SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort

Abstract

Background Syndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. Methods We estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models. Findings Swabs taken at 32,937/1,352,979 (2.4%) assessments tested positive for SARS-CoV-2, 181/14,939 (1.2%) for RSV and 130/14,939 (0.9%) for influenza A/B, varying by age over time. Positivity and incidence peaks were earliest for RSV, then influenza A/B, then SARS-CoV-2, and were highest for RSV in the youngest and for SARS-CoV-2 in the oldest age-groups. Many test-positives did not report key symptoms: middle-aged participants were generally more symptomatic than older or younger participants, but still only ~25% reported ILI-WHO and ~60% ILI-ECDC. Most symptomatic participants did not test positive for any of the three viruses. Influenza A/B-positivity was lower in participants reporting influenza vaccination in the current and previous seasons (odds ratio=0.55 (95% CI 0.32,0.95)) versus neither season. Interpretation Symptom profiles varied little by aetiology, making distinguishing SARS-CoV-2, influenza and RSV using symptoms challenging. Most symptoms were not explained by these viruses, indicating the importance of other pathogens in syndromic surveillance. Influenza vaccination was associated with lower rates of community influenza test positivity. Funding UK Health Security Agency, Department of Health and Social Care, National Institute for Health Research.

Nanopore sequencing of influenza A and B in Oxfordshire and the United Kingdom, 2022-23

“…In total 130 samples were positive for influenza A/B (positivity=0.9%); these positive samples were obtained from study participants in England (n=106), Scotland (n=11), Northern Ireland (n=8), and Wales (n=5). Most participants had been vaccinated in the current and/or previous influenza season (n=90, 69%), most reported some form of symptoms at the point the swab was taken (n=86/124, 69%, data missing for 6, see 11 for details), there was an equal split of participant sexes (n=65 female/male) and a wide spread of ages ranging from ≤5 to ≥80 years, median range 30-40 years (IQR: 10-20 years, 50-60 years) (only age groups available). Median (IQR) Ct values on initial testing (combined influenza A/B) were 29.9 (27.3-32.1).…”

“…From October 2022, a random subset of ∼750 swabs received per week were additionally tested by multiplex PCR (ThermoFisher TaqPath™ COVID-19, Flu A/B, RSV ComboKit A49867); PCR results, symptoms and temporal patterns have been described previously. 11 Samples positive for influenza A/B were sent to the University of Oxford for sequencing, together with PCR results and sample metadata (age provided as groups).…”

“…The 996 influenza A or B positive samples identified by the OUH microbiology laboratory represented 941 infections in 940 unique patients (one patient had an influenza B infection 53 days after testing influenza A positive). Although serial samples were obtained from 42 patients (median [IQR] 8 [1][2][3][4][5][6][7][8][9][10][11][12] days between first and last samples), these were not routinely sequenced; only 2 pairs (obtained ≤1 days apart) were sequenced with 0 and 4 SNPs between HA segments and 10 and 8 SNPs between six segment alignments (excluding S2 and S3, as above).…”