Extensive multiplex PCR diagnostics reveal new insights into the epidemiology of viral respiratory infections

Abstract

Viral respiratory infections continue to pose a major global healthcare burden. At the community level, the co-circulation of respiratory viruses is common and yet studies generally focus on single aetiologies. We conducted the first comprehensive epidemiological analysis to encompass all major respiratory viruses in a single population. Using extensive multiplex PCR diagnostic data generated by the largest NHS board in Scotland, we analysed 44230 patient episodes of respiratory illness that were simultaneously tested for 11 virus groups between 2005 and 2013, spanning the 2009 influenza A pandemic. We measured viral infection prevalence, described co-infections, and identified factors independently associated with viral infection using multivariable logistic regression. Our study provides baseline measures and reveals new insights that will direct future research into the epidemiological consequences of virus co-circulation. In particular, our study shows that (i) human coronavirus infections are more common during influenza seasons and in co-infections than previously recognized, (ii) factors associated with co-infection differ from those associated with viral infection overall, (iii) virus prevalence has increased over time especially in infants aged <1 year, and (iv) viral infection risk is greater in the post-2009 pandemic era, likely reflecting a widespread change in the viral population that warrants further investigation.

Keywords: Co-infections; pandemic influenza; risk factor analysis; surveillance.

Fig. 1.

Trends in episodes of respiratory illness and viral infection prevalence in patients seeking healthcare services within NHS Greater Glasgow and Clyde during 2005–2013. (a) Episodes of respiratory illness tested in each month highlighting the three major waves of A(H1N1)pdm09 virus circulation. (b) Distribution of episodes across age groups in each 6-month period. (c) Age-specific prevalence of confirned viral infection and virus-negative illness detected in each 6-month period. (d) Relative prevalence of each viral infection and virus-negative illness (Neg) in each 6-month period; A, typical non-influenza period (April–September); B, typical influenza period (October–March). Note that January–March 2005 and October–December 2013 were excluded from panel (d).

Fig. 2.

Episodes of viral respiratory infection by patient subgroup. Distribution of each viral infection and virus-negative illness (Neg) by (a) age group, (b) gender, and (c) patient origin. These results are based on 26 974 patient episodes of respiratory illness; excluding patients tested during the major waves of influenza A(H1N1)pdm09 virus circulation. GP, General Practitioner's surgery; Hospital (general), outpatients and non-critical care patients; Hospital (critical care), patients admitted to an intensive care, intensive therapy, high dependency, or coronary care unit.

Fig. 3.

Distribution of virus-positive/negative episodes of illness and respiratory infection types detected in each calendar month. (a, b) Patients attending primary healthcare services (General Practitioners) and (c, d) patients attending secondary healthcare services (hospital inpatients and outpatients). These results are based on 26 974 patient episodes of respiratory illness; excluding patients tested during the major waves of influenza A(H1N1)pdm09 virus circulation.

Fig. 4.

Prevalence of severe cases in patients with confirmed viral infection attending primary and secondary healthcare facilities in NHS Greater Glasgow and Clyde during 2005–2013. Comparison across viral infection types and virus-negative patients (Neg). Absolute numbers of severe cases are indicated in parentheses. Severe cases were identified based on patients’ admission to intensive care, intensive therapy, high dependency or coronary care units.

Fig. 5.

Co-infection and virus mixing patterns in patients tested for all virus groups. Comparing mono-infection and co-infection distributions for each virus group in (a) children aged ⩽5 years, and (b) patients aged >5 years. (c) A network of co-infections: each node represents a respiratory virus and links between viruses are proportional to the frequency at which each virus pair was observed in co-infected patients. Viruses are coloured according to their prevalence in co-infections (darker represents greater prevalence). (d) Correlation between mono-infection and co-infection frequencies across virus groups; –––, Fitted linear regression model with corresponding R² value.

Fig. 6.

Stratification of viral infection and co-infection associations. Age-specific viral infection (a, b) and co-infection (c, d) prevalences stratified by gender and patient origin. Significant interactions with age are indicated by an asterisk (*).