Home News Newsletters 2022 Newsletters Discrepancy in COVID-19 results explained

Discrepancy in COVID-19 results explained


I tested positive for COVID-19, I did another swab test and it came out negative. How is that possible?

  • The PCR (polymerase chain reaction) test for SARS-CoV-2, which is the virus that causes COVID-19 infection, is robust and very specific.
  • False positives results rarely occur because the specificity of the test (ability to differentiate SARS-CoV-2 from other viruses) is quite high - this means a positive PCR result on a sample is a real positive result.
  • The sensitivity of the PCR test can vary and be lower - meaning that some negative results may be false negatives whereby some people who are truly infected may test negative yet they are positive.
  • False negative results are especially true for people with early infection, asymptomatically infected individuals who have lower quantities of the virus and those recovering from mild illness while having lower quantities of virus in their nose, nasopharyngeal, throat and the lining of the airwaves.
  • Additionally, intermittent viral shedding may occur in the respiratory tract lining of the nasal passage and throat thus the amount of viral material collected on swabs taken in quick succession and tested in the same laboratory or in different laboratories can actually yield different results. Sequential testing is not recommended for a negative result if there are clinical reasons to suspect infection.
  • Results between different laboratories can also vary due to the sensitivity and the specificity of the assay (type of PCR kit and machines used), with some assays having better performance at detecting very low levels of SARS-CoV-2 than others, therefore a low level of virus can be missed during analysis if the sensitivity is low. Likewise sample handling and quality assurance in the lab can affect a result.
  • Generally speaking, a positive SARS-CoV-2 result supersedes a negative result if the two are done within a short time-interval of each other, and any positive result should be used to guide isolation and contact tracing.
  • If a result is suspected to be false, it is best to communicate with the laboratory to have the result audited and conrmed as having no errors, then have the results correlated to the individual circumstances to inform follow-up testing under relevant conditions based on the clinical indications for re-testing.

About SARS-CoV-2 PCR Testing at Pathologists Lancet Kenya (PLK)

  • Pathologists Lancet Kenya currently has capacity to process between 270 - 450 samples a day with room to scale up to over 1,000 samples a day as demand may dictate. We have conducted over 10,000 tests to date. Our PCR lab is ISO 15189 accredited and has undertaken validation of the SARS-CoV-2 test kits with National Influenza Centre (NIC) and the Lancet Laboratories in South Africa which are also ISO 15189 accredited by SANAS.
  • PLK participates in LGC Thistle external quality assurance (EQA) scheme for proficiency testing to ensure the quality of the analysis and has scored excellent results in the recent EQA round.
  • The assay used at PLK is FDA-approved for highly accurate results. The Seegene Allplex assay has Consistently shown a very good sensitivity compared to most other assays, and from the experience on several occasions we have detected SARS-CoV-2 where other assays yielded negative results.

SARS-CoV-2 Molecular Evaluation by Foundation for Innovative New Diagnostics (FIND) - A Global Non-Prot Organization

  • Results just released from FIND conrm Seegene Allplex assay for SARS-CoV-2 has 100% sensitivity and 100% specicity performing better than most other assays including Altona and similar kits that use E-gene and ORF1/S-gene
  • FIND conducted independent evaluations at the Hôpitaux Universitaires de Genève, to verify the limit of detection (LOD) and the clinical performance (as reported by the manufacturers) of the following molecular test kits.
  • The LOD analysis was performed using cultured viral stocks from a clinical isolate from Switzerland, and quantied using an E gene standard.
  • The clinical performance analysis was conducted on extracted samples from individuals suspected to have COVID-19 that were tested using an in-house PCR protocol that was optimized based on the Tib Molbiol assay.

For more details on the data for the first test evaluated see data on their website:

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