Whole genome molecular analysis of respiratory syncytial virus pre and during the COVID-19 pandemic in Free State province, South Africa

Abstract

Respiratory syncytial virus (RSV) is the most predominant viral pathogen worldwide in children with lower respiratory tract infections. The Coronavirus disease 2019 (COVID-19) pandemic and resulting nonpharmaceutical interventions perturbed the transmission pattern of respiratory pathogens in South Africa. A seasonality shift and RSV resurgence was observed in 2020 and 2021, with several infected children observed. Conventional RSV-positive nasopharyngeal swabs were collected from various hospitals in the Free State province, Bloemfontein, South Africa, from children suffering from respiratory distress and severe acute respiratory infection between 2020 to 2021. Overlapping genome fragments were amplified and complete genomes were sequenced using the Illumina MiSeq platform. Maximum likelihood phylogenetic and evolutionary analysis were performed on both RSV-A/-B G-genes with published reference sequences from GISAID and GenBank. Our study strains belonged to the RSV-A GA2.3.2 and RSV-B GB5.0.5a clades. The upsurge of RSV was due to pre-existing strains that predominated in South Africa and circulating globally also driving these off-season RSV outbreaks during the COVID-19 pandemic. The variants responsible for the resurgence were phylogenetically related to pre-pandemic strains and could have contributed to the immune debt resulting from pandemic imposed restrictions. The deviation of the RSV season from the usual pattern affected by the COVID-19 pandemic highlights the need for ongoing genomic surveillance and the identification of genetic variants to prevent unforeseen outbreaks in the future.

Keywords: COVID-19 pandemic; Respiratory syncytial virus; Whole genome sequencing.

Fig. 1.1

Recombination analysis of the complete genome of the sequenced study strains. The consensus of non-recombinant RSV-A study strains was used as the reference whilst the consensus of RSV/B study strains is presented by “UFS-RSV-B”.

Fig. 1.2

Depiction of RSV epidemiology in South Africa. The key indicate the number of specimens tested and positive tests by year/week among children below 5 years over the period of 2016–2022. The red dotted line marks and represents the beginning of NPI's impelmentation in South Africa.

Fig. 1.3

Phylogenetic tree of major RSV-A clades generated using NextClade. Previously characterised South African taxa are represented by circles coloured based on clade. The strains from this study formed two separate clusters (indicated with black arrows) within GA2 clade GA2.3.5 sub-genotype.

Fig. 1.4

Phylogenetic tree of major RSV-B clades generated using NextClade. Previously characterised South African taxa are represented by circles coloured based on clade. The strains from this study formed two separate clusters (indicated with black arrows) within GB5 clade GB5.0.5a sub-genotype.

Fig. 1.5

Phylogenetic tree of global representative GA2.3.5 strains constructed by maximum likelihood method at 10000 bootstrap replicates. Study strains are indicated by a red circle. The bootstrap values are not displayed at the branch nodes of the tree. A detailed phylogenetic tree with bootstrap support shown is presented in Supplementary Figure 1S1. The phylogenetic tree is drawn to scale; the scale bar represents the number of nucleotide substitutions per site.

Fig. 1.6

Maximum likelihood phylogenetic tree Global G-Gene GB5.0.5a strains. Study strains sequenced in this study are shown in a red circle. A detailed phylogenetic tree with bootstrap support shown is presented in Supplementary Figure 1S2. The scale number indicates the number of nucleotide substitutions per site.

Fig. 1.7

The relative genetic diversity of South African GA2.3.5 and GB5.0.5a strains. A measure of relative genetic diversity is given on the y-axis with the 95 % highest posterior density shown in solid colour and the median as a dashed line.