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Jelley L, Douglas J, O'Neill M, Berquist K, Claasen A, Wang J, Utekar S, Johnston H, Judy B, Allais M, de Ligt J, Tan CE, Seeds R, Wood T, Aminisani N, Jennings T, Welch D, Turner N, McIntyre P, Dowell T, Trenholme A, Byrnes C, Webby R, French N, Winter D, Huang QS, Geoghegan JL. Spatial and temporal transmission dynamics of respiratory syncytial virus in New Zealand before and after the COVID-19 pandemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24310412. [PMID: 39072023 PMCID: PMC11275701 DOI: 10.1101/2024.07.15.24310412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Human respiratory syncytial virus (RSV) is a major cause of acute respiratory infection. In 2020, RSV was effectively eliminated from the community in New Zealand due to non-pharmaceutical interventions (NPI) used to control the spread of COVID-19. However, in April 2021, following a brief quarantine-free travel agreement with Australia, there was a large-scale nationwide outbreak of RSV that led to reported cases more than five times higher, and hospitalisations more than three times higher, than the typical seasonal pattern. In this study, we generated 1,471 viral genomes of both RSV-A and RSV-B sampled between 2015 and 2022 from across New Zealand. Using a phylodynamics approach, we used these data to better understand RSV transmission patterns in New Zealand prior to 2020, and how RSV became re-established in the community following the relaxation of COVID-19 restrictions. We found that in 2021, there was a large epidemic of RSV in New Zealand that affected a broader age group range compared to the usual pattern of RSV infections. This epidemic was due to an increase in RSV importations, leading to several large genomic clusters of both RSV-A ON1 and RSV-B BA9 genotypes in New Zealand. However, while a number of importations were detected, there was also a major reduction in RSV genetic diversity compared to pre-pandemic seasonal outbreaks. These genomic clusters were temporally associated with the increase of migration in 2021 due to quarantine-free travel from Australia at the time. The closest genetic relatives to the New Zealand RSV genomes, when sampled, were viral genomes sampled in Australia during a large, off-season summer outbreak several months prior, rather than cryptic lineages that were sustained but not detected in New Zealand. These data reveal the impact of NPI used during the COVID-19 pandemic on other respiratory infections and highlight the important insights that can be gained from viral genomes.
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Moumbeket Yifomnjou MH, Monamele GC, Modiyinji AF, Njankouo-Ripa M, Onana B, Njouom R. Genetic Diversity of Human Respiratory Syncytial Virus during COVID-19 Pandemic in Yaoundé, Cameroon, 2020-2021. Microorganisms 2024; 12:952. [PMID: 38792782 PMCID: PMC11123827 DOI: 10.3390/microorganisms12050952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Worldwide, human respiratory syncytial virus (HRSV) is a major cause of severe infections of the lower respiratory system, affecting individuals of all ages. This study investigated the genetic variability of HRSV during the COVID-19 outbreak in Yaoundé; nasopharyngeal samples positive for HRSV were collected from different age groups between July 2020 and October 2021. A semi-nested RT-PCR was performed on the second hypervariable region of the G gene of detected HRSV, followed by sequencing and phylogenetic assessment. Throughout the study, 40 (37.7%) of the 106 HRSV-positive samples successfully underwent G-gene amplification. HRSV A and HRSV B co-circulated at rates of 47.5% and 52.5%, respectively. HRSV A clustered in the GA2.3.5 genetic lineage (ON1) and HRSV B clustered in the GB5.0.5a genetic lineage (BA9). Differences in circulating genotypes were observed between pre- and post-pandemic years for HRSV A. Predictions revealed potential N-glycosylation sites at positions 237-318 of HRSV A and positions 228-232-294 of HRSV B. This study reports the molecular epidemiology of HRSV in Cameroon during the COVID-19 pandemic. It describes the exclusive co-circulation of two genetic lineages. These findings highlight the importance of implementing comprehensive molecular surveillance to prevent the unexpected emergence of other diseases.
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Affiliation(s)
- Moïse Henri Moumbeket Yifomnjou
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Gwladys Chavely Monamele
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Abdou Fatawou Modiyinji
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Mohamadou Njankouo-Ripa
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
| | - Boyomo Onana
- Laboratory of Microbiology, University of Yaoundé I, Yaoundé P.O. Box 812, Cameroon;
| | - Richard Njouom
- Virology Unit, Centre Pasteur du Cameroun, 451 Rue 2005, Yaoundé P.O. Box 1274, Cameroon; (M.H.M.Y.); (G.C.M.); (A.F.M.); (M.N.-R.)
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Diouf FS, Tidjani Alou M, Bassene H, Cortaredona S, Diatta G, Raoult D, Sokhna C, Lagier JC. Seasonal variation of asymptomatic viral and bacterial nasopharyngeal carriage in rural Senegal. J Infect Public Health 2024; 17:922-928. [PMID: 38579539 DOI: 10.1016/j.jiph.2024.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/26/2024] [Accepted: 03/17/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The surveillance of respiratory pathogens in rural areas of West Africa has, to date, largely been focussed on symptoms. In this prospective study conducted prior to the COVID-19 pandemic, we aimed to assess the asymptomatic prevalence of respiratory pathogen carriage in a group of individuals living in a rural area of Senegalese. METHODS Longitudinal follow up was performed through monthly nasopharyngeal swabbing during the dry season and weekly swabbing during the rainy season. We enrolled 15 individuals from the village of Ndiop. A total of 368 nasopharyngeal swabs were collected over a one-year period. We investigated the prevalence of 18 respiratory viruses and eight respiratory bacteria in different age groups using singleplex and multiplex PCR. RESULTS In total, 19.56% of the samples (72/368) were positive for respiratory viruses and 13.60% of the samples (50/368) were positive for respiratory bacteria. Coronaviruses (19/72, 26.39%), adenoviruses (17/72, 23.61%), rhinoviruses (14/72, 19.44%), Streptococcus pneumoniae (17/50, 34%), and Moraxella catarrhalis (15/50, 30%) were the most frequently detected viruses. Interestingly, the carriage of respiratory pathogens was shown to be more frequent during the rainy season, as pluviometry was shown to be positively associated with the occurrence of respiratory viruses such as influenza (P = .0078, r2 =.523) and RSV (P = .0055, r2 =.554). CONCLUSIONS Our results show a non-negligible circulation of respiratory pathogens in a rural area in Senegal (West Africa) with an underestimated proportion of asymptomatic individuals. This study highlights the fact that the circulation of viruses and bacteria in the community has been overlooked.
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Affiliation(s)
- Fatou Samba Diouf
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Maryam Tidjani Alou
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Hubert Bassene
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Sebastien Cortaredona
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Georges Diatta
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal
| | - Didier Raoult
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- VITROME IRD, Campus International de Recherche IRD-UCAD Hann, Dakar, Senegal; IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- IHU Méditerranée Infection, Marseille, France; Aix-Marseille Université, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France.
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Tayachew A, Teka G, Gebeyehu A, Shure W, Biru M, Chekol L, Berkessa T, Tigabu E, Gizachew L, Agune A, Gonta M, Hailemariam A, Gedefaw E, Woldeab A, Alemu A, Getaneh Y, Lisanwork L, Yibeltal K, Abate E, Abayneh A, Wossen M, Hailu M, Workineh F. Prevalence of respiratory syncytial virus infection and associated factors in children aged under five years with severe acute respiratory illness and influenza-like illness in Ethiopia. IJID REGIONS 2024; 10:191-196. [PMID: 38356999 PMCID: PMC10864198 DOI: 10.1016/j.ijregi.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Objectives Acute respiratory infections because of respiratory syncytial viruses (RSVs) are among the major leading causes of morbidity and mortality in children worldwide. RSV prevalence and its contributing factors among children aged under 5 years in Ethiopia are not well studied. To assess the prevalence and associated factors of RSV infection in children aged under 5 years using influenza sentinel surveillance sites in Ethiopia. Methods A cross-sectional study design was used utilizing influenza-like illness/sever acute respiratory illness surveillance data from January 2021 to December 2022 at the Ethiopian Public Health Institute. Results In total, 2234 cases were included, with an overall RSV positivity rate of 16.2%. The RSV positivity rate was high in children aged under 1 year (22.8%) and during fall season (24.8%). The RSV positivity rate was significantly associated with ages under 1 year (adjusted odds ratio [AOR] 2.8, 95% confidence interval [CI]: 1.89-4.15) and 1-2 years (AOR 1.9, 95% CI: 1.26-2.73) and the fall season (AOR 1.67, 95% CI: 1.17-2.38). Conclusion The study revealed that a considerably high RSV positivity rate was detected in children aged under 5 years. The age of children and season have a significant association with RSV positivity rate. Further studies of RSV viral genotype, clinical characteristics, and disease outcome need to be conducted for a better understanding of the virus and disease outcome.
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Affiliation(s)
- Adamu Tayachew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Addis Continental Institute of Public Health, Addis Ababa
| | - Gizaw Teka
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayele Gebeyehu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Wolde Shure
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mengistu Biru
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Eyasu Tigabu
- The Ohio State University Global One Health, Addis Ababa, Ethiopia
| | | | - Admikew Agune
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Melaku Gonta
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Ergetu Gedefaw
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Adane Woldeab
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- The Ohio State University Global One Health, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yimam Getaneh
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Leuel Lisanwork
- The Ohio State University Global One Health, Addis Ababa, Ethiopia
| | | | - Ebba Abate
- The Ohio State University Global One Health, Addis Ababa, Ethiopia
| | | | - Mesfin Wossen
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mesay Hailu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
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Tejiokem MC, Barry A, Ratovoson R, Yambiyo B, Hamidou Lazoumar R, Herrant M, Madaha E, Richard V. African countries from the Pasteur Network reexamine their syndromic sentinel surveillance system associated with household contact within the AFROSCREEN program. Front Public Health 2024; 11:1292435. [PMID: 38249384 PMCID: PMC10796548 DOI: 10.3389/fpubh.2023.1292435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
Surveillance to better detect and respond to new pathogens remains a major challenge for global public health. The Pasteur Network recently held a brainstorming workshop located in Cameroon attended by Pasteur epidemiological teams from Niger, Central African Republic (CAR), Cameroon, Senegal, and Madagascar to discuss how the Pasteur Network in Africa could use the lessons of COVID-19 to set-up a pilot sentinel surveillance scheme given its expertise and involvement during the pandemic. The possibility of coupling sentinel syndromic and biological surveillance already implemented for influenza surveillance with the recent sequencing capacity put in place by the AFROSCREEN program prompted us to consider strengthening surveillance tools to target "Pathogen X" detection in Africa. The perspective project provided by the Pasteur Network teams and shared with other partners of the AFROSCREEN program will target strengthening of the diagnosis of severe acute respiratory infections (IRAS) and the surveillance of IRAS, the evaluation of the impact of SARS-CoV-2 on the epidemiology of IRAS, and the addition of the detection of new pathogens, called "Pathogen X," based on sequencing capacity and epidemiological criteria from One Health approaches.
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Affiliation(s)
| | | | - Rila Ratovoson
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Brice Yambiyo
- Institut Pasteur de Bangui, Bangui, Central African Republic
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Huang L, Xu Y, Yang Y, Dong H, Luo Q, Chen Z, Du H, Mei G, Wang X, Guan Y, Zhao C, Han J, Lu G. Molecular epidemiology and clinical characteristics of respiratory syncytial virus in hospitalized children during winter 2021-2022 in Bengbu, China. Front Public Health 2024; 11:1310293. [PMID: 38235154 PMCID: PMC10791987 DOI: 10.3389/fpubh.2023.1310293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/01/2023] [Indexed: 01/19/2024] Open
Abstract
Objective This study aimed to study the molecular epidemiology and clinical characteristics of respiratory syncytial virus (RSV) infection from hospitalized children with ARTI in Bengbu. Methods One hundred twenty-four nasopharyngeal swab specimens and clinical data from children with ARTI cases were collected in Bengbu, China, during winter 2021-2022. The samples were detected by qPCR of 13 respiratory viruses. Phylogenetic analysis was constructed using MEGA 7.0. All analyses were performed using SAS software, version 9.4. Results In winter 2021-2022, URTI, NSCAP, SCAP, and bronchiolitis accounted for 41.03%, 27.35%, 17.09%, and 14.53% of hospitalized children in Bengbu, China. The detection rates of the top three were RSV (41.94%), ADV (5.65%), and FluB (5.65%) in hospitalized children through 13 virus detection. RSV is the main pathogen of hospitalized children under 2 years old. Forty-eight sequences of G protein of RSV were obtained through PCR amplification, including RSV-A 37 strains and RSV-B 11 strains. Phylogenetic analysis showed that all RSV-A and RSV-B were ON1 and BA9 genotypes, respectively. ON1 genotypes were further divided into two clades. The majority of ON1 strains formed a unique genetic clade with T113I, V131D, N178 G, and H258Q mutations. Furthermore, RSV infection was an independent risk factor for ventilator use (OR = 9.55, 95% CI 1.87-48.64). Conclusion There was a high incidence of RSV among hospitalized children during winter 2021-2022 in Bengbu with ON1 and BA9 being the dominant strains. This study demonstrated the molecular epidemiological characteristics of RSV in children with respiratory infections in Bengbu, China.
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Affiliation(s)
- Limin Huang
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
- Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yuanyou Xu
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Yanqing Yang
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongming Dong
- School of Basic Medicine, North China University of Science and Technology, Tangshan, China
| | - Qin Luo
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhen Chen
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haijun Du
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyong Mei
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xinyue Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- College of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, China
| | - Yake Guan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chihong Zhao
- Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jun Han
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guoyu Lu
- The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
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Jallow MM, Diagne MM, Sagne SN, Tall F, Diouf JBN, Boiro D, Mendy MP, Ndiaye NK, Kiori D, Sy S, Goudiaby D, Loucoubar C, Fall G, Barry MA, Dia N. Respiratory syncytial virus in pediatric patients with severe acute respiratory infections in Senegal: findings from the 2022 sentinel surveillance season. Sci Rep 2023; 13:20404. [PMID: 37990112 PMCID: PMC10663443 DOI: 10.1038/s41598-023-47015-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
In 2022, many regions around the world experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start and increased numbers of paediatric patients in emergency departments. Here we carried out this study to describe the epidemiology and genetic characteristics of RSV infection in patients hospitalized with severe acute respiratory infections in 2022. Samples were tested for RSV by multiplex real time reverse transcription polymerase chain reaction. Subsequently, a subset of RSV positive samples was selected for NGS sequencing. RSV was detected in 16.04%, among which RSV-A was confirmed in 7.5% and RSV-B in 76.7%. RSV infection were more identified in infants aged ≤ 11 months (83.3%) and a shift in the circulation pattern was observed, with highest incidences between September-November. Phylogenetic analyses revealed that all RSV-A strains belonged to GA2.3.5 genotype and all RSV-B strains to GB5.0.5a genotype. Three putative N-glycosylation sites at amino acid positions 103, 135, 237 were predicted among RSV-A strains, while four N-linked glycosylation sites at positions 81, 86, 231 and 294 were identified in RSV-B strains. Globally, our findings reveal an exclusive co-circulation of two genetic lineages of RSV within the pediatric population in Senegal, especially in infants aged ≤ 11 months.
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Affiliation(s)
| | | | - Samba Niang Sagne
- Institut Pasteur de Dakar, Unité d'Epidémiologie Des Maladies Infectieuses, 36, Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Fatime Tall
- Hôpital Des Enfants Albert Royer de Fann, Dakar, Senegal
| | | | | | | | | | - Davy Kiori
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Déborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Cheikh Loucoubar
- Institut Pasteur de Dakar, Unité d'Epidémiologie Des Maladies Infectieuses, 36, Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Gamou Fall
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d'Epidémiologie Des Maladies Infectieuses, 36, Avenue Pasteur, B.P. 220, Dakar, Senegal
| | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar, Senegal.
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Bimouhen A, Regragui Z, El Falaki F, Ihazmade H, Benkerroum S, Barakat A, Rguig A, Benamar T, Triki S, Bakri Y, Oumzil H. Circulation patterns and molecular epidemiology of human respiratory syncytial virus over five consecutive seasons in Morocco. Influenza Other Respir Viruses 2023; 17:e13203. [PMID: 37859975 PMCID: PMC10582604 DOI: 10.1111/irv.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/05/2023] [Accepted: 09/10/2023] [Indexed: 10/21/2023] Open
Abstract
Background Respiratory syncytial virus (HRSV) is the leading cause of respiratory tract infections in infants and young children. we investigated the prevalence and characteristics of HRSV in Morocco and explored trends in circulating genotypes through partial G gene analysis of HRSV strains prevalent from 2012 to 2017. Methods Respiratory samples were gathered from both outpatients and inpatients meeting ILI or SARI case definitions. The patients' ages varied from 1 month to 99 years old. Nucleic acids were extracted and HRSV type/subtype was detected by RT-qPCR. A subset of positive samples was randomly selected in each epidemic year, the complete viral genome was sequenced, phylogenetic analysis was performed using the MEGA7 program and the genotypes were confirmed. Results The 3679 specimens were collected from 2012 to 2017, of which 726 (19.7%) were positive for HRSV. The 35% (257/726) of HRSV-positives were of the HRSV-A subtype, while the HRSV-B subtype accounted for 61% (442/726). The co-infection rate was 3.7% (27/726). The virus circulates in a periodic pattern, where epidemics occur during the fall months through early spring. HRSV genotype was confirmed in 127 specimens (56 HRSV-A and 71 HRSV-B). Based on phylogenetic analysis, all HRSV-A were ON1 genotype, and HRSV-B were mostly BA9 genotype. HRSV-B belonging to the BA10 genotype was detected in 2012 exclusively. Conclusions BA9, BA10, and ON1 were the only HRSV genotypes detected between 2012 and 2017. Variations in the G gene amino acid chain were identified in local strains, which suggests an increased need for continuous genomic surveillance.
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Affiliation(s)
- Abderrahman Bimouhen
- Laboratory of Human Pathologies Biology, Faculty of SciencesMohammed V University in RabatRabatMorocco
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Zakia Regragui
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Fatima El Falaki
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Hassan Ihazmade
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Samira Benkerroum
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
| | - Amal Barakat
- World Health Organization Regional Office for the Eastern MediterraneanCairoEgypt
| | - Ahmed Rguig
- Directorate of Epidemiology and Disease ControlMinistry of HealthRabatMorocco
| | - Touria Benamar
- Directorate of Epidemiology and Disease ControlMinistry of HealthRabatMorocco
| | - Soumia Triki
- World Health Organization Country Office of MoroccoRabatMorocco
| | - Youssef Bakri
- Laboratory of Human Pathologies Biology, Faculty of SciencesMohammed V University in RabatRabatMorocco
- Center of human pathologies genomic, faculty of Medicine and PharmacyMohammed V university in RabatRabatMorocco
| | - Hicham Oumzil
- National Influenza Center, Virology DepartmentNational Institute of Hygiene, Ministry of HealthRabatMorocco
- Pedagogy and Research Unit of Microbiology, School of Medicine and PharmacyMohammed V University in RabatRabatMorocco
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Wagatsuma K, Koolhof IS, Saito R. Nonlinear and Multidelayed Effects of Meteorological Drivers on Human Respiratory Syncytial Virus Infection in Japan. Viruses 2023; 15:1914. [PMID: 37766320 PMCID: PMC10535838 DOI: 10.3390/v15091914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
In this study, we aimed to characterize the nonlinear and multidelayed effects of multiple meteorological drivers on human respiratory syncytial virus (HRSV) infection epidemics in Japan. The prefecture-specific weekly time-series of the number of newly confirmed HRSV infection cases and multiple meteorological variables were collected for 47 Japanese prefectures from 1 January 2014 to 31 December 2019. We combined standard time-series generalized linear models with distributed lag nonlinear models to determine the exposure-lag-response association between the incidence relative risks (IRRs) of HRSV infection and its meteorological drivers. Pooling the 2-week cumulative estimates showed that overall high ambient temperatures (22.7 °C at the 75th percentile compared to 16.3 °C) and high relative humidity (76.4% at the 75th percentile compared to 70.4%) were associated with higher HRSV infection incidence (IRR for ambient temperature 1.068, 95% confidence interval [CI], 1.056-1.079; IRR for relative humidity 1.045, 95% CI, 1.032-1.059). Precipitation revealed a positive association trend, and for wind speed, clear evidence of a negative association was found. Our findings provide a basic picture of the seasonality of HRSV transmission and its nonlinear association with multiple meteorological drivers in the pre-HRSV-vaccination and pre-coronavirus disease 2019 (COVID-19) era in Japan.
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Affiliation(s)
- Keita Wagatsuma
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan;
- Japan Society for the Promotion of Science, Tokyo 102-0083, Japan
| | - Iain S. Koolhof
- College of Health and Medicine, School of Medicine, University of Tasmania, Hobart 7000, Australia;
| | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan;
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10
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Regassa BT, Gebrewold LA, Mekuria WT, Kassa NA. Molecular epidemiology of respiratory syncytial virus in children with acute respiratory illnesses in Africa: A systematic review and meta-analysis. J Glob Health 2023; 13:04001. [PMID: 36637855 PMCID: PMC9840062 DOI: 10.7189/jogh.13.04001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Background Globally, the respiratory syncytial virus (RSV) is the most common etiologic agent of acute respiratory illnesses in children. However, its burden has not been well addressed in developing countries. We aimed to estimate the molecular epidemiology of RSV in children less than 18 years of age with acute respiratory infections in Africa by conducting a systematic review and meta-analysis. Methods We systematically searched PubMed, Scopus, CINAHL, and Global Index Medicus databases to identify studies published from January 1, 2002, to April 27, 2022, following the PRISMA 2020 guideline. We assessed the study quality using the Joanna Brigg's Institute (JBI) critical appraisal checklists. We conducted a qualitative synthesis by describing the characteristics of included studies and performed the quantitative synthesis with random effects model using STATA-14. We checked for heterogeneity with Q statistics, quantified by I2, and determined the prediction interval. We performed subgroup analyses to explain the sources of heterogeneity and assessed publication biases by funnel plots augmented with Egger's test. Results Eighty-eight studies with 105 139 participants were included in the review. The overall pooled prevalence of RSV in children <18 years of age was 23% (95% confidence interval (CI) = 20, 25%). Considerable heterogeneity was present across the included studies. The adjusted prediction interval was found to be 19%-27%. Heterogeneities were explained by subgroups analyses. The highest prevalence of RSV was found among inpatients, 28% (95% CI = 25, 31%) compared with inpatients/outpatients and outpatients, with statistically significant differences (P < 0.01). The RSV estimate was also highest among those with acute lower respiratory tract illnesses (ALRTIs), 28% (95% CI = 25, 31%) compared with acute upper respiratory tract illnesses (AURTIs) and both acute upper/lower respiratory manifestations, with statistically different prevalence (P < 0.01). RSV infection estimates in each sub-region of Africa were statistically different (P < 0.01). There were no statistically significant differences in RSV infections by designs, specimen types, and specimen conditions, despite them contributing to heterogeneity. Conclusions We found a high prevalence of RSV in pediatric populations with acute respiratory tract illnesses in Africa, highlighting that the prevention and control of RSV infections in children deserve more attention. Registration PROSPERO CRD42022327054.
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Affiliation(s)
- Belay Tafa Regassa
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Lami Abebe Gebrewold
- Department of Public Health, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Wagi Tosisa Mekuria
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Ambo University, Ethiopia
| | - Nega Assefa Kassa
- School of Public Health, College of Health and Medical Sciences, Haramaya University, Ethiopia
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11
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Faye MN, Barry MA, Jallow MM, Wade SF, Mendy MP, Sy S, Fall A, Kiori DE, Ndiaye NK, Goudiaby D, Diamanka A, Niang MN, Dia N. Epidemiology of Non-SARS-CoV2 Human Coronaviruses (HCoVs) in People Presenting with Influenza-like Illness (ILI) or Severe Acute Respiratory Infections (SARI) in Senegal from 2012 to 2020. Viruses 2022; 15:20. [PMID: 36680061 PMCID: PMC9864203 DOI: 10.3390/v15010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In addition to emerging coronaviruses (SARS-CoV, MERS, SARS-CoV-2), there are seasonal human coronaviruses (HCoVs): HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1. With a wide distribution around the world, HCoVs are usually associated with mild respiratory disease. In the elderly, young children and immunocompromised patients, more severe or even fatal respiratory infections may be observed. In Africa, data on seasonal HCoV are scarce. This retrospective study investigated the epidemiology and genetic diversity of seasonal HCoVs during nine consecutive years of influenza-like illness surveillance in Senegal. Nasopharyngeal swabs were collected from ILI outpatients or from SARI hospitalized patients. HCoVs were diagnosed by qRT-PCR and the positive samples were selected for molecular characterization. Among 9337 samples tested for HCoV, 406 (4.3%) were positive: 235 (57.9%) OC43, 102 (25.1%) NL63, 58 (14.3%) 229E and 17 (4.2%) HKU1. The four types circulated during the study period and a peak was noted between November and January. Children under five were the most affected. Co-infections were observed between HCoV types (1.2%) or with other viruses (76.1%). Genetically, HCoVs types showed diversity. The results highlighted that the impact of HCoVs must be taken into account in public health; monitoring them is therefore particularly necessary both in the most sensitive populations and in animals.
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Affiliation(s)
- Modeste Name Faye
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Mamadou Malado Jallow
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Serigne Fallou Wade
- Ecole Supérieure des Sciences Agricoles et de l’Alimentation (ES2A), Université Amadou Makhtar MBOW de Dakar (UAM), Dakar 12900, Senegal
| | - Marie Pedapa Mendy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Amary Fall
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Davy Evrard Kiori
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | | | - Deborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Arfang Diamanka
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | | | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
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12
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Goumballa N, Sambou M, Samba DF, Bassene H, Bedotto M, Aidara A, Dieng M, Hoang VT, Parola P, Sokhna C, Gautret P. PCR investigation of infections in patients consulting at a healthcare centre over a four-year period during the Grand Magal of Touba. Travel Med Infect Dis 2022; 52:102515. [PMID: 36470351 DOI: 10.1016/j.tmaid.2022.102515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Respiratory and gastrointestinal symptoms and febrile illness are the most common complaints among ill pilgrims attending the Grand Magal of Touba (GMT) in Senegal. METHODS Patients presenting with respiratory or gastrointestinal symptoms or febrile systemic illnesses were recruited between 2018 and 2021 at a healthcare centre close to Touba. Respiratory, gastrointestinal and blood samples were tested for potential pathogens using qPCR. RESULTS 538 patients were included. 45.5% of these were female, with a median age of 17 years. Of the 326 samples collected from patients with a cough, 62.8% tested positive for at least one virus, including influenza viruses (33.1%). A high positivity rate of bacterial carriage was observed for Haemophilus influenzae (72.7%), Streptococcus pneumoniae (51.2%) and Moraxella catarrhalis (46.0%). Of the 95 samples collected from patients with diarrhoea, 71.3% were positive, with high rates of bacterial carriage, ranging from 4.2% for Tropheryma whipplei to 45.3% for Entero-pathogenic Escherichia coli. Of the 141 blood samples collected from patients with fever, 31.9% were positive including Plasmodium falciparum (21.3%), Borrelia sp. (5.7%) and dengue virus (5.0%). CONCLUSION This study provides insight into the aetiology of most common infections at the GMT on which to base therapeutic options.
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Affiliation(s)
- Ndiaw Goumballa
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal; IHU-Méditerranée Infection, Marseille, France
| | - Masse Sambou
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal
| | - Diouf Fatou Samba
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal; IHU-Méditerranée Infection, Marseille, France
| | - Hubert Bassene
- VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal
| | | | - Adama Aidara
- Région Médicale de Diourbel, Senegal; Centre de Santé de Mbacké, Senegal
| | | | - Van Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Philippe Parola
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Cheikh Sokhna
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Gautret
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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13
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Barr IG, Williams TC, Salimi V, Buchholz UJ. Addendum to Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level. Emerg Infect Dis 2022; 28:764. [PMID: 35202531 PMCID: PMC8888225 DOI: 10.3201/eid2803.212438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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14
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Komoyo GF, Yambiyo BM, Manirakiza A, Gody JC, Muller CP, Hübschen JM, Nakoune E, Snoeck CJ. Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018. Health Sci Rep 2021; 4:e298. [PMID: 34013070 PMCID: PMC8112815 DOI: 10.1002/hsr2.298] [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] [Received: 08/20/2020] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.
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Affiliation(s)
- Giscard F. Komoyo
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
- Ecole Doctorale d'Infectiologie Tropicale de Franceville, GabonFrancevilleGabon
| | - Brice M. Yambiyo
- Service d'épidémiologieInstitut Pasteur de BanguiBanguiCentral African Republic
| | | | - Jean C. Gody
- Complexe pédiatrique de BanguiCentre National Hospitalier Universitaire de BanguiBanguiCentral African Republic
| | - Claude P. Muller
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Judith M. Hübschen
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Emmanuel Nakoune
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
| | - Chantal J. Snoeck
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
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15
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Weldetsadik AY, Riedel F. Respiratory syncytial virus in severe lower respiratory infections in previously healthy young Ethiopian infants. BMC Pediatr 2021; 21:201. [PMID: 33910510 PMCID: PMC8080344 DOI: 10.1186/s12887-021-02675-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Respiratory Syncytial Virus (RSV) is the commonest cause of acute lower respiratory infections (ALRI) in infants. However, the burden of RSV is unknown in Ethiopia. We aimed to determine the prevalence, seasonality and predictors of RSV infection in young infants with ALRI for the first time in Ethiopia. METHODS We performed RSV immuno-chromatographic assay from nasopharyngeal swabs of infants, 29 days to 6 months of age. We included the first 10 eligible infants in each month from June 2018 to May 2019 admitted in a tertiary pediatric center. Clinical, laboratory and imaging data were also collected, and chi-square test and regression were used to assess associated factors with RSV infection. RESULTS Among a total of 117 study children, 65% were male and mean age was 3 months. Bronchiolitis was the commonest diagnosis (49%). RSV was isolated from 26 subjects (22.2%) of all ALRI, 37% of bronchiolitis and 11% of pneumonia patients. Although RSV infection occurred year round, highest rate extended from June to November. No clinical or laboratory parameter predicted RSV infection and only rainy season (Adjusted Odds Ratio (AOR) 10.46 [95%. C.I. 1.95, 56.18]) was independent predictor of RSV infection. CONCLUSIONS RSV was isolated in a fifth of young infants with severe ALRI, mostly in the rainy season. Diagnosis of RSV infection in our setting require specific tests as no clinical parameter predicted RSV infection. Since RSV caused less than a quarter of ALRI in our setting, the other causes should be looked for in future studies.
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Affiliation(s)
| | - Frank Riedel
- Pediatric Pulmonology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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Fall A, Elawar F, Hodcroft EB, Jallow MM, Toure CT, Barry MA, Kiori DE, Sy S, Diaw Y, Goudiaby D, Niang MN, Dia N. Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal. INFECTION GENETICS AND EVOLUTION 2021; 91:104864. [PMID: 33866019 DOI: 10.1016/j.meegid.2021.104864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Amary Fall
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Farah Elawar
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Mamadou Malado Jallow
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Cheikh Talibouya Toure
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Mamadou A Barry
- Unit Epidemiology of Infectious Diseases, Institute Pasteur of Dakar, Senegal.
| | | | - Sara Sy
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Yague Diaw
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | | | | | - Ndongo Dia
- Virology Department, Institute Pasteur of Dakar, Senegal.
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17
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Ihling CM, Schnitzler P, Heinrich N, Mangu C, Sudi L, Souares A, Gies S, Sié A, Coulibaly B, Ouédraogo AT, Mordmüller B, Held J, Adegnika AA, Fernandes JF, Eckerle I, May J, Hogan B, Eibach D, Tabatabai J. Molecular epidemiology of respiratory syncytial virus in children in sub-Saharan Africa. Trop Med Int Health 2021; 26:810-822. [PMID: 33683751 DOI: 10.1111/tmi.13573] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES This study investigated the molecular epidemiology of respiratory syncytial virus (RSV) among febrile children with acute respiratory tract infection in Ghana, Gabon, Tanzania and Burkina Faso between 2014 and 2017 as well as the evolution and diversification of RSV strains from other sub-Saharan countries. METHODS Pharyngeal swabs were collected at four study sites (Agogo, Ghana: n = 490; Lambaréné, Gabon: n = 182; Mbeya, Tanzania: n = 293; Nouna, Burkina Faso: n = 115) and analysed for RSV and other respiratory viruses using rtPCR. For RSV-positive samples, sequence analysis of the second hypervariable region of the G gene was performed. A dataset of RSV strains from sub-Saharan Africa (2011-2017) currently available in GenBank was compiled. Phylogenetic analysis was conducted to identify the diversity of circulating RSV genotypes. RESULTS In total, 46 samples were tested RSV positive (Ghana n = 31 (6.3%), Gabon n = 4 (2.2%), Tanzania n = 9 (3.1%) and Burkina Faso n = 2 (1.7%)). The most common RSV co-infection was with rhinovirus. All RSV A strains clustered with genotype ON1 strains with a 72-nucleotide duplication and all RSV B strains belonged to genotype BAIX. Phylogenetic analysis of amino acid sequences from sub-Saharan Africa revealed the diversification into 11 different ON1 and 22 different BAIX lineages and differentiation of ON1 and BAIX strains into potential new sub-genotypes, provisionally named ON1-NGR, BAIX-KEN1, BAIX-KEN2 and BAIX-KEN3. CONCLUSION The study contributes to an improved understanding of the molecular epidemiology of RSV infection in sub-Saharan Africa. It provides the first phylogenetic data for RSV from Tanzania, Gabon and Burkina Faso and combines it with RSV strains from all other sub-Saharan countries currently available in GenBank.
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Affiliation(s)
- Clara Marlene Ihling
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg, Germany.,Dr. von Haunersches Kinderspital, University Hospital of the LMU Munich, Munich, Germany
| | - Paul Schnitzler
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Norbert Heinrich
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Division for Infectious Diseases, University Hospital of the LMU Munich, Munich, Germany
| | - Chacha Mangu
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Lwitiho Sudi
- NIMR-Mbeya Medical Research Center, Mbeya, Tanzania
| | - Aurélia Souares
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Heidelberg Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany
| | - Sabine Gies
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Heidelberg Institute of Global Health, Heidelberg University Hospital, Heidelberg, Germany
| | - Ali Sié
- Centre de Recherche en Santé de Nouna, Nouna, Burkina Faso
| | | | | | - Benjamin Mordmüller
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Jana Held
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Eberhard Karls University Tuebingen, Tübingen, Germany
| | - Ayola Akim Adegnika
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Eberhard Karls University Tuebingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - José F Fernandes
- Eberhard Karls University Tuebingen, Tübingen, Germany.,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Isabella Eckerle
- Institute of Virology, University of Bonn Medical Center, Bonn, Germany.,Faculty of Medicine, Geneva Center for Emerging Viral Diseases, University Hospitals of Geneva, University of Geneva, Geneva, Switzerland
| | - Juergen May
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Benedikt Hogan
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Daniel Eibach
- German Center for Infection Research (DZIF), Heidelberg, Germany.,Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Julia Tabatabai
- Center of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany.,German Center for Infection Research (DZIF), Heidelberg, Germany.,Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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18
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Krivitskaya V, Komissarova K, Pisareva M, Sverlova M, Fadeev A, Petrova E, Timonina V, Sominina A, Danilenko D. Respiratory Syncytial Virus G Protein Sequence Variability among Isolates from St. Petersburg, Russia, during the 2013-2014 Epidemic Season. Viruses 2021; 13:119. [PMID: 33477301 PMCID: PMC7830914 DOI: 10.3390/v13010119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
Human respiratory syncytial virus (RSV) is the most common cause of upper and lower respiratory tract infections in infants and young children. It is actively evolving under environmental and herd immunity influences. This work presents, for the first time, sequence variability analysis of RSV G gene and G protein using St. Petersburg (Russia) isolates. Viruses were isolated in a cell culture from the clinical samples of 61 children hospitalized (January-April 2014) with laboratory-confirmed RSV infection. Real-time RT-PCR data showed that 56 isolates (91.8%) belonged to RSV-A and 5 isolates (8.2%) belonged to RSV-B. The G genes were sequenced for 27 RSV-A isolates and all of them belonged to genotype ON1/GA2. Of these RSV-A, 77.8% belonged to the ON1(1.1) genetic sub-cluster, and 14.8% belonged to the ON1(1.2) sub-cluster. The ON1(1.3) sub-cluster constituted a minor group (3.7%). Many single-amino acid substitutions were identified in the G proteins of St. Petersburg isolates, compared with the Canadian ON1/GA2 reference virus (ON67-1210A). Most of the amino acid replacements were found in immunodominant B- and T-cell antigenic determinants of G protein. These may affect the antigenic characteristics of RSV and influence the host antiviral immune response to currently circulating viruses.
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Affiliation(s)
- Vera Krivitskaya
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Kseniya Komissarova
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Maria Pisareva
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Maria Sverlova
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Artem Fadeev
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Ekaterina Petrova
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Veronika Timonina
- Children’s City Hospital of St. Olga, 194017 Saint-Petersburg, Russia;
| | - Anna Sominina
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
| | - Daria Danilenko
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint-Petersburg, Russia; (V.K.); (M.P.); (M.S.); (A.F.); (E.P.); (A.S.); (D.D.)
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Global Molecular Epidemiology of Respiratory Syncytial Virus from the 2017-2018 INFORM-RSV Study. J Clin Microbiol 2020; 59:JCM.01828-20. [PMID: 33087438 PMCID: PMC7771447 DOI: 10.1128/jcm.01828-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 02/07/2023] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships with clinical features of RSV disease. During the pilot season (2017–2018), 410 RSV G-F gene sequences were obtained from 476 RSV-positive nasal samples collected from 8 countries (United Kingdom, Spain, The Netherlands, Finland, Japan, Brazil, South Africa, and Australia). Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection among infants and young children, resulting in annual epidemics worldwide. INFORM-RSV is a multiyear clinical study designed to describe the global molecular epidemiology of RSV in children under 5 years of age by monitoring temporal and geographical evolution of current circulating RSV strains, F protein antigenic sites, and their relationships with clinical features of RSV disease. During the pilot season (2017–2018), 410 RSV G-F gene sequences were obtained from 476 RSV-positive nasal samples collected from 8 countries (United Kingdom, Spain, The Netherlands, Finland, Japan, Brazil, South Africa, and Australia). RSV B (all BA9 genotype) predominated over RSV A (all ON1 genotype) globally (69.0% versus 31.0%) and in all countries except South Africa. Geographic clustering patterns highlighted wide transmission and continued evolution with viral spread. Most RSV strains were from infants of <1 year of age (81.2%), males (56.3%), and patients hospitalized for >24 h (70.5%), with no differences in subtype distribution. Compared to 2013 reference sequences, variations at F protein antigenic sites were observed for both RSV A and B strains, with high-frequency polymorphisms at antigenic site Ø (I206M/Q209R) and site V (L172Q/S173L/K191R) in RSV B strains. The INFORM-RSV 2017–2018 pilot season establishes an important molecular baseline of RSV strain distribution and sequence variability with which to track the emergence of new strains and provide an early warning system of neutralization escape variants that may impact transmission or the effectiveness of vaccines and MAbs under development.
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Carbonell-Estrany X, Rodgers-Gray BS, Paes B. Challenges in the prevention or treatment of RSV with emerging new agents in children from low- and middle-income countries. Expert Rev Anti Infect Ther 2020; 19:419-441. [PMID: 32972198 DOI: 10.1080/14787210.2021.1828866] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) causes approximately 120,000 deaths annually in children <5 years, with 99% of fatalities occurring in low- and middle-income countries (LMICs). AREAS COVERED There are numerous RSV interventions in development, including long-acting monoclonal antibodies, vaccines (maternal and child) and treatments which are expected to become available soon. We reviewed the key challenges and issues that need to be addressed to maximize the impact of these interventions in LMICs. The epidemiology of RSV in LMICs was reviewed (PubMed search to 30 June 2020 inclusive) and the need for more and better-quality data, encompassing hospital admissions, community contacts, and longer-term respiratory morbidity, emphasized. The requirement for an agreed clinical definition of RSV lower respiratory tract infection was proposed. The pros and cons of the new RSV interventions are reviewed from the perspective of LMICs. EXPERT OPINION We believe that a vaccine (or combination of vaccines, if practicable) is the only viable solution to the burden of RSV in LMICs. A coordinated program, analogous to that with polio, involving governments, non-governmental organizations, the World Health Organization, the manufacturers and the healthcare community is required to realize the full potential of vaccine(s) and end the devastation of RSV in LMICs.
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Affiliation(s)
- Xavier Carbonell-Estrany
- Neonatology Service, Hospital Clinic, Institut d'Investigacions Biomediques August Pi Suñer (IDIBAPS), Barcelona, Spain
| | | | - Bosco Paes
- Department of Pediatrics (Neonatal Division), McMaster University, Hamilton, Ontario, Canada
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21
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Respiratory syncytial virus infection trend is associated with meteorological factors. Sci Rep 2020; 10:10931. [PMID: 32616819 PMCID: PMC7331681 DOI: 10.1038/s41598-020-67969-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 06/16/2020] [Indexed: 11/10/2022] Open
Abstract
Respiratory syncytial virus (RSV) infects young children and causes influenza-like illness. RSV circulation and prevalence differ among countries and climates. To better understand whether climate factors influence the seasonality of RSV in Thailand, we examined RSV data from children ≤ 5 years-old who presented with respiratory symptoms from January 2012–December 2018. From a total of 8,209 nasopharyngeal samples, 13.2% (1,082/8,209) was RSV-positive, of which 37.5% (406/1,082) were RSV-A and 36.4% (394/1,082) were RSV-B. The annual unimodal RSV activity from July–November overlaps with the rainy season. Association between meteorological data including monthly average temperature, relative humidity, rainfall, and wind speed for central Thailand and the incidence of RSV over 7-years was analyzed using Spearman’s rank and partial correlation. Multivariate time-series analysis with an autoregressive integrated moving average (ARIMA) model showed that RSV activity correlated positively with rainfall (r = 0.41) and relative humidity (r = 0.25), but negatively with mean temperature (r = − 0.27). The best-fitting ARIMA (1,0,0)(2,1,0)12 model suggests that peak RSV activity lags the hottest month of the year by 4 months. Our results enable possible prediction of RSV activity based on the climate and could help to anticipate the yearly upsurge of RSV in this region.
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Razanajatovo Rahombanjanahary NH, Rybkina K, Randriambolamanantsoa TH, Razafimanjato H, Heraud JM. Genetic diversity and molecular epidemiology of respiratory syncytial virus circulated in Antananarivo, Madagascar, from 2011 to 2017: Predominance of ON1 and BA9 genotypes. J Clin Virol 2020; 129:104506. [PMID: 32585620 DOI: 10.1016/j.jcv.2020.104506] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Respiratory syncytial virus is the main cause of acute respiratory infections leading to a considerable morbidity and mortality among under-5 years children. A comprehensive scheme of RSV virus evolution is of great value in implementing effective universal RSV vaccine. OBJECTIVE We investigated the clinical spectrum and molecular characteristics of detected RSV over a period of seven years (January 2011 to June 2017) in Antananarivo, the capital city of Madagascar. STUDY DESIGN 671 nasopharyngeal samples taken from children aged less than 5 years suffered from ARI were screened for RSV by real-time PCR. Clinical data were retrieved from case report forms. Genotype identification was performed by reverse-transcription PCR and sequencing of the second hyper variable region (HVR2) of the G glycoprotein. RESULTS Amongst samples tested, 292 (43.5 %) were found positive for RSV. RSV A predominated during the study period which accounted for 62.3 % (182/292) of positive samples while RSV B represented 37.0 % (108/292). Phylogenetic analyses identified NA1 and ON1 genotypes among RSV A. Though NA1 widespread from 2011 to 2013, ON1 became prevalent during the following years. Among RSV B, THB, CB1 and BA9 genotypes were detected. A co-circulation of THB and CB1 strains occurred during the 2011 season that was substituted by the BA9 from 2012. Malagasy ON1 strains carried some characteristic amino acid substitutions that distinguish them from the worldwide ON1 strains. By analyzing clinical spectrum, ON1 and BA genotypes seemed to prevail in mild infections compared to NA1. CONCLUSION Results obtained here will have its implication in predicting temporal evolution of RSV at the local level. Considering the insularity of the country, information obtained should help in comparative analysis with global RSV strains to optimize vaccine efficacy.
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Affiliation(s)
| | - Ksenia Rybkina
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Helisoa Razafimanjato
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- National Influenza Center, Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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Jensen KJ, Biering-Sørensen S, Ursing J, Kofoed PEL, Aaby P, Benn CS. Seasonal variation in the non-specific effects of BCG vaccination on neonatal mortality: three randomised controlled trials in Guinea-Bissau. BMJ Glob Health 2020; 5:e001873. [PMID: 32201619 PMCID: PMC7059430 DOI: 10.1136/bmjgh-2019-001873] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/11/2019] [Accepted: 09/15/2019] [Indexed: 11/23/2022] Open
Abstract
The BCG vaccine protects non-specifically against other diseases than tuberculosis. Three randomised controlled trials of early BCG in Guinea-Bissau found a 38% reduction in all-cause neonatal mortality. Little is known about the underlying mechanisms. In Guinea-Bissau, prevalent infectious diseases display distinct seasonality. Revisiting the three trials (>6500 infants) comparing early BCG versus no early BCG in low weight infants on all-cause neonatal mortality over 12 consecutive years, we explored the seasonal variation in BCG’s effect on mortality. In a subgroup of participants, adaptive and innate cytokine responses were measured 4 weeks after randomisation. Consistently over the course of the three trials and 12 years, the effect of BCG on all-cause neonatal mortality was particularly beneficial when administered in November to January, coincident with peaking malaria infections. During these months, BCG was also associated with stronger proinflammatory responses to heterologous challenge. Recent studies have suggested a protective effect of BCG against malaria. BCG may also ameliorate immune-compromising fatal effects of placental malaria in the newborn.
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Affiliation(s)
- Kristoffer Jarlov Jensen
- Bandim Health Project, University of Southern Denmark, Copenhagen, Denmark.,Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | - Johan Ursing
- Department of Infectious Diseases, Danderyd University Hospital, Stockholm, Sweden.,Department of Clinical Sciences, Karolinska Institute, Stockholm, Sweden
| | - Poul-Erik Lund Kofoed
- Department of Pediatrics, Kolding Hospital, Kolding, Denmark.,Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Peter Aaby
- Bandim Health Project, University of Southern Denmark, Copenhagen, Denmark.,Bandim Health Project, INDEPTH Network, Bissau, Guinea-Bissau
| | - Christine Stabell Benn
- Bandim Health Project, University of Southern Denmark, Copenhagen, Denmark.,OPEN, Institute of Clinical Research, University of Southern Denmark, Odense, Syddanmark, Denmark
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Respiratory syncytial, parainfluenza and influenza virus infection in young children with acute lower respiratory infection in rural Gambia. Sci Rep 2019; 9:17965. [PMID: 31784567 PMCID: PMC6884537 DOI: 10.1038/s41598-019-54059-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/23/2019] [Indexed: 01/06/2023] Open
Abstract
Respiratory viral infections contribute significantly to morbidity and mortality worldwide, but representative data from sub-Saharan Africa are needed to inform vaccination strategies. We conducted population-based surveillance in rural Gambia using standardized criteria to identify and investigate children with acute lower respiratory infection (ALRI). Naso- and oropharyngeal swabs were collected. Each month from February through December 2015, specimens from 50 children aged 2–23 months were randomly selected to test for respiratory syncytial (RSV), parainfluenza (PIV) and influenza viruses. The expected number of viral-associated ALRI cases in the population was estimated using statistical simulation that accounted for the sampling design. RSV G and F proteins and influenza hemagglutinin genes were sequenced. 2385 children with ALRI were enrolled, 519 were randomly selected for viral testing. One or more viruses were detected in 303/519 children (58.4%). RSV-A was detected in 237 and RSV-B in seven. The expected incidence of ALRI associated with RSV, PIV or influenza was 140 cases (95% CI, 131–149) per 1000 person-years; RSV incidence was 112 cases (95% CI, 102–122) per 1000 person-years. Multiple strains of RSV and influenza circulated during the year. RSV circulated throughout most of the year and was associated with eight times the number of ALRI cases compared to PIV or IV. Gambian RSV viruses were closely related to viruses detected in other continents. An effective RSV vaccination strategy could have a major impact on the burden of ALRI in this setting.
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Sáez-López E, Cristóvão P, Costa I, Pechirra P, Conde P, Guiomar R, Peres MJ, Viseu R, Lopes P, Soares V, Vale F, Fonseca P, Freitas L, Alves J, Pessanha MA, Toscano C, Mota-Vieira L, Veloso RC, Côrte-Real R, Branquinho P, Pereira-Vaz J, Rodrigues F, Cunha M, Martins L, Mota P, Couto AR, Bruges-Armas J, Almeida S, Rodrigues D. Epidemiology and genetic variability of respiratory syncytial virus in Portugal, 2014-2018. J Clin Virol 2019; 121:104200. [PMID: 31707201 PMCID: PMC7106440 DOI: 10.1016/j.jcv.2019.104200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Respiratory syncytial virus (RSV) is associated with substantial morbidity and mortality since it is a predominant viral agent causing respiratory tract infections in infants, young children and the elderly. Considering the availability of the RSV vaccines in the coming years, molecular understanding in RSV is necessary. OBJECTIVE The objective of the present study was to describe RSV epidemiology and genotype variability in Portugal during the 2014/15-2017/18 period. MATERIAL AND METHODS Epidemiological data and RSV-positive samples from patients with a respiratory infection were collected through the non-sentinel and sentinel influenza surveillance system (ISS). RSV detection, subtyping in A and B, and sequencing of the second hypervariable region (HVR2) of G gene were performed by molecular methods. Phylogenetic trees were generated using the Neighbor-Joining method and p-distance model on MEGA 7.0. RESULTS RSV prevalence varied between the sentinel (2.5%, 97/3891) and the non-sentinel ISS (20.7%, 3138/16779), being higher (P < 0.0001) among children aged <5 years. Bronchiolitis (62.9%, 183/291) and influenza-like illness (24.6%, 14/57) were associated (P < 0.0001) with RSV laboratory confirmation among children aged <6 months and adults ≥65 years, respectively. The HVR2 was sequenced for 562 samples. RSV-A (46.4%, 261/562) and RSV-B (53.6%, 301/562) strains clustered mainly to ON1 (89.2%, 233/261) and BA9 (92%, 277/301) genotypes, respectively, although NA1 and BA10 were also present until 2015/2016. CONCLUSION The sequence and phylogenetic analysis reflected the relatively high diversity of Portuguese RSV strains. BA9 and ON1 genotypes, which have been circulating in Portugal since 2010/2011 and 2011/2012 respectively, predominated during the whole study period.
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Affiliation(s)
- Emma Sáez-López
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal; European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 16973, Solna, Sweden.
| | - Paula Cristóvão
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Inês Costa
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Pedro Pechirra
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Patrícia Conde
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
| | - Raquel Guiomar
- Department of Infectious Diseases, National Health Institute Doutor Ricardo Jorge (INSA), Avenida Padre Cruz, 1649-016, Lisbon, Portugal.
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Epidemiology of respiratory syncytial virus infections in Chennai, south India. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2019. [DOI: 10.1016/j.cegh.2018.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Streng A, Goettler D, Haerlein M, Lehmann L, Ulrich K, Prifert C, Krempl C, Weißbrich B, Liese JG. Spread and clinical severity of respiratory syncytial virus A genotype ON1 in Germany, 2011-2017. BMC Infect Dis 2019; 19:613. [PMID: 31299924 PMCID: PMC6624929 DOI: 10.1186/s12879-019-4266-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/05/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Respiratory Syncytial Virus (RSV) A genotype ON1, which was first detected in Ontario (Canada) in 2010/11, appeared in Germany in 2011/12. Preliminary observations suggested a higher clinical severity in children infected with this new genotype. We investigated spread and disease severity of RSV-A ON1 in pediatric in- and outpatient settings. Methods During 2010/11 to 2016/17, clinical characteristics and respiratory samples from children with acute respiratory tract infections (RTI) were obtained from ongoing surveillance studies in 33 pediatric practices (PP), one pediatric hospital ward (PW) and 23 pediatric intensive care units (PICU) in Germany. RSV was detected in the respiratory samples by PCR; genotypes were identified by sequencing. Within each setting, clinical severity markers were compared between RSV-A ON1 and RSV-A non-ON1 genotypes. Results A total of 603 children with RSV-RTI were included (132 children in PP, 288 in PW, and 183 in PICU). Of these children, 341 (56.6%) were infected with RSV-A, 235 (39.0%) with RSV-B, and one child (0.2%) with both RSV-A and RSV-B; in 26 (4.3%) children, the subtype could not be identified. In the 341 RSV-A positive samples, genotype ON1 was detected in 247 (72.4%), NA1 in 92 (26.9%), and GA5 in 2 children (0.6%). RSV-A ON1, rarely observed in 2011/12, was the predominant RSV-A genotype in all settings by 2012/13 and remained predominant until 2016/17. Children in PP or PW infected with RSV-A ON1 did not show a more severe clinical course of disease compared with RSV-A non-ON1 infections. In the PICU group, hospital stay was one day longer (median 8 days, inter-quartile range (IQR) 7–12 vs. 7 days, IQR 5–9; p = 0.02) and duration of oxygen treatment two days longer (median 6 days, IQR 4–9 vs. 4 days, IQR 2–6; p = 0.03) for children infected with RSV-A ON1. Conclusions In children, RSV-A ON1 largely replaced RSV-A non-ON1 genotypes within two seasons and remained the predominant RSV-A genotype in Germany during subsequent seasons. A higher clinical severity of RSV-A ON1 was observed within the group of children receiving PICU treatment, whereas in other settings clinical severity of RSV-A ON1 and non-ON1 genotypes was largely similar. Electronic supplementary material The online version of this article (10.1186/s12879-019-4266-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrea Streng
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - David Goettler
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Miriam Haerlein
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Lisa Lehmann
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Kristina Ulrich
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Christiane Prifert
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Christine Krempl
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Benedikt Weißbrich
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Johannes G Liese
- Department of Pediatrics, University Hospital of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
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Jallow MM, Fall A, Kiori D, Sy S, Goudiaby D, Barry MA, Fall M, Niang MN, Dia N. Epidemiological, clinical and genotypic features of human Metapneumovirus in patients with influenza-like illness in Senegal, 2012 to 2016. BMC Infect Dis 2019; 19:457. [PMID: 31117983 PMCID: PMC6532257 DOI: 10.1186/s12879-019-4096-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is a causal agent of acute respiratory infection, especially in primarily children. At the clinical level, HMPV is associated to several diseases including bronchitis, croup, pneumonia, bronchiolitis, reactive airway disease, chronic obstructive pulmonary disease and asthma exacerbations, specifically in children less than 5 years. Here, we carried out a retrospective pilot study, based on the processing of nasopharyngeal swabs, with a focus on the epidemiology and molecular characteristics of HMPV in Senegal. METHODS This retrospective study was conducted from January 2012 to December 2016. Briefly, all outpatients presenting to healthcare sentinel sites were screened for surveillance enrollment and included if they met criteria for ILI. Naso-oropharyngeal swabs were collected from eligible participants. For viral respiratory pathogens detection, including HMPV, the Anyplex™ II RV16 Detection kit was used. A fragment of the hMPV F gene was targeted for sequencing. RESULTS In total, 8209 patients with ILI were enrolled. Half of them (49.7%) were children under 5 years. Fever was the most common symptom followed by cough, and rhinitis. Three hundred eight patients were positive for HMPV (3.75%). 89 (28.9%) were detected as single infection. In co-infection cases, the most common co-infecting viruses were influenza, adenovirus and rhinovirus. HMPV detection rates in the different age groups varied significantly with the children under 5 years group accounting for 71.7% of positive patients. The temporal distribution pattern for HMPV infection showed a clear seasonal pattern with a higher activity during the rainy period (July-September). Phylogenetic analyses revealed that HMPV specimens circulating in Senegal were distributed into the two main genetic lineages, A and B. We also noted a co-circulation of both genetic lineages during the whole study period except in 2014. CONCLUSION In summary, the present study characterized the recent prevalence, seasonality and genetic diversity of HMPV in a large outpatient population presented with ILI in Senegal between 2012 and 2016. Globally our results show a clear seasonal circulation pattern of HMPV in Senegal. Our findings identified children less than 5 years as more susceptible group to HMPV infection. Molecular studies identified A2, B1 and B2 as the major genotypes circulating.
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Affiliation(s)
- Mamadou Malado Jallow
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Amary Fall
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Davy Kiori
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Déborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d’Epidémiologie des maladies infectieuses, Dakar, Sénégal
| | - Malick Fall
- Département de Biologie, Animale Faculté des Sciences et Techniques Université Cheikh Anta DIOP de Dakar, Dakar, Sénégal
| | - Mbayame Ndiaye Niang
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
| | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, 36, Avenue Pasteur, B.P. 220, Dakar, Sénégal
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Thongpan I, Suntronwong N, Vichaiwattana P, Wanlapakorn N, Vongpunsawad S, Poovorawan Y. Respiratory syncytial virus, human metapneumovirus, and influenza virus infection in Bangkok, 2016-2017. PeerJ 2019; 7:e6748. [PMID: 30997293 PMCID: PMC6462397 DOI: 10.7717/peerj.6748] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
Children and adults residing in densely populated urban centers around the world are at risk of seasonal influenza-like illness caused by respiratory viruses such as influenza virus, human metapneumovirus (hMPV), and respiratory syncytial virus (RSV). In a large metropolitan of Thailand’s capital city Bangkok, most respiratory infections are rarely confirmed by molecular diagnostics. We therefore examined the frequency of RSV, hMPV, and influenza virus in 8,842 patients who presented influenza-like illness and sought medical care at a large hospital in Bangkok between 2016 and 2017. Using a multiplex real-time reverse-transcription polymerase chain reaction (RT-PCR), 30.5% (2,699/8,842) of nasopharyngeal (NP) swab samples tested positive for one or more of these viruses. Influenza virus comprised 17.3% (1,528/8,842), of which the majority were influenza A/H3N2. Such infection was most prevalent among adults and the elderly. RSV was identified in 11.4% (1,011/8,842) and were mostly ON1 and BA9 genotypes. Of the hMPV-positive samples (3.6%, 318/8,842), genotypes A2, B1, and B2 were detected. A small number of individuals experienced co-infections (1.8%, 155/8,842), most commonly between RSV and influenza A/H3N2. RSV and hMPV co-infections were also found, but mainly in young children. Viral respiratory tract infection peaked locally in the rainy season (June to September). These findings support the utility of rapid nucleic acid testing of RSV, hMPV, and influenza virus in patients with ILI.
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Affiliation(s)
- Ilada Thongpan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nungruthai Suntronwong
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Preeyaporn Vichaiwattana
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nasamon Wanlapakorn
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Kini S, Kalal BS, Chandy S, Shamsundar R, Shet A. Prevalence of respiratory syncytial virus infection among children hospitalized with acute lower respiratory tract infections in Southern India. World J Clin Pediatr 2019; 8:33-42. [PMID: 31065544 PMCID: PMC6477150 DOI: 10.5409/wjcp.v8.i2.33] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a leading cause of lower respiratory infections among children.
AIM To investigate the proportion of RSV and non-RSV respiratory viral infections among hospitalized children ≤ 5 years.
METHODS Hospitalized children aged < 5 years, with a diagnosis of acute lower respiratory infections (ALRI), admitted between August 2011-August 2013, were included. Cases were defined as laboratory-confirmed RSV and non-RSV respiratory viruses by direct fluorescence assay from the nasopharyngeal wash.
RESULTS Of 383 1-59 mo old children hospitalized with an acute lower respiratory infection, 33.9% (130/383) had evidence of viral infection, and RSV was detected in 24.5% (94/383). Co-infections with RSV and other respiratory viruses (influenza A or B, adenovirus, para influenza 1, 2 or 3) were seen in children 5.5% (21/383). Over 90% of the RSV-positive children were under 2 years of age. RSV was detected throughout the year with peaks seen after the monsoon season. Children hospitalized with RSV infection were more likely to have been exposed to a shorter duration of breastfeeding of less than 3 mo. RSV positive children had a shorter hospital stay, although there were significant complications requiring intensive care. Use of antibiotics was high among those with RSV and non-RSV viral infections.
CONCLUSION Our study provides evidence of a high proportion of RSV and other virus-associated ALRI among hospitalized children in India. RSV infection was associated with fewer days of hospital stay compared to other causes of lower respiratory infections. A high level of antibiotic use was seen among all respiratory virus-associated hospitalizations. These results suggest the need for implementing routine diagnostics for respiratory pathogens in order to minimize the use of unnecessary antibiotics and plan prevention strategies among pediatric populations.
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Affiliation(s)
- Sandesh Kini
- Department of Paediatrics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Bhuvanesh Sukhlal Kalal
- Department of Biochemistry, Yenepoya Medical College, Yenepoya (Deemed to be University), Mangaluru 575018, Karnataka, India
| | - Sara Chandy
- Pushpagiri Research Centre, Pushpagiri Institute of Medical Science and Research Centre, Thiruvalla 689101, Kerala, India
| | - Ranjani Shamsundar
- Department of Microbiology, St. John’s Medical College, Bengaluru 560034, Karnataka, India
| | - Anita Shet
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States
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Kenmoe S, Bigna JJ, Well EA, Simo FBN, Penlap VB, Vabret A, Njouom R. Prevalence of human respiratory syncytial virus infection in people with acute respiratory tract infections in Africa: A systematic review and meta-analysis. Influenza Other Respir Viruses 2018; 12:793-803. [PMID: 29908103 PMCID: PMC6185896 DOI: 10.1111/irv.12584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2018] [Indexed: 12/31/2022] Open
Abstract
AIM The epidemiology of human respiratory syncytial virus (HRSV) infection has not yet been systematically investigated in Africa. This systematic review and meta-analysis are to estimate the prevalence of HRSV infections in people with acute respiratory tract infections (ARTI) in Africa. METHOD We searched PubMed, EMBASE, Africa Journal Online, and Global Index Medicus to identify observational studies published from January 1, 2000, to August 1, 2017. We used a random-effects model to estimate the prevalence across studies. Heterogeneity (I2 ) was assessed via the chi-square test on Cochran's Q statistic. Review registration: PROSPERO CRD42017076352. RESULTS A total of 67 studies (154 000 participants) were included. Sixty (90%), seven (10%), and no studies had low, moderate, and high risk of bias, respectively. The prevalence of HRSV infection varied widely (range 0.4%-60.4%). The pooled prevalence was 14.6% (95% CI 13.0-16.4, I2 = 98.8%). The prevalence was higher in children (18.5%; 95% CI 15.8-21.5) compared to adults (4.0%; 95% CI 2.2-6.1) and in people with severe respiratory tract infections (17.9%; 95% CI 15.8-20.1) compared to those with benign forms (9.4%; 95% CI 7.4-11.5); P-values <0.0001. The HRSV prevalence was not associated with sex, subregion in Africa, setting, altitude, latitude, longitude, and seasonality. CONCLUSION This study suggests a high prevalence of HRSV in people with ARTI in Africa, particularly among children and people with severe clinical form. All innovative strategies to curb the burden should first focus on children which present the highest HRSV-related burden.
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Affiliation(s)
- Sebastien Kenmoe
- Department of VirologyNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
| | - Jean Joel Bigna
- Department of Epidemiology and Public HealthNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
- School of Public HealthFaculty of MedicineUniversity of Paris SudLe Kremlin‐BicêtreFrance
| | | | - Fredy Brice N. Simo
- Department of BiochemistryFaculty of SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Véronique B. Penlap
- Department of BiochemistryFaculty of SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Astrid Vabret
- Normandie UniversitéCaenFrance
- Groupe de Recherche sur l'Adaptation Microbienne (GRAM)Université de CaenCaenFrance
- Laboratoire de VirologieCentre Hospitalo‐Universitaire de CaenCaenFrance
| | - Richard Njouom
- Department of VirologyNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
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Tracing the emerging genotypes of human respiratory syncytial virus in Beijing by evolution analysis of the attachment glycoprotein (G) gene. INFECTION GENETICS AND EVOLUTION 2018; 65:18-27. [DOI: 10.1016/j.meegid.2018.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 02/08/2023]
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Bigna JJ, Kenmoe S, Well EA, Simo FBN, Penlap VB, Vabret A, Njouom R. Contemporaneous data on the prevalence of Human Respiratory Syncytial Virus infection in people with acute respiratory tract infections in Africa (2000-2017). Data Brief 2018; 20:940-947. [PMID: 30225305 PMCID: PMC6138983 DOI: 10.1016/j.dib.2018.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/24/2018] [Accepted: 08/15/2018] [Indexed: 11/28/2022] Open
Abstract
Availability of accurate data on the burden of the Human Respiratory Syncytial Virus (HRSV) can help to implement better strategies to curb this burden in Africa continent among people with acute respiratory tract infections (ARTI). We summarize here available contemporaneous data published from January 1, 2000 to August 31, 2017 on the prevalence of HSRV infection among people with ARTI in the continent.
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Affiliation(s)
- Jean Joel Bigna
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Sebastien Kenmoe
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Estelle Amandine Well
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, P.O. Box 1364, Yaoundé, Cameroon
| | - Fredy Brice N. Simo
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Véronique B. Penlap
- Department of Biochemistry, Faculty of Sciences, University of Yaoundé 1, P.O. Box 337, Yaoundé, Cameroon
| | - Astrid Vabret
- Normandie Université, 14032 Caen, France
- Université de Caen, Groupe de Recherche sur l’Adaptation Microbienne (GRAM), F-14000 Caen, France
- Laboratoire de Virologie, Centre Hospitalo-Universitaire de Caen, F-14033 Caen, France
| | - Richard Njouom
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
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Obodai E, Odoom JK, Adiku T, Goka B, Wolff T, Biere B, Schweiger B, Reiche J. The significance of human respiratory syncytial virus (HRSV) in children from Ghana with acute lower respiratory tract infection: A molecular epidemiological analysis, 2006 and 2013-2014. PLoS One 2018; 13:e0203788. [PMID: 30199549 PMCID: PMC6130863 DOI: 10.1371/journal.pone.0203788] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Background Acute lower respiratory tract infection (ALRI) is a leading cause of childhood morbidity and mortality in developing countries. Globally, human respiratory syncytial virus (HRSV) is the most common pathogen of ALRI in infants and children. However, age-stratified HRSV disease burden data are largely absent from Africa, which is a key gap in informing an evidence-based recommendation for the introduction of an HRSV vaccine by the WHO. Methods This study investigated the presence of HRSV in respiratory specimens from 552 children <5 years old with ALRI from Accra, Ghana in 2006 and 2013–2014 by real-time PCR. Of HRSV-positive samples the second hypervariable region of the viral G protein gene was sequenced and analyzed for phylogeny, characteristic amino acid substitutions, and potential glycosylation patterns. Further, HRSV infections have been characterized by age, symptoms and timely occurrence. Results HRSV was observed in 23% (127/552) of the children with ALRI, with the highest incidence in infants younger than one year (33%, 97/295, p = 0.013). Within the observed seasonal circulation time of HRSV from June (mid-wet season) to December (beginning of the dry season) the incidence of ALRI due to HRSV was as high as 46% (125/273). HRSV disease was significantly associated with (broncho-) pneumonia, bronchiolitis, LRTI, and difficulty in breathing. Phylogenetic characterization of HRSV strains from Ghana identified the circulation of the currently worldwide prevailing genotypes ON1 and BA9, and shows evidence of an independent molecular evolution of ON1 and BA9 strains in Ghana resulting in potentially new subgenotypes within ON1 and BA9, provisionally named ON1.5, ON1.6, and BA9-IV. Conclusion This study addresses important knowledge gaps in the forefront of introducing the HRSV vaccine by providing information on the molecular evolution and incidence of HRSV in Accra (Ghana, Africa).
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Affiliation(s)
- Evangeline Obodai
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
| | - John Kofi Odoom
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Theophilus Adiku
- Department of Biomedical Sciences, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Volta Region, Ghana
| | - Bamenla Goka
- Department of Child Health, School of Medicine and Dentistry, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Thorsten Wolff
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Barbara Biere
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Brunhilde Schweiger
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
| | - Janine Reiche
- Department of Infectious Diseases, Unit 17, Influenza and Other Respiratory Viruses, Robert Koch Institute, Berlin, Germany
- * E-mail: (EO); (JR)
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Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia. Viruses 2018; 10:v10090476. [PMID: 30200580 PMCID: PMC6164696 DOI: 10.3390/v10090476] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/01/2018] [Accepted: 09/05/2018] [Indexed: 01/06/2023] Open
Abstract
There is an ongoing global pandemic of human respiratory syncytial virus (RSV) infection that results in substantial annual morbidity and mortality. In Australia, RSV is a major cause of acute lower respiratory tract infections (ALRI). Nevertheless, little is known about the extent and origins of the genetic diversity of RSV in Australia, nor the factors that shape this diversity. We have conducted a genome-scale analysis of RSV infections in New South Wales (NSW). RSV genomes were successfully sequenced for 144 specimens collected between 2010⁻2016. Of these, 64 belonged to the RSVA and 80 to the RSVB subtype. Phylogenetic analysis revealed a wide diversity of RSV lineages within NSW and that both subtypes evolved rapidly in a strongly clock-like manner, with mean rates of approximately 6⁻8 × 10-4 nucleotide substitutions per site per year. There was only weak evidence for geographic clustering of sequences, indicative of fluid patterns of transmission within the infected population and no evidence of any clustering by patient age such that viruses in the same lineages circulate through the entire host population. Importantly, we show that both subtypes circulated concurrently in NSW with multiple introductions into the Australian population in each year and only limited evidence for multi-year persistence.
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Kenmoe S, Vernet MA, Miszczak F, Dina J, Schoenhals M, Beng VP, Vabret A, Njouom R. Genetic diversity of human respiratory syncytial virus isolated among children with acute respiratory infections in Southern Cameroon during three consecutive epidemic seasons, 2011-2013. Trop Med Health 2018; 46:7. [PMID: 29618942 PMCID: PMC5881174 DOI: 10.1186/s41182-018-0088-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/20/2018] [Indexed: 02/07/2023] Open
Abstract
Background Human respiratory syncytial virus (HRSV) is the main viral cause of severe lower respiratory tract disease in infants and young children. The aim of this study was to describe for the first time the genetic variability of HRSV in Cameroonian patients living in Yaounde for three consecutive epidemic seasons. Methods HRSV-positive nasopharyngeal samples detected in children less than 15 years in Yaounde were collected from September 2011 to December 2013. Semi-nested RT-PCR, sequencing, and phylogenetic analyses of the second hypervariable region of the G gene were performed. Results A total of 57 HRSV-positive samples were collected during the study period. Among these, 46 (80.7%) could be amplified in the G gene. HRSV group A (HRSV-A) and group B (HRSV-B) co-circulated in this population at 17.4 and 82.6%, respectively. HRSV-A strains clustered in the NA-1 genotype while HRSV-B strains clustered in the BA-9 genotype. HRSV-A strains accounted for 33.3% (2/6), 4.3% (1/23), and 29.4% (5/17) of the viruses isolated in 2011, 2012, and 2013, respectively. Conclusions This study reports molecular epidemiology data of HRSV in Cameroon for the first time. Additional studies are required to clarify evolutionary patterns of HRSV throughout sub-Saharan Africa to support antiviral and vaccine development.
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Affiliation(s)
- Sebastien Kenmoe
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon.,2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France.,5Département de Biochimie, Université de Yaoundé I, BP 812 Yaoundé, Cameroon
| | - Marie-Astrid Vernet
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon
| | - Fabien Miszczak
- 2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France
| | - Julia Dina
- 2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France
| | - Matthieu Schoenhals
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon
| | | | - Astrid Vabret
- 2Normandie Université, 14032 Caen, France.,3UNICAEN, UNIROUEN, GRAM, 14000 Caen, France.,4Department of Virology, University Hospital of Caen, 14000 Caen, France
| | - Richard Njouom
- Virology Department, Centre Pasteur of Cameroon, P.O.Box 1274, Yaounde, Cameroon
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Haider MSH, Deeba F, Khan WH, Naqvi IH, Ali S, Ahmed A, Broor S, Alsenaidy HA, Alsenaidy AM, Dohare R, Parveen S. Global distribution of NA1 genotype of respiratory syncytial virus and its evolutionary dynamics assessed from the past 11 years. INFECTION GENETICS AND EVOLUTION 2018; 60:140-150. [PMID: 29427763 DOI: 10.1016/j.meegid.2018.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 01/29/2023]
Abstract
Respiratory syncytial virus (RSV) is a potent pathogen having global distribution. The main purpose of this study was to gain an insight into distribution pattern of the NA1 genotype of group A RSV across the globe together with its evolutionary dynamics. We focused on the second hypervariable region of the G protein gene and used the same for Phylogenetic, Bayesian and Network analyses. Eighteen percent of the samples collected from 500 symptomatic pediatric patients with acute respiratory tract infection (ARI) were found to be positive for RSV during 2011-15 from New Delhi, India. Of these, group B RSV was predominant and clustered into two different genotypes (BA and SAB4). Similarly, group A viruses clustered into two genotypes (NA1 and ON1). The data set from the group A viruses included 543 sequences from 23 different countries including 67 strains from India. The local evolutionary dynamics suggested consistent virus population of NA1 genotype in India during 2009 to 2014. The molecular clock analysis suggested that most recent common ancestor of group A and NA1 genotype have emerged in during the years 1953 and 2000, respectively. The global evolutionary rates of group A viruses and NA1 genotype were estimated to be 3.49 × 10-3 (95% HPD, 2.90-4.17 × 10-3) and 3.56 × 10-3 (95% HPD, 2.91 × 10-3-4.18 × 10-3) substitution/site/year, respectively. Analysis of the NA1 genotype of group A RSV reported during 11 years i.e. from 2004 to 2014 showed its dominance in 21 different countries across the globe reflecting its evolutionary dynamics. The Network analysis showed highly intricate but an inconsistent pattern of haplotypes of NA1 genotype circulating in the world. Present study seems to be first comprehensive attempt on global distribution and evolution of NA1 genotype augmenting the optimism towards the vaccine development.
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Affiliation(s)
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Wajihul Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India; Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Irshad H Naqvi
- Dr. M.A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia; Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shobha Broor
- Department of Microbiology, Faculty of Medicine and Health Science, Shree Guru Gobind Singh Tricentenary University, Gurgaon, Haryana, India
| | | | | | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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Hibino A, Saito R, Taniguchi K, Zaraket H, Shobugawa Y, Matsui T, Suzuki H. Molecular epidemiology of human respiratory syncytial virus among children in Japan during three seasons and hospitalization risk of genotype ON1. PLoS One 2018; 13:e0192085. [PMID: 29377949 PMCID: PMC5788364 DOI: 10.1371/journal.pone.0192085] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/16/2018] [Indexed: 12/25/2022] Open
Abstract
We investigated the genetic diversity, the circulation patterns, and risk for hospital admission of human respiratory syncytial virus (HRSV) strains in Japan between 2012 through 2015. During the study period, 744 HRSV-positive cases were identified by rapid diagnostic test. Of these, 572 samples were positive by real-time PCR; 400 (69.9%) were HRSV-A, and 172 (30.1%) were HRSV-B. HRSV-A and -B alternated as the dominant strain in the subsequent seasons. Phylogenetic tree analysis of the second hyper-variable region of the G protein classified the HRSV-A specimens into NA1 (n = 242) and ON1 (n = 114) genotypes and the HRSV-B specimens into BA9 (n = 60), and BA10 (n = 27). The ON1 genotype, containing a 72-nucleotide duplication in the G protein’s second hyper-variable region, was first detected in the 2012–2013 season but it predominated and replaced the older NA1 HRSV-A in the 2014–2015 season, which also coincided with a record number of HRSV cases reported to the National Infectious Disease Surveillance in Japan. The risk of hospitalization was 6.9 times higher for the ON1 genotype compared to NA1. In conclusion, our data showed that the emergence and predominance of the relatively new ON1 genotype in Japan was associated with a record high number of cases and increased risk for hospitalization.
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Affiliation(s)
- Akinobu Hibino
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Reiko Saito
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- * E-mail:
| | | | - Hassan Zaraket
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- Department of Pathology, Immunology, and Microbiology, Faculty of Medicine American University of Beirut, Beirut, Lebanon
- Center for Infectious Disease Research, Faculty of Medicine American University of Beirut, Beirut, Lebanon
| | - Yugo Shobugawa
- Division of International Health (Public Health), Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tamano Matsui
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Suzuki
- School of Nursing, Niigata Seiryo University, Niigata, Japan
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Comas-García A, Noyola DE, Cadena-Mota S, Rico-Hernández M, Bernal-Silva S. Respiratory Syncytial Virus-A ON1 Genotype Emergence in Central Mexico in 2009 and Evidence of Multiple Duplication Events. J Infect Dis 2018; 217:1089-1098. [DOI: 10.1093/infdis/jiy025] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Daniel E Noyola
- Microbiology Department, Facultad de Medicina, San Luis Potosí, México
| | | | | | - Sofía Bernal-Silva
- Microbiology Department, Facultad de Medicina, San Luis Potosí, México
- Research Center for Health Sciences and Biomedicine, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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Genetic diversity of human respiratory syncytial virus circulating among children in Ibadan, Nigeria. PLoS One 2018; 13:e0191494. [PMID: 29360861 PMCID: PMC5779668 DOI: 10.1371/journal.pone.0191494] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/06/2018] [Indexed: 11/19/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is the most common viral cause of acute lower respiratory tract infections (LRTIs) in infants and young children however, without an effective vaccine licensed for human use till date. Information on the circulating genotypes of HRSV from regions with high-burden of infection is vital in the global efforts towards the development of protective vaccine. We report here the genotypes of HRSV circulating among children in Ibadan, the first of such from Nigeria.Nasopharyngeal and oropharyngeal swabs collected from 231 children presenting with respiratory infections in some health facilities for care as well as those attending immunization centers for routine vaccination in Ibadan, Nigeria were used for the study. The 2nd hypervariable (HVR2) region of the glycoprotein (G) gene of HRSV was amplified and sequenced using HRSV group specific primers. HRSV was detected in 41 out of the 231 samples. Thirty-three of the isolates were successfully subtyped(22 subtype A and 11 subtype B). Fourteen of the subtype A and all the subtype B were successfully sequenced and genotyped. Phylogenetic analysis showed that genotype ON1 with 72 nucleotide (nt) duplication was the major subgroup A virus (11 of 14) detected together with genotype NA2. All the HRSV subtype B detected belong to the BA genotype with characteristic 60nt duplication. The ON1 genotypes vary considerably from the prototype strain due to amino acid substitutions including T292I which has not been reported elsewhere. The NA2 genotypes have mutations on four antigenic sites within the HVR2relative to the prototype A2. In conclusion, three genotypes of HRSV were found circulating in Ibadan, Nigeria. Additional study that will include isolates from other parts of the country will be done to determine the extent of genotype diversity of HRSV circulating in Nigeria.
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Tahamtan A, Samieipoor Y, Nayeri FS, Rahbarimanesh AA, Izadi A, Rashidi-Nezhad A, Tavakoli-Yaraki M, Farahmand M, Bont L, Shokri F, Mokhatri-Azad T, Salimi V. Effects of cannabinoid receptor type 2 in respiratory syncytial virus infection in human subjects and mice. Virulence 2017; 9:217-230. [PMID: 28992427 PMCID: PMC5955186 DOI: 10.1080/21505594.2017.1389369] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
An accumulating body of evidence suggests that the endocannabinoid system plays a significant role in pathophysiological processes and impacts disease severity. Here we investigate the possible role of a cannabinoid receptor type 2 (CB2) functional variant in determining disease severity and the potential pharmacological therapeutic effects of CB2 activation in viral respiratory infection. The common missense variant (CAA/CGG; Q63R) of the gene-encoding CB2 receptor (CNR2) was evaluated in 90 inpatient and 90 outpatient children with acute respiratory tract infection (ARTI). The frequency distribution of respiratory syncytial virus (RSV)-the main cause of severe cases of bronchiolitis and pneumonia in children-was studied in all collected samples. The mechanism through which CB2 affects clinical outcomes in case of RSV infection was studied in Balb/c mice model using AM630 as a CB2 antagonist. The potential therapeutic effect of CB2 activation during RSV infection was studied using a selective agonist, JWH133. The CB2 Q63R variation was associated with increased risk of hospitalization in children with ARTI. Children carrying the QQ genotype were more prone to developing severe ARTI (OR = 3.275, 95% CI: 1.221–8.705; p = 0.019). Of all the children enrolled in the study, 83 patients (46.1%) were found positive for RSV infection. The associated risk of developing severe ARTI following RSV infection increased more than two-fold in children carrying the Q allele (OR = 2.148, 95% CI: 1.092–4.224; p = 0.026). In mice, the blockade of CB2 by AM630 during RSV infection enhanced the influx of BAL cells and production of cytokines/chemokines while exaggerating lung pathology. CB2 activation by JWH133 reduces the influx of BAL cells and production of cytokines/chemokines while alleviating lung pathology. Collectively, CB2 is associated with RSV severity during infancy and may serve as a therapeutic target in RSV infection through the alleviation of virus-associated immunopathology.
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Affiliation(s)
- Alireza Tahamtan
- a Department of Virology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran
| | - Yazdan Samieipoor
- a Department of Virology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran
| | - Fatemeh Sadat Nayeri
- b Fetal and Neonatal Research Center , Tehran University of Medical Sciences , Tehran , Iran
| | | | - Anahita Izadi
- c Bahrami Children Hospital , Tehran University of Medical Sciences , Tehran , Iran
| | - Ali Rashidi-Nezhad
- d Maternal, Fetal and Neonatal Research Center , Tehran University of Medical Sciences , Tehran , Iran
| | | | - Mohammad Farahmand
- a Department of Virology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran
| | - Louis Bont
- f University Medical Center Utrecht (UMCU), Wilhelmina Children's Hospital (WKZ) , Department of Pediatrics , Utrecht , The Netherlands
| | - Fazel Shokri
- g Department of Immunology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran
| | - Talat Mokhatri-Azad
- a Department of Virology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran
| | - Vahid Salimi
- a Department of Virology , School of Public Health, Tehran University of Medical Sciences , Tehran , Iran
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Thongpan I, Mauleekoonphairoj J, Vichiwattana P, Korkong S, Wasitthankasem R, Vongpunsawad S, Poovorawan Y. Respiratory syncytial virus genotypes NA1, ON1, and BA9 are prevalent in Thailand, 2012-2015. PeerJ 2017; 5:e3970. [PMID: 29085762 PMCID: PMC5661434 DOI: 10.7717/peerj.3970] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/09/2017] [Indexed: 01/04/2023] Open
Abstract
Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in infants and young children worldwide. To investigate the RSV burden in Thailand over four consecutive years (January 2012 to December 2015), we screened 3,306 samples obtained from children ≤5 years old with acute respiratory tract infection using semi-nested reverse-transcription polymerase chain reaction (RT-PCR). In all, 8.4% (277/3,306) of the specimens tested positive for RSV, most of which appeared in the rainy months of July to November. We then genotyped RSV by sequencing the G glycoprotein gene and performed phylogenetic analysis to determine the RSV antigenic subgroup. The majority (57.4%, 159/277) of the RSV belonged to subgroup A (RSV-A), of which NA1 genotype was the most common in 2012 while ON1 genotype became prevalent the following year. Among samples tested positive for RSV-B subgroup B (RSV-B) (42.6%, 118/277), most were genotype BA9 (92.6%, 87/94) with some BA10 and BA-C. Predicted amino acid sequence from the partial G region showed highly conserved N-linked glycosylation site at residue N237 among all RSV-A ON1 strains (68/68), and at residues N296 (86/87) and N310 (87/87) among RSV-B BA9 strains. Positive selection of key residues combined with notable sequence variations on the G gene contributed to the continued circulation of this rapidly evolving virus.
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Affiliation(s)
- Ilada Thongpan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - John Mauleekoonphairoj
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Preeyaporn Vichiwattana
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sumeth Korkong
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Rujipat Wasitthankasem
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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43
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Molecular and clinical characterization of human respiratory syncytial virus in South Korea between 2009 and 2014. Epidemiol Infect 2017; 145:3226-3242. [PMID: 28988544 DOI: 10.1017/s0950268817002230] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Respiratory syncytial virus (RSV) can cause serious respiratory infections, second only to influenza virus. In order to know RSV's genetic changes we examined 4028 respiratory specimens from local hospital outpatients in Gyeonggi Province, South Korea over six consecutive years by real-time one-step RT-PCR; 183 patients were positive for RSV infection. To investigate the specific distribution of RSV genotypes, we performed partial sequencing of the glycoprotein gene. Of the 131 RSV-A specimens sequenced, 61 (43·3%) belonged to the ON1 genotype, 66 (46·8%) were NA1 genotype, 3 (2·1%) were GA5 genotype, and 1 (0·7%) belonged to the GA1 genotype. Of the 31 RSV-B specimens sequenced, 29 were BA9 genotype (87·9%) and 2 were BA10 genotype (6·1%). The most common clinical symptoms were fever, cough, nasal discharge, and phlegm; multiple logistic regression analysis showed that RSV-positive infection on pediatric patients was strongly associated with cough (OR = 2·8, 95% CI 1·6-5·1) and wheezing (OR = 2·8, 95% CI 1·7-4·4). The ON1 genotype was significantly associated with phlegm (OR = 11·8, 95% CI 3·8-46·7), while the NA1 genotype was associated with the pediatric patients' gender (males, OR = 2·4, 95% CI 1·1-5·4) and presence of chills (OR = 5·1, 95% CI 1·1-27·2). RSV subgroup B was showed association with nasal obstruction (OR = 4·6, 95% CI 1·2-20·0). The majority of respiratory virus coinfections with RSV were human rhinovirus (47·2%). This study contributes to our understanding of the molecular epidemiological characteristics of RSV, which promotes the potential for improving RSV vaccines.
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44
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Korsun N, Angelova S, Tzotcheva I, Georgieva I, Lazova S, Parina S, Alexiev I, Perenovska P. Prevalence and genetic characterisation of respiratory syncytial viruses circulating in Bulgaria during the 2014/15 and 2015/16 winter seasons. Pathog Glob Health 2017; 111:351-361. [PMID: 28948867 DOI: 10.1080/20477724.2017.1375708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The respiratory syncytial virus (RSV) is a leading cause of acute respiratory illnesses (ARI) in infants and young children. The objectives of this study were to investigate the RSV circulation among children aged <5 years in Bulgaria, to identify the RSV-A and RSV-B genotypes and to perform an amino acid sequence analysis of second hypervariable region (HVR2) of the G gene. During the 2014/15 and 2015/16 winter seasons, nasopharyngeal specimens of 610 children aged <5 years with ARI were tested using Real Time RT-PCR for influenza viruses, RSV, metapneumovirus, parainfluenza viruses, rhinoviruses and adenoviruses. Viral respiratory pathogens were detected in 429 (70%) out of 610 patients examined and RSV was the most frequently identified virus (26%) followed by influenza A(H1N1)pdm09 virus (14%) (p < .05). RSV was the most prevalent pathogen in patients with bronchiolitis (48%) and pneumonia (38%). In the 2014/15 season, RSV-A dominated slightly (53%), while in the next season RSV-B viruses prevailed more strongly (66%). The phylogenetic analysis based on the G gene indicated that all 21 studied RSV-A strains belonged to the ON1 genotype; the vast majority (96%) of the RSV-B strains were classified into BA9 genotype and only one - into BA10 genotype. All Bulgarian RSV-A and RSV-B sequences contained a 72-nt and a 60-nt duplication in the HVR2, respectively. The study showed the leading role of this pathogen as a causative agent of serious respiratory illnesses in early childhood, year-on-year fluctuations in RSV incidence, a shift from RSV-A to RSV-B subgroup dominance and relatively low genetic divergence in the circulating strains.
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Affiliation(s)
- Neli Korsun
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Svetla Angelova
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Iren Tzotcheva
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Irina Georgieva
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Snezhina Lazova
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Snezhana Parina
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
| | - Ivaylo Alexiev
- a Department of Virology , National Centre of Infectious and Parasitic Diseases , Sofia , Bulgaria
| | - Penka Perenovska
- b Paediatric clinic , University Hospital Alexandrovska, Medical University , Sofia , Bulgaria
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45
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Infections Caused by HRSV A ON1 Are Predominant among Hospitalized Infants with Bronchiolitis in São Paulo City. BIOMED RESEARCH INTERNATIONAL 2017. [PMID: 28626754 PMCID: PMC5463120 DOI: 10.1155/2017/3459785] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human respiratory syncytial virus is the main cause of respiratory infections in infants. Several HRSV genotypes have been described. Goals. To describe the main genotypes that caused infections in São Paulo (2013-2015) and to analyze their clinical/epidemiological features. Methods. 94 infants (0-6 months) with bronchiolitis were studied. Clinical/epidemiological information was collected; a search for 16 viruses in nasopharyngeal secretion (PCR-real-time and conventional, sequencing, and phylogenetic analyses) was performed. Results. The mean age was 2.4 m; 48% were male. The mean length of hospital stay was 4.4 d (14% in the Intensive Care Unit). The positive rate of respiratory virus was 98.9%; 73 cases (77.6%) were HRSV (76,7% HRSVA). HRSVA formed three clusters: ON1 (n = 34), NA1 (n = 1), and NA2 (n = 4). All HRSVB were found to cluster in the BA genotype (BA9-n = 10; BA10-n = 3). Clinical analyses showed no significant differences between the genotype AON1 and other genotypes. Conclusion. This study showed a high rate of HRSV detection in bronchiolitis. HRSVA ON1, which has recently been described in other countries and has not been identified in previous studies in the southeast region of Brazil, was predominant. The clinical characteristics of the infants that were infected with AON1 were similar to infants with infections by other genotypes.
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46
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Ábrego LE, Delfraro A, Franco D, Castillo J, Castillo M, Moreno B, López-Vergès S, Pascale JM, Arbiza J. Genetic variability of human respiratory syncytial virus group B in Panama reveals a novel genotype BA14. J Med Virol 2017; 89:1734-1742. [PMID: 28464479 DOI: 10.1002/jmv.24838] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/24/2017] [Accepted: 04/17/2017] [Indexed: 11/10/2022]
Abstract
In Panama, human respiratory syncytial virus (HRSV) is responsible of 20-40% of acute respiratory infections in children under 5 years old. Currently, little is known about the genetic variability of HRSV in Central America and the Caribbean. Recently, we reported the genetic variability of HRSV-A, however; no studies on HRSV-B in Panama have been described yet. In this study, 24 sequences of Panamanian HRSV-B, from children (<5 years) with acute respiratory infections (ARI), collected from July 2008 to November 2012 were analyzed. All sequences share the characteristic 60-nt duplication of the BA strains. Six Panamanian strains grouped with the BA10 genotype and 12 samples clustered together in a separate monophyletic clade with an aLRT support value of 0.92 and an intra-group p-distance less than 0.07. This fulfills the criteria to consider a new genotype in HRSV, which we named BA14 genotype. Another six strains remain unclassified, but closely related to BA9, BA11, or the new BA14 genotypes, according to their genetic p-distance. Different amino acid substitutions in the Panamanian HRSV-B strains were observed, some previously described and others found only on Panamanian strains. This study contributes to the knowledge of the genetic variability and evolution of HRSV in Central America.
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Affiliation(s)
- Leyda E Ábrego
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Adriana Delfraro
- Virology Section, School of Sciences, University of the Republic, Montevideo, Uruguay
| | - Danilo Franco
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama.,School of Medicine, University of Panama, Panama City, Panama
| | - Juan Castillo
- Department of Genomic and Proteomic, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Marlene Castillo
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Brechla Moreno
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Sandra López-Vergès
- Deparment of Research in Virology and Biotechnology, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan M Pascale
- School of Medicine, University of Panama, Panama City, Panama.,Department of Genomic and Proteomic, Gorgas Memorial Institute of Health Studies, Panama City, Panama
| | - Juan Arbiza
- Virology Section, School of Sciences, University of the Republic, Montevideo, Uruguay
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47
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Moreira FB, Rosario CS, Santos JS, Avanzi VM, Nogueira MB, Vidal LR, Raboni SM. Molecular characterization and clinical epidemiology of human respiratory syncytial virus (HRSV) A and B in hospitalized children, Southern Brazil. J Med Virol 2017; 89:1489-1493. [PMID: 28213974 DOI: 10.1002/jmv.24795] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/22/2017] [Indexed: 01/01/2023]
Abstract
Human respiratory syncytial virus (HRSV) is a major etiologic agent of pediatric respiratory infections. Genetic variability of its glycoprotein G enables HRSV to evade the immune response and determines its seasonal dissemination. This study reports genetic variability and clinical profiles of HRSV-infected patients from Southern Brazil. Seventy positive samples, 78% type A and 22% type B, were analyzed. Of the patients (median age, 6 months; interquartile range, 2-11 years), 16% had co-morbidities and 17% developed severe disease. The ON1 HRSV genotype first appeared in 2012, and patients infected with this genotype showed an increased tendency to develop severe disease.
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Affiliation(s)
- Francielli B Moreira
- Postgraduate Program in Microbiology, Parasitology and Pathology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Cristine S Rosario
- Department of Pediatrics, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Jucelia S Santos
- Postgraduate Program in Internal Medicine and Health Science, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Valéria M Avanzi
- Postgraduate Program in Internal Medicine and Health Science, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Meri Bordignon Nogueira
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Luine R Vidal
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Sonia Mara Raboni
- Postgraduate Program in Microbiology, Parasitology and Pathology, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.,Postgraduate Program in Internal Medicine and Health Science, Universidade Federal do Paraná, Curitiba, Paraná, Brazil.,Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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