Erratum: Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

[This corrects the article DOI: 10.1093/ve/vey027.][This corrects the article DOI: 10.1093/ve/vey027.].

Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains.

The respiratory syncytial virus (RSV) group A variant with the 72-nucleotide duplication in the G gene, genotype ON1, was first detected in Kilifi in 2012 and has almost completely replaced circulating genotype GA2 strains. This replacement suggests some fitness advantage of ON1 over the GA2 viruses in Kilifi, and might be accompanied by important genomic substitutions in ON1 viruses. Close observation of such a new virus genotype introduction over time provides an opportunity to better understand the transmission and evolutionary dynamics of the pathogen. We have generated and analysed 184 RSV-A whole-genome sequences (WGSs) from Kilifi (Kenya) collected between 2011 and 2016, the first ON1 genomes from Africa and the largest collection globally from a single location. Phylogenetic analysis indicates that RSV-A circulation in this coastal Kenya location is characterized by multiple introductions of viral lineages from diverse origins but with varied success in local transmission. We identified signature amino acid substitutions between ON1 and GA2 viruses' surface proteins (G and F), polymerase (L), and matrix M2-1 proteins, some of which were positively selected, and thereby provide an enhanced picture of RSV-A diversity. Furthermore, five of the eleven RSV open reading frames (ORFs) (G, F, L, N, and P) formed distinct phylogenetic clusters for the two genotypes. This might suggest that coding regions outside of the most frequently studied G ORF also play a role in the adaptation of RSV to host populations, with the alternative possibility that some of the substitutions are neutral and provide no selective advantage. Our analysis provides insight into the epidemiological processes that define RSV spread, highlights the genetic substitutions that characterize emerging strains, and demonstrates the utility of large-scale WGS in molecular epidemiological studies.

Comparison of three methods of collecting nasal specimens for respiratory virus analysis.

BACKGROUND: Nasopharyngeal aspiration (NPA) is used widely in the collection of nasal specimens for respiratory virus diagnosis. The method has limitations in relation to technical expertise, patient anxiety, and apparatus dependence. Nasal washing (NW) offers an alternative approach. OBJECTIVE: To identify the merits of two different NW methods in comparison with NPA. DESIGN: Two hundred children with acute respiratory infection (ARI) were randomised to receive one of three collection devices: (i) standard NPA, (ii) NW using a 30ml ear-syringe bulb (NWb), or (iii) NW using a 5ml syringe (NWs) with a shortened (9cm) 8FG tube. Assessment focused on ease of procedure, acceptability to parent and child, and adequacy of epithelial cell yield for immunofluorescence testing. A short questionnaire was delivered. SETTING: Paediatric Ward of Kilifi District Hospital, (KDH) Kilifi, Kenya. SUBJECTS: Any child admitted with ARI between 5th November 2001 and 24th January 2002. RESULTS: Children recruited into NPA, NWb and NWs procedures numbered 62, 76 and 62, respectively (median age of 8 months). A higher proportion of children receiving NWb did not cry (43%) compared to those receiving NPA (13%) (OR 5.18; 95% CI 2.17-12.4). Whereas 66% of mothers were comfortable with NPA procedure, the proportion for NWs was 40% (OR 0.341; 0.163-0.714). Acceptability to the operator was marginally lower for NWs than NPA (79% vs 92%, OR 0.324, 0.107-0.974). For other observations there were no differences between the procedures; these were length of procedure (98% <5mins), the acceptable time interval for repeating a procedure (64% <1 week), comparison with blood collection (77% preferred the nasal specimen) and slides with 20 or more epithelial cells (overall 82%). CONCLUSION: Nasal washing methods provide simple and effective alternatives to NPA, with the NWb being the more acceptable, and have merits for use in resource poor and home settings.

Causes and outcome of young infant admissions to a Kenyan district hospital.

AIMS: To provide a comprehensive description of young infant admissions to a first referral level health facility in Kenya. These data, currently lacking, are important given present efforts to standardise their care through the integrated management of childhood illness (IMCI) and for prioritising both health care provision and disease prevention strategies. METHODS: Prospective, 18 month observational study in a Kenyan district hospital of all admissions less than 3 months of age to the paediatric ward. RESULTS: A total of 1080 infants were studied. Mortality was 18% overall, though in those aged 0-7 days it was 34%. Within two months of discharge a further 5% of infants aged <60 days on admission had died. Severe infection and prematurity together accounted for 57% of inpatient deaths in those aged <60 days, while jaundice and tetanus accounted for another 27%. S pneumoniae, group B streptococcus, E coli, and Klebsiella spp. were the most common causes of invasive bacterial disease. Hypoxaemia, hypoglycaemia, and an inability to feed were each present in more than 20% of infants aged 0-7 days. Both hypoxaemia and the inability to feed were associated with inpatient death (OR 3.8 (95% CI 2.5 to 5.8) and 7.4 (95% CI 4.8 to 11.2) respectively). CONCLUSIONS: Young infants contribute substantially to paediatric inpatient mortality at the first referral level, highlighting the need both for basic supportive care facilities and improved disease prevention strategies.