Key role of PCR amidst flu and ongoing COVID-19

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Predictable seasonal patterns of influenza viruses worldwide is the backbone of worldwide influenza surveillance systems and vaccination programs over the past several decades.

However, the public health measures implemented worldwide to contain the SARS-CoV-2 virus (between early 2020 and early 2022) resulted in a dramatic impact on the circulation of influenza and other respiratory viruses (Table 1).  The total absence (0) of influenza detections between March to June 2021, is in stark contrast to 3296 detections in 2019 (Table 1).

By Dr Sudha Pottumarthy-Boddu
Dr Sudha Pottumarthy-Boddu has a distinguished career in microbiology with extensive experience in the US New Zealand and Australia. Sudha is a Diplomate of the American Board of Medical Microbiology, and a member of both the Antimicrobial Stewardship Committees and Infection Prevention and Control Committees at multiple St John of God hospitals in WA. 

The gradual relaxation of public health measures in WA since March 2022, along with the resumption of international travel, has been associated with increasing influenza detections since March 2022 (2 in March, versus 593 in June, Table 2).

  • Australian National Notifiable Diseases Surveillance System (NNDSS) reported that influenza-like illness (ILI) activity has increased since March and peaked in May and June 2022.
  • 16,707 influenza notifications were reported to NNDSS in the fortnight ending July 17th, 2022, with 204,911 total notifications to date in 2022.
  • Influenza A notifications constituted 82.7 % of laboratory-confirmed influenza reported to NNDSS, of which 94.4% were influenza A (unsubtyped).
  • The weekly notifications of laboratory-confirmed influenza to NNDSS from mid-April 2022, has been reported to exceed the 5-year average. 
  • Summarising the United States influenza activity of 2021-2022, Centers for Disease Control and Prevention (CDC), reports that:
    • unlike the typical influenza season which begins in fall and peaks in February each year, in the 2021-22 season, influenza activity began to increase in November and remained elevated until mid-June;
    • it featured two distinct waves, with A(H3N2) viruses predominating for the entire season, with the second wave resulting in higher percentage of positive laboratory detections and higher number of hospitalisations than the first. 
  • The CDC further highlights the need to remain vigilant for influenza infections even in summer and stresses the ongoing need to perform testing for influenza viruses and monitoring for novel influenza A virus infections.
  • A recent report from UK noted that viral co-infections were noted in 8.4% of the 6965 patients with SARS-CoV-2 infections (227 had influenza viruses, 220 had RSV and 136 had adenovirus detections).
  • Despite the limitations acknowledged in the study, SARS-CoV-2 co-infection with influenza viruses, was associated with receipt of invasive mechanical ventilation, compared to SARS-CoV-2 mono-infection.
  • Testing guidance from CDC when SARS-CoV-2 and influenza viruses are co-circulating emphasizes the need for multiplex respiratory nucleic acid detection assay which includes both influenza A/B and SARS-CoV-2 viruses.
Why test for respiratory viruses?

The multiplex PCR to diagnose influenza and respiratory viral infections, including SARS-CoV-2 allows the clinician to have a rapid and accurate diagnosis. This will enable the clinician to initiate targeted treatment early, avoiding inappropriate antibiotic therapy.

The ongoing evolution in the trends of respiratory infections in the current winter of 2022, emphasizes the testing for a broad range of respiratory pathogens in addition to SARS-CoV-2, if clinically indicated. 

References on request

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