PP5 -Prevalence of co-infection with influenza A, influenza B and SARS-CoV-2 viruses among samples referred to the national laboratory in 2024

Abstract

Introduction   

Co-infection with respiratory pathogens, such as influenza and SARS-CoV-2, poses a significant challenge in clinical diagnosis and treatment. Understanding the prevalence and clinical characteristics of such cases is crucial for guiding effective healthcare interventions. The National Influenza Centre/Laboratory adopted testing all surveillance samples for both viruses, as recommended by the WHO, which was later expanded to include all clinical samples. This provides prevalence data from a larger sample and reflects the co-circulation of the viruses. 

Objectives

To determine the prevalence of co-infection with influenza and SARS-CoV-2 viruses among patient samples referred to the National Reference Respiratory Laboratory, Colombo.

Design, setting, and methods

All samples sent from OPD and in-ward patients from all over the country between January and December 2024 were tested using CDC in-house multiplex PCR, and Altona Diagnostics (IVD, CE) assays to detect influenza A/B and SARS-CoV-2. The analysis included patient demographics and clinical symptoms. Co-infection was defined as the simultaneous detection of both viruses in the same sample, and all those were sent to the WHO reference laboratory in Australia for confirmation.

Results

Out of the 5,364 samples analyzed, 23(0.42%) were confirmed as co-infected with SARS-CoV-2 and influenza A/B. Twelve were from the OPD, three from the intensive care/emergency treatment units, and eight from wards. This co-infected group consisted of 15 females and eight males, with ages ranging from 1 to 81 years (mean age: 32.5 years). The age groups were 1-12 years (5), 13-45 years (7), 46-65 years (6), and over 66 years (5). Most co-infected patients presented with fever 65% (15), cough 69% (16), sore throat 39% (9), shortness of breath 17% (4). The request forms did not mention the co-morbid factors of the co-infected patients. Twenty patients were co-infected with influenza A and SARS-CoV-2, and three with influenza B and SARS-CoV-2. The influenza A subtypes were H1 (13), H3 (4), and not typed (3). All influenza B cases (3) were of Victoria lineage.

Conclusion

The study highlights a very low prevalence of co-infection among this cohort. Continued routine testing for both viruses raises questions in a low-resource setting due to the significant costs involved.