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

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).

Fig 1. Ghana and its ten administrative regions.

The two study sites, the Korle Bu Teaching Hospital (KBTH) and the Princess Marie Louise Children’s Hospital (PMLCH), were located in Accra within the Greater Accra region. Accra is mapped with a black star.

Fig 2. Monthly distribution of specimens from children with ALRI and HRSV positivity rate.

Dry and wet seasons are indicated.

Fig 3. Maximum likelihood analysis of the VR2 region of HRSV G protein gene sequences from Ghana.

The phylogenetic trees were constructed with MEGA version 5.2 using the Tamura-Nei and the Hasegawa-Kishino-Yano methods for (a) HRSV-A and (b) HRSV–B, respectively, with 1,000 replicates. Reference sequences representing the different HRSV genotypes were obtained from GenBank and are indicated by their accession numbers. Sequences from this study are shown in bold and designated by the geographic location (GHA), patient number and year of collection. The genotype clusters are indicated on the right of each figure. Only bootstrap values greater than 70% are displayed at the branch nodes. Characteristic amino acid substitutions are indicated at branch nodes.

Fig 4. Deduced amino acid alignment of the VR2 region of HRSV G protein gene sequences.

Alignments of (a) HRSV- group A and (b) HRSV group B viruses from Ghana are shown in relation to prototype strains, and genotype specific strains. Identical residues are indicated by dots. Stop codons are indicated by asterisks. Rectangles indicate the two copies of amino acid duplicated regions. Potential N-glycosylation sites (NXT/S, where X is not a proline) are underlined. Potential sites for extensive O-glycosylation KPXnTTKXn motifs (where X is any amino acid) are indicated by gray shading.