Viruses (Nov 2023)

Influenza A, like Omicron SARS-CoV-2, Is Similarly Detected in Saliva or Nasopharyngeal Samples via RT-qPCR

  • Hellen Abreu,
  • Carla Adriane Royer,
  • Carolina Gracia Poitevin,
  • Ana Flávia Kohler,
  • Ana Carolina Rodrigues,
  • Sonia Mara Raboni,
  • Meri Bordignon Nogueira,
  • Pedro Henrique Cardoso,
  • Monica Barcellos Arruda,
  • Patrícia Alvarez da Silva Baptista,
  • Ana Claudia Bonatto,
  • Daniela Fiori Gradia,
  • Douglas Adamoski,
  • Emanuel Maltempi de Souza,
  • Jaqueline Carvalho de Oliveira

DOI
https://doi.org/10.3390/v15122352
Journal volume & issue
Vol. 15, no. 12
p. 2352

Abstract

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After the Coronavirus pandemic, the importance of virus surveillance was highlighted, reinforcing the constant necessity of discussing and updating the methods for collection and diagnoses, including for other respiratory viruses. Although the nasopharyngeal swab is the gold-standard sample for detecting and genotyping SARS-CoV-2 and Influenza viruses, its collection is uncomfortable and requires specialized teams, which can be costly. During the pandemic, non-invasive saliva samples proved to be a suitable alternative for SARS-CoV-2 diagnosis, but for Influenza virus the use of this sample source is not recognized yet. In addition, most SARS-CoV-2 comparisons were conducted before the Omicron variant emerged. Here, we aimed to compare Influenza A and Omicron RT-qPCR analysis of nasopharyngeal swabs and saliva self-collection in paired samples from 663 individuals. We found that both nasopharyngeal swab and saliva collection are efficient for the diagnosis of Omicron (including sub-lineages) and for Influenza A, with high sensitivity and accuracy (>90%). The kappa index is 0.938 for Influenza A and 0.905 for SARS-CoV-2. These results showed excellent agreement between the two samples reinforcing saliva samples as a reliable source for detecting Omicron and highlighting saliva as a valid sample source for Influenza detection, considering this cheaper and more comfortable alternative.

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