Impact of Viral Co-Detection on the Within-Host Viral Diversity of Influenza Patients

Abstract

Numerous studies have documented the evidence of virus-virus interactions at the population, host, and cellular levels. However, the impact of these interactions on the within-host diversity of influenza viral populations remains unexplored. Our study identified 13 respiratory viral pathogens from the nasopharyngeal swab samples (NPSs) of influenza-like-illness (ILI) patients during the 2012/13 influenza season using multiplex RT-PCR. Subsequent next-generation sequencing (NGS) of RT-PCR-confirmed influenza A infections revealed all samples as subtype A/H3N2. Out of the 2305 samples tested, 538 (23.3%) were positive for the influenza A virus (IAV), while rhinovirus (RV) and adenoviruses (Adv) were detected in 264 (11.5%) and 44 (1.9%) samples, respectively. Among these, the co-detection of more than one virus was observed in ninety-six samples, and five samples showed co-detections involving more than two viruses. The most frequent viral co-detection was IAV-RV, identified in 48 out of the 96 co-detection cases. Of the total samples, 150 were processed for whole-genome sequencing (WGS), and 132 met the criteria for intra-host single-nucleotide variant (iSNV) calling. Across the genome, 397 unique iSNVs were identified, with most samples containing fewer than five iSNVs at frequencies below 10%. Seven samples had no detectable iSNVs. Notably, the majority of iSNVs (86%) were unique and rarely shared across samples. We conducted a negative binomial regression analysis to examine factors associated with the number of iSNVs detected within hosts. Two age groups-elderly individuals (>64 years old) and school-aged children (6-18 years old)-were significantly associated with higher iSNV counts, with incidence rate ratios (IRR) of 1.80 (95% confidence interval [CI]: 1.09-3.06) and 1.38 (95% CI: 1.01-1.90), respectively. Our findings suggest a minor or negligible contribution of these viral co-detections to the evolution of influenza viruses. However, the data available in this study may not be exhaustive, warranting further, more in-depth investigations to conclusively determine the impact of virus-virus interactions on influenza virus genetic diversity.

Keywords: A/H3N2; co-detection or co-infection; influenza.

Figure 1

Epidemic curve of the daily number of influenza-like illness (ILI) cases reported by the hospital influenza surveillance system.

Figure 2

Co-circulating viruses by season (A) and by age group (B). Each color represents the individual virus detected.

Figure 3

Maximum likelihood phylogenetic tree of WGS of A/H3N2 sequences in the 2012/13 influenza season. The co-detected virus, along with A/H3N2, was color-coded. Non-color-coded instances (black) are influenza-only cases.

Figure 4

Number of iSNVs per sample (A), number of iSNVs by segment for influenza-only cases versus co-detected cases (B), number of iSNVs by days of symptoms between the groups (C).