Spotlight influenza: Extending influenza surveillance to detect non-influenza respiratory viruses of public health relevance: analysis of surveillance data, Belgium, 2015 to 2019

Abstract

Background Seasonal influenza-like illness (ILI) affects millions of people yearly. Severe acute respiratory infections (SARI), mainly influenza, are a leading cause of hospitalisation and mortality. Increasing evidence indicates that non-influenza respiratory viruses (NIRV) also contribute to the burden of SARI. In Belgium, SARI surveillance by a network of sentinel hospitals has been ongoing since 2011. Aim We report the results of using in-house multiplex qPCR for the detection of a flexible panel of viruses in respiratory ILI and SARI samples and the estimated incidence rates of SARI associated with each virus. Methods We defined ILI as an illness with onset of fever and cough or dyspnoea. SARI was defined as an illness requiring hospitalisation with onset of fever and cough or dyspnoea within the previous 10 days. Samples were collected in four winter seasons and tested by multiplex qPCR for influenza virus and NIRV. Using catchment population estimates, we calculated incidence rates of SARI associated with each virus. Results One third of the SARI cases were positive for NIRV, reaching 49.4% among children younger than 15 years. In children younger than 5 years, incidence rates of NIRV-associated SARI were twice that of influenza (103.5 vs 57.6/100,000 person-months); co-infections with several NIRV, respiratory syncytial viruses, human metapneumoviruses and picornaviruses contributed most (33.1, 13.6, 15.8 and 18.2/100,000 person-months, respectively). Conclusion Early testing for NIRV could be beneficial to clinical management of SARI patients, especially in children younger than 5 years, for whom the burden of NIRV-associated disease exceeds that of influenza.

Preparing for an influenza season 2021/22 with a likely co-circulation of influenza virus and SARS-CoV-2

“…Equally, the detection of other viruses causing respiratory symptoms can indicate unusual situations and provide important information for disease management, like in the case of respiratory syncytial virus (RSV) and the protection of vulnerable infants with monoclonal antibodies. Reagents for molecular detection of multiple respiratory pathogens are available from a number of commercial producers or in the form of in-house-designed multiplex PCR systems as described by Subissi at al [ 12 ]. Testing for other respiratory viruses besides influenza shows that they are a frequent cause of severe illness and of respiratory infections outside the usual influenza seasons [ 13 ].…”

Genomic monitoring of SARS‐CoV‐2 variants using sentinel SARI hospital surveillance

“…This should ideally involve an increase of the number of the participating hospitals to improve the catchment population and being more representative for the whole country but should also require better resources for sampling and faster sample shipment. Not only pandemic preparedness and response will be strengthened, but also the public health management of the yearly epidemics of a number of respiratory viruses will benefit from this system 27–29,56 . The performance of the SARI surveillance system can be increased by including different pathogen‐specific labs or institutions.…”

“…Although SARI surveillance is less timely and sensitive compared to the baseline genomic surveillance in its current format, it gives a well‐founded assessment on the disease impact of pathogen circulation in a country. This allows for monitoring of locally circulating viruses for antiviral sensitivity or strain identification for the vaccine composition for the upcoming season, both existing already for influenza and possibly applicable for SARS‐CoV‐2 and other pathogens as well 9,27–29,31,66–68 …”

“…Additionally, an active genomic surveillance was also set up to target specific indications, including unusual outbreaks, persisting infections in immunocompromised patients, and returning travelers from a zone at risk 23,24,26 . Patients hospitalized with severe acute respiratory infections (SARI) were at first not included in these indications, although being a very important group to evaluate the impact of SARS‐CoV‐2 on human health 27–30 …”

“…[27][28][29][30] Sentinel surveillance networks have been operating for influenza virus for many years. [27][28][29]31,32 In Belgium, SARI surveillance exists since 2012 and consists presently of a network of six hospitals sending respiratory samples and clinical information from patients fulfilling the case definition to the National Influenza Centre. In particular, SARI surveillance has proven to be very useful to evaluate the severity of infections caused by different respiratory viruses, including influenza virus.…”