scholarly journals Genetic diversity and evolutionary insights of respiratory syncytial virus A ON1 genotype: global and local transmission dynamics

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Venkata R. Duvvuri ◽  
Andrea Granados ◽  
Paul Rosenfeld ◽  
Justin Bahl ◽  
Alireza Eshaghi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Respiratory Syncytial Virus ◽  
Transmission Dynamics ◽  
Syncytial Virus ◽  
Global And Local ◽  
Local Transmission

scholarly journals Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya

2016 ◽  
Vol 90 (10) ◽  
pp. 4990-5002 ◽  
Author(s):  
James R. Otieno ◽  
Charles N. Agoti ◽  
Caroline W. Gitahi ◽  
Ann Bett ◽  
Mwanajuma Ngama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Respiratory Syncytial Virus ◽  
Time Scales ◽  
Evolutionary Dynamics ◽  
Nucleotide Substitutions ◽  
High Genetic Diversity ◽  
Data Set ◽  
New Variant ◽  
Syncytial Virus ◽  
Highest Posterior Density

ABSTRACTThe characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing the efficiency of preexisting immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 to 2012) in Kilifi (n= 649), Kenya, and contemporaneous sequences (n= 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2 and then GA2 by ON1. Within these genotypes, there was considerable variation in potentialN-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi data set was estimated at 3.58 × 10−3(95% highest posterior density interval = 3.04 to 4.16) nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating RSV-A strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics.IMPORTANCEThe mechanisms underlying recurrent epidemics of RSV are poorly understood. We observe high genetic diversity in circulating strains within and between epidemics in both local and global settings. On longer time scales (∼7 years) there is sequential replacement of genotypes, whereas on shorter time scales (one epidemic to the next or within epidemics) there is a high turnover of variants within genotypes. Further, this genetic diversity is predicted to be associated with variation in antigenic profiles. These observations provide an explanation for recurrent RSV epidemics and have potential implications on the long-term effectiveness of vaccines.

scholarly journals Understanding the transmission dynamics of respiratory syncytial virus using multiple time series and nested models

2007 ◽  
Vol 209 (1) ◽  
pp. 222-239 ◽  
Author(s):  
L.J. White ◽  
J.N. Mandl ◽  
M.G.M. Gomes ◽  
A.T. Bodley-Tickell ◽  
P.A. Cane ◽  
...  
Keyword(s):  
Time Series ◽  
Respiratory Syncytial Virus ◽  
Transmission Dynamics ◽  
Multiple Time ◽  
Multiple Time Series ◽  
Nested Models ◽  
Syncytial Virus

scholarly journals Conservation of G-Protein Epitopes in Respiratory Syncytial Virus (Group A) Despite Broad Genetic Diversity: Is Antibody Selection Involved in Virus Evolution?

2015 ◽  
Vol 89 (15) ◽  
pp. 7776-7785 ◽  
Author(s):  
Alfonsina Trento ◽  
Leyda Ábrego ◽  
Rosa Rodriguez-Fernandez ◽  
Maria Isabel González-Sánchez ◽  
Felipe González-Martínez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Respiratory Syncytial Virus ◽  
Positive Selection ◽  
G Protein ◽  
Human Respiratory Syncytial Virus ◽  
Antigenic Drift ◽  
Clear Correlation ◽  
Published Data ◽  
Group A ◽  
Syncytial Virus

ABSTRACTWorldwide G-glycoprotein phylogeny of human respiratory syncytial virus (hRSV) group A sequences revealed diversification in major clades and genotypes over more than 50 years of recorded history. Multiple genotypes cocirculated during prolonged periods of time, but recent dominance of the GA2 genotype was noticed in several studies, and it is highlighted here with sequences from viruses circulating recently in Spain and Panama. Reactivity of group A viruses with monoclonal antibodies (MAbs) that recognize strain-variable epitopes of the G glycoprotein failed to correlate genotype diversification with antibody reactivity. Additionally, no clear correlation was found between changes in strain-variable epitopes and predicted sites of positive selection, despite both traits being associated with the C-terminal third of the G glycoprotein. Hence, our data do not lend support to the proposed antibody-driven selection of variants as a major determinant of hRSV evolution. Other alternative mechanisms are considered to account for the high degree of hRSV G-protein variability.IMPORTANCEAn unusual characteristic of the G glycoprotein of human respiratory syncytial virus (hRSV) is the accumulation of nonsynonymous (N) changes at higher rates than synonymous (S) changes, reaching dN/dS values at certain sites predictive of positive selection. Since these sites cluster preferentially in the C-terminal third of the G protein, like certain epitopes recognized by murine antibodies, it was proposed that immune (antibody) selection might be driving the apparent positive selection, analogous to the antigenic drift observed in the influenza virus hemagglutinin (HA). However, careful antigenic and genetic comparison of the G glycoprotein does not provide evidence of antigenic drift in the G molecule, in agreement with recently published data which did not indicate antigenic drift in the G protein with human sera. Alternative explanations to the immune-driven selection hypothesis are offered to account for the high level of G-protein genetic diversity highlighted in this study.

scholarly journals Seasonality, molecular epidemiology, and virulence of Respiratory Syncytial Virus (RSV): A perspective into the Brazilian Influenza Surveillance Program

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0251361
Author(s):  
Lucas A. Vianna ◽  
Marilda M. Siqueira ◽  
Lays P. B. Volpini ◽  
Iuri D. Louro ◽  
Paola C. Resende
Keyword(s):  
Genetic Diversity ◽  
Viral Load ◽  
Respiratory Syncytial Virus ◽  
Disease Severity ◽  
Clinical Severity ◽  
Influenza Surveillance ◽  
Surveillance Program ◽  
Inverse Association ◽  
Severe Acute Respiratory Infection ◽  
Syncytial Virus

Background Respiratory Syncytial Virus (RSV) is the main cause of pediatric morbidity and mortality. The complex evolution of RSV creates a need for worldwide surveillance, which may assist in the understanding of multiple viral aspects. Objectives This study aimed to investigate RSV features under the Brazilian Influenza Surveillance Program, evaluating the role of viral load and genetic diversity in disease severity and the influence of climatic factors in viral seasonality. Methodology We have investigated the prevalence of RSV in children up to 3 years of age with severe acute respiratory infection (SARI) in the state of Espirito Santo (ES), Brazil, from 2016 to 2018. RT-qPCR allowed for viral detection and viral load quantification, to evaluate association with clinical features and mapping of local viral seasonality. Gene G sequencing and phylogenetic reconstruction demonstrated local genetic diversity. Results Of 632 evaluated cases, 56% were caused by RSV, with both subtypes A and B co-circulating throughout the years. A discrete inverse association between average temperature and viral circulation was observed. No correlation between viral load and disease severity was observed, but children infected with RSV-A presented a higher clinical severity score (CSS), stayed longer in the hospital, and required intensive care, and ventilatory support more frequently than those infected by RSV-B. Regarding RSV diversity, some local genetic groups were observed within the main genotypes circulation RSV-A ON1 and RSV-B BA, with strains showing modifications in the G gene amino acid chain. Conclusion Local RSV studies using the Brazilian Influenza Surveillance Program are relevant as they can bring useful information to the global RSV surveillance. Understanding seasonality, virulence, and genetic diversity can aid in the development and suitability of antiviral drugs, vaccines, and assist in the administration of prophylactic strategies.

scholarly journals Cohort Profile: a Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa (PHIRST), 2016-2018

2021 ◽  
Author(s):  
Cheryl Cohen ◽  
Meredith L. McMorrow ◽  
Neil A. Martinson ◽  
Kathleen Kahn ◽  
Florette K. Treurnicht ◽  
...  
Keyword(s):  
South Africa ◽  
Cohort Study ◽  
Respiratory Syncytial Virus ◽  
Disease Burden ◽  
Influenza Viruses ◽  
Transmission Dynamics ◽  
Respiratory Pathogens ◽  
Household Members ◽  
Syncytial Virus

AbstractPurposeThe PHIRST study (Prospective Household cohort study of Influenza, Respiratory Syncytial virus, and other respiratory pathogens community burden and Transmission dynamics in South Africa) aimed to estimate the community burden of influenza and respiratory syncytial virus (RSV) including the incidence of infection, symptomatic fraction, and disease severity, and to assess household transmission. We further aimed to estimate the impact of HIV infection and age on disease burden and transmission, and to assess the burden of Bordetella pertussis and Streptococcus pneumoniae.ParticipantsWe enrolled 1684 individuals in 327 randomly selected households in two sites (rural Agincourt subdistrict, Mpumalanga Province and urban Jouberton Township, North West Province) over 3 consecutive influenza and RSV seasons. A new cohort of households was enrolled each year. Eligible households included those with >2 household members where ≥80% of household members provided consent (and assent for children aged 7-17 years). Enrolled household members were sampled with nasopharyngeal swabs twice weekly during the RSV and influenza seasons of the year of enrolment. Serology samples were collected at enrolment and before and after the influenza season annually.Findings to dateThere were 122,113 potential individual follow-up visits over the 3 years, and participants were interviewed for 105,783 (87%) of these. Out of 105,683 nasopharyngeal swabs from follow-up visits, 1,258 (1%), 1,026 (1%), 273 (<1%), 38,829 (37%) tested positive on PCR for influenza viruses, respiratory syncytial virus, pertussis and pneumococcus respectively.Future plansFuture planned analyses include analysis of influenza serology results and RSV burden and transmission. Households enrolled in the PHIRST study during 2016-2018 were eligible for inclusion in a study of SARS-CoV-2 transmission initiated in July 2020. This study uses similar testing frequency and household selection methods to assess the community burden of SARS-CoV-2 infection and the role of asymptomatic infection in virus transmission.RegistrationClinical trials.gov NCT02519803Article summaryStrengths and limitations of this studyPHIRST was conducted in urban and rural African settings with high HIV prevalence, allowing assessment of the effect of HIV on community burden and transmission dynamics of respiratory pathogens.Households were selected randomly to provide a representative sample of the community. Twice weekly sampling from each cohort of individuals for 6-10 months irrespective of symptoms allows estimation of community burden, household secondary infection risk, and serial interval including asymptomatic or paucisymptomatic episodes.Polymerase chain reaction testing of >100,000 nasopharyngeal swab samples for multiple pathogens (influenza, respiratory syncytial virus, pertussis and Streptoccocus pneumonia) allows detailed examination of disease burden and transmission and pathogen interactionsPHIRST was not powered to assess severe outcomes (i.e. hospitalisation and death).We only examined four pathogens, but other micro-organisms may be important. Samples have been stored which could allow us to implement broader multi-pathogen testing in the future.

Genetic diversity and molecular epidemiology of respiratory syncytial virus circulated in Antananarivo, Madagascar, from 2011 to 2017: Predominance of ON1 and BA9 genotypes

2020 ◽  
Vol 129 ◽  
pp. 104506
Author(s):  
Norosoa Harline Razanajatovo Rahombanjanahary ◽  
Ksenia Rybkina ◽  
Tsiry Hasina Randriambolamanantsoa ◽  
Helisoa Razafimanjato ◽  
Jean-Michel Heraud
Keyword(s):  
Genetic Diversity ◽  
Respiratory Syncytial Virus ◽  
Molecular Epidemiology ◽  
Syncytial Virus
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