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Cepheid's Multi-Target Test Design Enables Detection of Influenza Variants

SUNNYVALE, Calif., Dec. 8, 2022 /PRNewswire/ -- Currently circulating mutant strains of influenza highlight the need for multi-target diagnostic tests. Two recently identified mutations in the matrix genes of the Human Influenza A virus have been reported to cause matrix gene target failure (MGTF) for several commercial diagnostic tests1. Cepheid's respiratory test design enables detection of these new variants, and with similar symptoms across various illnesses such as the flu, respiratory syncytial virus (RSV) disease, and COVID-19, an accurate and fast diagnosis is critical to patient care.

Variants of the (H1N1)pdm09 and A(H3N2) viruses containing matrix gene mutations are currently circulating around the world1. Recombination and other mutations of the viruses impact the performance of molecular diagnostic tests – which may lead to an increase in false negative test results. The greatest impact occurs in tests that detect only one genetic target of the influenza genome.2, 3

"In developing our portfolio of respiratory tests, we include multiple conserved gene targets to account for genetic drift within the influenza genome," said David Persing, M.D., Ph.D., EVP and Chief Scientific Officer of Cepheid. "The resulting target redundancy mitigates the impact of mutational drift. Our three-gene target design for detection of influenza A reduces the risk of false-negative test results, even in the event of an MGTF."

Cepheid's respiratory tests all utilize a multi-target approach for the detection of influenza, providing target redundancy to mitigate the potential impact of genetic shift and drift on strain detection:

  • Xpert Xpress Flu/RSV
  • Xpert Xpress SARS-CoV-2/Flu/RSV^
  • Xpert Xpress CoV-2/Flu/RSV plus^

Table 1. Influenza genes targeted by Cepheid tests

Influenza virus type



3-Gene Target Detection

  • Matrix (M)
  • Basic polymerase (PB2)
  • Acidic polymerase (PA)

2-Gene Target Detection

  • Matrix (M)
  • Non-structural (NS)

"The Medicines and Healthcare Products Regulatory Agency (MHRA), United Kingdom (UK) has asked all influenza test manufacturers in the UK to analyze their tests for any impact to diagnostic performance against the H1N1pdm09 strain. Our Scientific Affairs team performed in silico testing of the performance of our portfolio of influenza tests against the new H1N1pdm09 strain," said Mike Loeffelholz, Ph.D., D(ABMM) and Senior Director, Scientific Affairs. "Our analysis shows 100% predicted coverage for this strain."

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  1. Jørgensen RL, et al. Emergence of circulating influenza A H3N2 viruses with genetic drift in the matrix gene: be alert of false-negative test results. 2022. APMIS. 130(10): 612–617.
  2. Overmeire Y et al. Severe sensitivity loss in an influenza A molecular assay due to antigenic drift variants during the 2014/15 influenza season. 2016. Diagnostic Microbiology and Infectious Disease. 85(1):42-46.
  3. Binnicker MJ, et al. Identification of an Influenza A H1N1/2009 Virus with Mutations in the Matrix Gene Causing a Negative Result by a Commercial Molecular Assay.  2013. J Clinical Microbiology. 51(6):2006-2007.
About Cepheid

Based in Sunnyvale, Calif., Cepheid is a leading molecular diagnostics company. Cepheid is dedicated to improving healthcare by developing, manufacturing, and marketing accurate yet easy-to-use molecular systems and tests. By automating highly complex and time-consuming manual procedures, the company's solutions deliver a better way for institutions of any size to perform sophisticated molecular diagnostic testing for organisms and genetic-based diseases. Through its strong molecular biology capabilities, the company is focusing on those applications where accurate, rapid, and actionable test results are needed most, such as managing infectious diseases and cancer. For more information, visit

US-IVD and CE-IVD. In Vitro Diagnostic Medical Device.
^ For use under an Emergency Use Authorization in the United States.

For Cepheid Media Inquiries: 
Darwa Peterson 

SOURCE Cepheid

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