Molecular Analysis of Human Respiratory Syncytial Virus Group B Strains Isolated in Kenya Before and During the Emergence of Pandemic Influenza A/H1N1

Abstract

Background: We conducted a retrospective study to explore molecular insights into human respiratory syncytial virus (HRSV) group B strains among patients attending outpatient clinics at government medical facilities both prior and during the onset of Influenza A/H1N1/2009 pandemic outbreak.

Methods: We screened 2300 nasopharyngeal swabs using multiplex real time reverse transcriptase polymerase chain reaction. We amplified a segment of the first and second hypervariable regions, as well as the conserved portion of the third domain of the G-gene using HRSV-B specific primers, sequenced by Sanger di-deoxy chain termination method and thereafter analyzed the sequences.

Results: We characterized the circulating strains into three known genotypes: SAB4 (1.4%), BA7 (1.4%), and multiple variants of BA9 (97.2%). The majority of BA9 viruses were uniquely Kenyan with only 4% aligning with BA9 lineages found elsewhere. The mean evolutionary rate of the HRSV-B was estimated to be 3.08 × 10^-3 substitutions per site per year.

Conclusion: Our findings indicate that the circulating HRSV-B viruses in Kenya underwent a slower evolution during the period of 2007-2010. Additionally, our findings reveal the existence of a unique lineage as well as new variants that have not been reported elsewhere to date.

Keywords: COVID‐19 pandemic; HRSV‐B genotypes; SARS‐CoV‐2; evolution; genetic variability; pandemic influenza; recombination; spatial–temporal trends.

FIGURE 1

Kenyan map showing the locations of health facilities in the previously known provinces. The five regions examined in this study comprise of one or two public hospitals. The Port Reitz and Malindi subcounty hospitals serve the Coast region, while the Mbagathi county hospital serves the Nairobi region and the Isiolo county hospital represents the Eastern region. The Highlands region encompasses the Kericho county hospital in the middle belt of the rift valley and the Kisii county hospital in the southeast of the larger Nyanza region. The Western region is represented by the Alupe subcounty hospital and the New Nyanza Children's Hospital, which is located in the northeast of Nyanza province.

FIGURE 2

(a–f) Temporal spatial distribution of HRSV‐B in Kenya. (a) Quarterly distribution of HRSV‐B from 2007 to 2010. It is displaying the proportion of cases in the five regions and the total number of samples tested per quarter. The quarters followed the calendar year starting January to December. (b–f) Temporal distribution of HRSV‐B in five regions. (b) Western (WES), (c) Coast (CST), (d) Nairobi (NRB), (e) Highlands (HLD), and (f) Eastern (NEA).

FIGURE 3

Phylogenetic tree based on the G‐gene segment of the HRSV‐B recovered from the ILI cases across Kenya. It is made up of 104 sequences rooted on the prototype isolated in 1962, accession number JX198143. The local sequences (73) are represented by the colored tips. Each individual cluster or subcluster has a distinct color for the tips. We only assigned genotype names to clusters comprising local sequences. The BA9 genotype comprised of seven clusters labeled as BA9.1–BA9.7. The nucleotide differences among these sequences were annotated based on the prototype sequence and therefore does not display the changes in the duplicated segment among these sequences.

FIGURE 4

Bayesian Markov chain Monte Carlo (MCMC) tree based on the G‐gene segment of the HRSV‐B recovered from the ILI cases across Kenya. The tree comprised of 74 sequences. It is rooted on the prototype, accession number JX198143. The two major lineages are represented by distinct colored clades. Lineage 1 comprises of 33 sequences found in cluster 9.3 of Figure 2 while lineage 2 comprises of the remaining 38 BA9 sequences and 1 BA7 sequence represented in different shades. The BA9 clusters shown in Figure 2 are labeled in black font while the BA7 and SAB4 genotypes are labeled in a colored font.

FIGURE 5

Sequences alignment of a segment of deduced amino acids of a segment of the G‐gene of the HRSV‐B sub‐group BA. The alignment shown is relative to a BA isolate from Argentina, GenBank Accession number AY333364. (a) The alignment covers 100 residues of the first hypervariable region starting from position 107 of the reference strain. The box frame represents a deletion in the local sequences. (b) This alignment covers the second hypervariable region from position 101, which is equivalent to position 208 of the reference strain. The boxes frame covers a region of 40 amino acids in the duplicated region. The box frame to the right is a copy of the 20‐amino acids insertion.