Circulation and Codetections of Influenza Virus, SARS-CoV-2, Respiratory Syncytial Virus, Rhinovirus, Adenovirus, Bocavirus, and Other Respiratory Viruses During 2022-2023 Season in Latvia

Abstract

This retrospective study analysed the routine data obtained by multiplex real-time RT-qPCR methods for respiratory virus detection. A total of 4814 respiratory specimens collected during 1 September 2022-31 August 2023 were included in the study. A total of 38% of the specimens were positive for at least one target, with the incidence maximum (82%) for the small children (age group 0-4 years). The five dominant virus groups were rhinovirus (RV, 12%), influenza virus A (IAV, 7%), adenovirus (AdV, 6%), respiratory syncytial virus (RSV, 5%), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, 5%). The specimens with multi-detections represented 19% of the positives, unevenly distributed (n = 225, 56, 43, 24) among the age groups 0-4, 5-14, 15-64, and 65< years, respectively. The dominant virus groups in multi-positive specimens were RV (53%), AdV (43%), and bocavirus (BoV, 35%)-in mutual pairs as well as all three together-followed by RSV (21%), and IAV (15%). Our study focused on the specimens with codetections and provides an insight into the variety of the respiratory virus interactions in Latvia during the first year since pandemic-related social restriction measures were eased. The observations also emphasise the need to consider the differentiation between rhinoviruses and enteroviruses, especially for the youngest patients in the age group 0-4.

Keywords: SARS-CoV-2; adenovirus; bocavirus; enterovirus; influenza viruses; patients’ median age; respiratory syncytial virus; respiratory viruses; rhinovirus.

Figure 1

The number of the specimens positive for adenovirus (AdV), bocavirus (BoV), coronviruses (CoV-229E, CoV-NL63, and CoV-OC43), enterovirus (EV), undifferentiated picornavirus group (EV/RV), influenza A virus (IAV), influenza B virus (IVB), metapneumovirus (MPV), parainfluenza virus 1/2/3/4 (PiV), respiratory syncytial virus A/B (RSV), rhinovirus (RV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) per each week from 1 September 2022 to 31 August 2023. Abbreviations: * EV tested until 31 January 2023; ** EV/RV not tested for the age group 0–4.

Figure 2

The number of the specimens with detected pairs of viruses in 88 virus combinations of two (upper part) or three and more (bottom part) during 1 September 2022–31 August 2023 (n > 10 painted in pink; negatives marked as gray “N”—not detected). Abbreviations: n = count of the multi-positive specimens (the total sum exceeds the number of the positive specimens since each incidence is recounted per virus involved); * EV tested until 31 January 2023; ** EV/RV undifferentiated picornavirus group (age group 0–4 not tested). A more detailed overview of these combinations is summarised in Table A5.

Figure 3

Difference matrices for the median age of the patients whose specimens tested positive per respiratory virus groups during 1 September 2022–31 August 2023 (A,E), the pre-epidemic (B,F), the influenza epidemic (C,G), and the post-epidemic (D,H). The upper parts of the matrices represent general positivity per target and the bottom parts represent multi-detections. The median age was measured in years (all age groups, A–D) and months (age group 0–4 years, E–H). The median age evaluated by the nonparametric Mann–Whitney U test; abbreviations of p values: * p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001; N p > 0.05; and “-” insufficient case count. Significant differences are coloured in blue and green for positives, and yellow for multi-detections. Abbreviation “∑ (other)” stands for a summarised group of all respiratory virus detections in a given timeframe without the positives for the respective virus group.