Pécs, Hungary.
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49
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Pun SB, Nakagomi T, Sherchand JB, Pandey BD, Cuevas LE, Cunliffe NA, Hart C, Nakagomi O. Detection of G12 human rotaviruses in Nepal. Emerg Infect Dis 2007; 13:482-4. [PMID: 17552107 PMCID: PMC2725908 DOI: 10.3201/eid1303.061367] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Of 731 stool specimens collected from children with diarrhea in Kathmandu, Nepal, from August 2004 through July 2005, 170 (23.3%) tested positive for rotavirus. Reverse transcription-PCR, including a revised G12-specific primer set, identified 56 (32.9%) as G2P[4] and 39 (23.0%) as G12 with P[6], P[8], or P[4].
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Affiliation(s)
| | - Toyoko Nakagomi
- Nagasaki University, Nagasaki, Japan
- University of Liverpool, Liverpool, United Kingdom
| | - Jeevan Bahadur Sherchand
- Tribhuvan University Institute of Medicine, Kathmandu, Nepal
- Infectious and Tropical Diseases Research Centre, Kathmandu, Nepal
| | - Basu Dev Pandey
- Sukra Raj Tropical and Infectious Disease Hospital, Kathmandu, Nepal
| | - Luis E. Cuevas
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | | | - C.A. Hart
- University of Liverpool, Liverpool, United Kingdom
| | - Osamu Nakagomi
- Nagasaki University, Nagasaki, Japan
- University of Liverpool, Liverpool, United Kingdom
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50
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Wang YH, Kobayashi N, Zhou DJ, Yang ZQ, Zhou X, Peng JS, Zhu ZR, Zhao DF, Liu MQ, Gong J. Molecular epidemiologic analysis of group A rotaviruses in adults and children with diarrhea in Wuhan city, China, 2000-2006. Arch Virol 2007; 152:669-85. [PMID: 17195953 DOI: 10.1007/s00705-006-0904-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 11/22/2006] [Indexed: 11/29/2022]
Abstract
To compare epidemiologic features and genetic characteristics of group A rotaviruses causing diarrhea in children and adults, a survey was conducted in Wuhan, China, during the period of Dec. 2000-May 2006. A total of 3839 stool specimens from diarrheal patients from eight hospitals were analyzed. Winter seasonality was observed for rotavirus diarrhea in both adults and children, showing overall rotavirus-positive rates of 9.0 and 23.9%, respectively. Throughout the study period, G3 was the most frequent G serotype in both adults and children (detection rates 86.2 and 87.8%, respectively), and was mostly associated with VP4 genotype P[8], VP 6 genotype II (subgroup II), and NSP4 genotype B. G3 rotaviruses were differentiated into eight electropherotypes, among which seven types were found in specimens from both adults and children. VP7 gene sequences of G3 rotaviruses from adults and children (6 and 4 strains, respectively), detected in different years and different hospitals, showed extremely high sequence identities (99-100%) to each other and to a few G3 rotavirus strains reported in Asia. However, lower sequence identities (82-96%) were observed to most of the human and animal G3 rotaviruses reported so far, including some Chinese strains. These findings indicate that in Wuhan, China, epidemic and genetic features of rotaviruses are similar in adults and children, and it has been suggested that G3 rotaviruses that might have originated from the same rotavirus were circulating among children and adults as prevailing viruses. In this study, two rotavirus strains, G9P[8] strain L169, derived from an adult, and G4P[6] strain R479, derived from a child, were isolated and genetically analyzed. The VP7 gene of L169 belongs to a major lineage of G9 rotaviruses that are globally widespread, but is distinct from G9 rotaviruses reported previously in China. The strain R479 had a VP7 gene which was divergent from most G4 human rotaviruses and showed an unusual dual subgroup specificity, I + II. The R479 VP6 gene does not belong to the main clusters of subgroup I and II rotaviruses phylogenetically, but is related to those of the porcine rotaviruses and some unusual human rotaviruses represented by the RMC321 strain isolated in eastern India.
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Affiliation(s)
- Y-H Wang
- State Key Laboratory of Virology, Institute of Virology, Wuhan University School of Medicine, Wuhan, Hubei Province, P.R. China
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