Cohort profile: A Prospective Household cohort study of Influenza, Respiratory syncytial virus and other respiratory pathogens community burden and Transmission dynamics in South Africa, 2016–2018

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.

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Full compliance with Respiratory syncytial virus prophylaxis was associated with fewer respiratory‐related hospital admissions in preterm children: A cohort study

Acta Paediatrica ◽

10.1111/apa.15697 ◽

2020 ◽

Author(s):

Heloise Torchin ◽

Marie‐Laure Charkaluk ◽

Jessica Rousseau ◽

Laetitia Marchand‐Martin ◽

Ludovic Treluyer ◽

...

Keyword(s):

Cohort Study ◽

Respiratory Syncytial Virus ◽

Hospital Admissions ◽

Preterm Children ◽

Full Compliance ◽

Syncytial Virus

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Bacterial and Viral Coinfections with the Human Respiratory Syncytial Virus

Microorganisms ◽

10.3390/microorganisms9061293 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1293

Author(s):

Gaspar A. Pacheco ◽

Nicolás M. S. Gálvez ◽

Jorge A. Soto ◽

Catalina A. Andrade ◽

Alexis M. Kalergis

Keyword(s):

Respiratory Syncytial Virus ◽

Influenza A ◽

Human Respiratory Syncytial Virus ◽

Respiratory Pathogens ◽

Parainfluenza Viruses ◽

Starting Point ◽

The Social ◽

Syncytial Virus ◽

Tract Infections ◽

Polymicrobial Infections

The human respiratory syncytial virus (hRSV) is one of the leading causes of acute lower respiratory tract infections in children under five years old. Notably, hRSV infections can give way to pneumonia and predispose to other respiratory complications later in life, such as asthma. Even though the social and economic burden associated with hRSV infections is tremendous, there are no approved vaccines to date to prevent the disease caused by this pathogen. Recently, coinfections and superinfections have turned into an active field of study, and interactions between many viral and bacterial pathogens have been studied. hRSV is not an exception since polymicrobial infections involving this virus are common, especially when illness has evolved into pneumonia. Here, we review the epidemiology and recent findings regarding the main polymicrobial infections involving hRSV and several prevalent bacterial and viral respiratory pathogens, such as Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Klebsiella pneumoniae, human rhinoviruses, influenza A virus, human metapneumovirus, and human parainfluenza viruses. As reports of most polymicrobial infections involving hRSV lack a molecular basis explaining the interaction between hRSV and these pathogens, we believe this review article can serve as a starting point to interesting and very much needed research in this area.

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Circulation of Respiratory Viruses in Hospitalized Adults before and during the COVID-19 Pandemic in Brescia, Italy: A Retrospective Study

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph18189525 ◽

2021 ◽

Vol 18 (18) ◽

pp. 9525

Author(s):

Maria Antonia De Francesco ◽

Caterina Pollara ◽

Franco Gargiulo ◽

Mauro Giacomelli ◽

Arnaldo Caruso

Keyword(s):

Respiratory Syncytial Virus ◽

Influenza A ◽

Statistical Significance ◽

Respiratory Viruses ◽

Influenza Viruses ◽

Contact Tracing ◽

Nucleic Acid Detection ◽

Respiratory Pathogens ◽

Syncytial Virus ◽

Human Coronaviruses

Different preventive public health measures were adopted globally to limit the spread of SARS-CoV-2, such as hand hygiene and the use of masks, travel restrictions, social distance actions such as the closure of schools and workplaces, case and contact tracing, quarantine and lockdown. These measures, in particular physical distancing and the use of masks, might have contributed to containing the spread of other respiratory viruses that occurs principally by contact and droplet routes. The aim of this study was to evaluate the prevalence of different respiratory viruses (influenza viruses A and B, respiratory syncytial virus, parainfluenza viruses 1, 2, 3 and 4, rhinovirus, adenovirus, metapneumovirus and human coronaviruses) after one year of the pandemic. Furthermore, another aim was to evaluate the possible impact of these non-pharmaceutical measures on the circulation of seasonal respiratory viruses. This single center study was conducted between January 2017–February 2020 (pre-pandemic period) and March 2020–May 2021 (pandemic period). All adults >18 years with respiratory symptoms and tested for respiratory pathogens were included in the study. Nucleic acid detection of all respiratory viruses was performed by multiplex real time PCR. Our results show that the test positivity for influenza A and B, metapneumovirus, parainfluenza virus, respiratory syncytial virus and human coronaviruses decreased with statistical significance during the pandemic. Contrary to this, for adenovirus the decrease was not statistically significant. Conversely, a statistically significant increase was detected for rhinovirus. Coinfections between different respiratory viruses were observed during the pre-pandemic period, while the only coinfection detected during pandemic was between SARS-CoV-2 and rhinovirus. To understand how the preventive strategies against SARS-CoV-2 might alter the transmission dynamics and epidemic patterns of respiratory viruses is fundamental to guide future preventive recommendations.

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Amino Acid Variation within the Fusion Protein of Respiratory Syncytial Virus Subtype A and B Strains during Annual Epidemics in South Africa

Virus Genes ◽

10.1007/s11262-004-5633-2 ◽

2005 ◽

Vol 30 (2) ◽

pp. 267-278 ◽

Cited By ~ 18

Author(s):

Elizabeth Agenbach ◽

Caroline T. Tiemessen ◽

Marietjie Venter

Keyword(s):

South Africa ◽

Respiratory Syncytial Virus ◽

Amino Acid ◽

Fusion Protein ◽

Amino Acid Variation ◽

Syncytial Virus ◽

Subtype A ◽

Virus Subtype

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Asthma and Immunoglobulin E Antibodies After Respiratory Syncytial Virus Bronchiolitis: A Prospective Cohort Study With Matched Controls

PEDIATRICS ◽

10.1542/peds.95.4.500 ◽

1995 ◽

Vol 95 (4) ◽

pp. 500-505 ◽

Cited By ~ 8

Author(s):

N. Sigurs ◽

R. Bjarnason ◽

F. Sigurbergsson ◽

B. Kjellman ◽

B. Björkstén

Keyword(s):

Risk Factor ◽

Cohort Study ◽

Respiratory Syncytial Virus ◽

Prospective Cohort ◽

Egg White ◽

Control Group ◽

Igg Antibodies ◽

Ige Antibodies ◽

Syncytial Virus

Objective. To study the occurrence of bronchial obstructive symptoms and immunoglobulin (Ig) E antibodies after respiratory syncytial virus (RSV) bronchiolitis in infancy. Previous studies of this subject have mostly been retrospective or without controls, or the controls have not been followed prospectively. Design. This was a prospective cohort study with matched controls. Participants. Forty-seven infants had experienced RSV bronchiolitis severe enough to cause hospitalization at a mean age of 3½ months. For each child with RSV infection, two controls were acquired from the local Child Health Center and matched for date of birth, sex, and residence. Only one control was obtained for one RSV child, and the control group thus contained 93 children. Methods. All the children underwent two follow-up examinations, the first one at a mean age of 1 year and the second at a mean age of 3 years. At the first follow-up, a skin-prick test against egg white was performed, and serum IgG antibodies against RSV were measured. At the second follow-up, serum IgE antibodies were measured using screening tests for common food and inhalant antibodies, and skin-prick tests against egg white, cat, birch, and mite allergen were performed. Hereditary and environmental factors (passive smoking, indoor furred animals) and duration of breast-feeding were recorded. Results. At the first follow-up, 89% in the RSV group and 27% in the control group had IgG antibodies against RSV (P < .001). At the second follow-up, asthma, defined as three episodes of bronchial obstruction verified by a physician, was found in 11 of 47 children (23%) in the RSV group and in 1 of 93 children (1%) in the control group (P < .001). A positive test for IgE antibodies was noted in 14 of 44 (32%) RSV children and in 8 of 92 (9%) children in the control group (P = .002). An analysis of risk factors for the development of asthma and IgE antibodies on the whole group of 140 children showed that RSV bronchiolitis was the most important risk factor, and a family history of atopy or asthma further increased the risk. Conclusions. Respiratory syncytial virus bronchiolitis during the first year of life apparently is an important risk factor for the development of asthma and sensitization to common allergens during the subsequent 2 years, particularly in children with heredity for atopy/asthma.

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ASTHMA AND IMMUNOGLOBULIN E (IgE) ANTIBODIES AFTER RESPIRATORY SYNCYTIAL VIRUS (RSV) BRONCHIOLITIS: A PROSPECTIVE COHORT STUDY WITH MATCHED CONTROLS

PEDIATRICS ◽

10.1542/peds.98.2.329 ◽

1996 ◽

Vol 98 (2) ◽

pp. 329-329

Author(s):

James E. Gern

Keyword(s):

Risk Factor ◽

Cohort Study ◽

Respiratory Syncytial Virus ◽

Family History ◽

Prospective Cohort ◽

Immunoglobulin E ◽

Specific Ige ◽

Ige Antibodies ◽

History Of ◽

Syncytial Virus

RSV bronchiolitis was the most important risk factor for the development of asthma and allergen-specific IgE, although a family history of atopy or asthma further increased the risk.

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Respiratory Pathogens in Children 1 Month to 5 Years of Age Presenting With Undifferentiated Acute Respiratory Distress in 2 District-Level Hospitals in Ghana

Journal of the Pediatric Infectious Diseases Society ◽

10.1093/jpids/piy090 ◽

2018 ◽

Vol 8 (4) ◽

pp. 361-364

Author(s):

Patrick T Wilson ◽

Frank Baiden ◽

Joshua C Brooks ◽

Katie M Giessler ◽

Gavin Apio ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Respiratory Syncytial Virus ◽

Respiratory Distress ◽

Polymerase Chain Reaction Assay ◽

Rainy Season ◽

Dry Season ◽

Respiratory Pathogens ◽

Chain Reaction ◽

Polymerase Chain ◽

Syncytial Virus

Abstract Ghanaian children (2176) aged <5 years who presented with undifferentiated acute respiratory distress were tested for respiratory pathogens using a BioFire FilmArray polymerase chain reaction assay. Rhinovirus and/or enterovirus was detected in 36% of the assays, respiratory syncytial virus in 11%, and parainfluenza in 7%. Respiratory syncytial virus and metapneumovirus were detected more frequently in the rainy season than in the dry season.

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Genotyping of Type A Human Respiratory Syncytial Virus Based on Direct F Gene Sequencing

Medicina ◽

10.3390/medicina55050169 ◽

2019 ◽

Vol 55 (5) ◽

pp. 169 ◽

Cited By ~ 1

Author(s):

Daifullah Al Aboud ◽

Nora M. Al Aboud ◽

Mater I. R. Al-Malky ◽

Ahmed S. Abdel-Moneim

Keyword(s):

Respiratory Syncytial Virus ◽

Mutational Analysis ◽

Gene Sequencing ◽

Human Respiratory Syncytial Virus ◽

Clinical Samples ◽

Escape Mutant ◽

Respiratory Pathogens ◽

Virus Genotype ◽

F Gene ◽

Syncytial Virus

Background and objectives: The human respiratory syncytial virus (hRSV) is among the important respiratory pathogens affecting children. Genotype-specific attachment (G) gene sequencing is usually used to determine the virus genotype. The reliability of the fusion (F) gene vs. G gene genotype-specific sequencing was screened. Materials and Methods: Archival RNA from Saudi children who tested positive for hRSV-A were used. Samples were subjected to a conventional one-step RT-PCR for both F and G genes and direct gene sequencing of the amplicons using the same primer sets. Phylogeny and mutational analysis of the obtained sequences were conducted. Results: The generic primer set succeeded to amplify target gene sequences. The phylogenetic tree based on partial F gene sequencing resulted in an efficient genotyping of hRSV-A strains equivalent to the partial G gene genotyping method. NA1, ON1, and GA5 genotypes were detected in the clinical samples. The latter was detected for the first time in Saudi Arabia. Different mutations in both conserved and escape-mutant domains were detected in both F and G. Conclusion: It was concluded that a partial F gene sequence can be used efficiently for hRSV-A genotyping.

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