Respitatory virus infections during the first year of life a longitudinal community-based dynamic birth cohort study

Abstract

Background: Viral acute respiratory infections (ARIs) are the commonest illnesses experienced by all age groups, especially in infants where infection rates are highest. Nevertheless, during the molecular era, outside of hospital-based studies, little is known about the current aetiology and community burden of viral ARIs in infants and young children. The observational research in childhood infectious disease (ORChID) project is a prospective community-based birth-cohort study of healthy Australian infants and children. It began in 2010 to investigate respiratory virus infections until two-years of age. My PhD established laboratory quality control techniques for studies of this nature and describes the respiratory viruses and molecular epidemiology of human rhinoviruses (RV) during the first year of life in a nested subgroup of this cohort. The hypotheses were: (i) During the first year of life and in otherwise healthy infants, RV is the most commonly detected respiratory virus in respiratory secretions. (ii) Various factors impact upon successful viral detection, including the ability of parents to collect appropriate samples and other laboratory-based technical issues. (iii) Repeated detection of RV-RNA in respiratory secretions over periods of more than 4-weeks results from genotype replacement and new infection events rather than from prolonged shedding of the same genotype. (iv) Many RV genotypes circulate in a single location in 1 year period. Methods The ongoing ORChID study completed sample collection at the end of 2014. Parents were approached antenatally and asked to collect weekly anterior nasal swabs from the time of their child's birth until their second birthday. Swabs were mailed to the laboratory where they were stored at-80ºC until analysis. Parents also completed a daily symptom diary, which was submitted monthly. My PhD focused on samples collected from an infant subgroup within this cohort and the first two-years of the ORChID study. Samples were extracted using an automated robotic system after spiking each sample with equid herpes virus (EHV-1). The extraction quality and presence of human DNA in extracts were assessed by real-time PCR for EHV-1 and endogenous retrovirus 3 (ERV-3) respectively. Respiratory virus

Observational research in childhood respiratory diseases

“…3 Ct value >38, respiratory virus detection declined significantly (odds ratio 0.35, 95% CI: 0.27, 0.44 when ERV-3 was undetectable)(249). Thus, virus-negative swabs with an ERV-3 Ct value >38 were deemed to be of poor quality and removed from parts of the analysis, such as incidence calculations.Swab quality was monitored throughout the study and the number of ERV-3 negative specimens ranged from 19.6% to 44.6% in the first 8 months of the study(250).Analysis of ERV-3 positive and respiratory virus positive specimens showed that ERV-3 positive sample rates increased with age and varied by season(249), with ERV-3 positive rates in the first six months of age as a reference. Following a cluster of specimens that were negative for ERV-3, study nurses contacted parents and reminded them of the optimal swab technique they had been shown at enrolment.After this feedback, the number of ERV-3 specimens declined.Each swab was resuspended in 2mL of phosphate buffered saline from which 200µL was used for nucleic acid extraction.…”