SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene

Ziegler, Katharina; Steininger, Philipp; Ziegler, Renate; Steinmann, Jörg; Korn, Klaus; Ensser, Armin

doi:10.2807/1560-7917.es.2020.25.39.2001650

Cited by 121 publications

(147 citation statements)

References 10 publications

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“…An example of a run of the N-gene triplex RT-PCR is shown in Figure S2 . Both laboratory-developed assays were able to reliably detect a SARS-CoV-2-positive patient sample (data not shown) for which a discrepant RT-PCR was reported due to a single mutation in the N-gene [ 18 ]. The N-gene triplex RT-PCR was also tested against a commercial RT-PCR designed for simultaneous detection of N-gene, RdRp-gene and a control.…”

Section: Resultsmentioning

confidence: 99%

Performance of a Point-of-Care Test for the Rapid Detection of SARS-CoV-2 Antigen

Strömer

Rose

Schäfer³

et al. 2020

Microorganisms

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The rapid detection of infections caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is necessary in the ongoing pandemic. Antigen-specific point-of-care tests (POCT) may be useful for this purpose. Here, such a POCT (SARS-CoV-2 NADAL® COVID-19 Ag) was compared to a laboratory-developed triplex real-time polymerase chain reaction (RT-PCR) designed for the detection of viral nucleoprotein gene and two control targets. This RT-PCR served as a reference to investigate POCT sensitivity by re-testing upper respiratory tract (URT) samples (n = 124) exhibiting different SARS-CoV-2 loads in terms of RT-PCR threshold cycle (Ct) values. The optical intensities of the antigen bands were compared to the Ct values of the RT-PCR. The infectivity of various virus loads was estimated by inoculating Vero cells with URT samples (n = 64, Ct 17-34). POCT sensitivity varied from 100% (Ct < 25) to 73.1% (Ct ≤ 30); higher SARS-CoV-2 loads correlated with higher band intensities. All samples with a Ct > 30 were negative; among SARS-CoV-2 free samples (n = 10) no false-positives were detected. A head-to-head comparison with another POCT (Abbott, Panbio™ COVID-19 Ag Rapid Test) yielded similar results. Isolation of SARS-CoV-2 in cell-culture was successful up to a Ct value of 29. The POCT reliably detects high SARS-CoV-2 loads and rapidly identifies infectious individuals.

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Section: Resultsmentioning

confidence: 99%

Performance of a Point-of-Care Test for the Rapid Detection of SARS-CoV-2 Antigen

Strömer

Rose

Schäfer³

et al. 2020

Microorganisms

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“…Most available diagnostic tests have limitations and are being continuously subjected to research and development for improving accuracy and precision (Figure 1). 30,42–45 The SARS‐CoV‐2 is rapidly evolving and undergoing mutations, and for ensuring efficacy, the local strains should be sequenced at regular intervals and checked for the mutations that can impact RT‐PCR based diagnosis 46 . Recently, a point mutation has been identified in nucleoprotein gene of SARS‐CoV‐2 which resulted in false negative RT‐PCR test 46 .…”

Section: Discussionmentioning

confidence: 99%

Guidelines on newly identified limitations of diagnostic tools for COVID‐19 and consequences

Syal

2020

Journal of Medical Virology

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Coronavirus disease 2019 (COVID‐19) caused by coronavirus has spread worldwide and has become the deadliest pandemic of the 21st century. Such rapid spread is predominantly attributed to the poor diagnosis and its asymptomatic transmission. In the absence of treatment regime, timely diagnosis is the best available remedy that can restrict its spread. An early diagnosis of COVID‐19 is critical for determining the line of treatment and preventing long term complications in the infected subject. Unfortunately, available rapid antigen and antibody kits are known to be erroneous whereas reverse transcription polymerase chain reaction based tests are expensive, viral load dependent and at times inconclusive. In current scenario, the false‐negative results imposed a major risk to the individual patient care and also to the efforts for containing the spread at the population level, where as false positives are traumatic for families and can lead to improper treatment resulting in severe complications. In this article, the limitations of available diagnostic procedures have been elaborated and plausible combination approach has been advised.

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“…Furthermore, Ziegler et al. [ 80 ] found that a single nucleotide polymorphism (SNP) in the E gene SARS-CoV-2 from a patient interfered with detection in a widely used RT-PCR assay. Consequently, this underscores the necessity of targeting two independent essential genes of SARS-CoV-2 for reliable detection.…”

Section: Sars-cov-2 Mutations and Consequences On Laboratory Testsmentioning

confidence: 99%

“…Prior to the discovery of the ability of SARS-CoV-2 to be involved in a number of re-infection cases, there have been several notions that individuals who recovered from COVID-19 infection develop immunity and are protected against viral re-infection due to the presence of immunological response by serum neutralising immunoglobulins. The notion which was held by certain governments on the grounds that patients who recovered from COVID-19 were fortified against re-infection and could afford to travel as well as resume work during the pandemic was however, debunked by WHO on the basis of the lack of substantial evidence to confirm the relationship between neutralising antibodies and immunity against re-infection [ 80 ]. Despite this development, several studies have demonstrated that the viral RNA can replicate and diminish in numerical strength in body fluids of convalescent infected individuals for up to 12 weeks [ 81 ].…”

Section: Implications Of Sars-cov-2 Re-infections On Pandemic Controlmentioning

confidence: 99%

Understanding the implications of SARS-CoV-2 re-infections on immune response milieu, laboratory tests and control measures against COVID-19

Mustapha¹,

Abdullahi²,

Ajagbe³

et al. 2021

Heliyon

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SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene

Abstract: SARS-CoV-2 samples may escape detection because of a single point mutation in the N gene.

Cited by 121 publications

References 10 publications

Performance of a Point-of-Care Test for the Rapid Detection of SARS-CoV-2 Antigen

Performance of a Point-of-Care Test for the Rapid Detection of SARS-CoV-2 Antigen

Guidelines on newly identified limitations of diagnostic tools for COVID‐19 and consequences

Understanding the implications of SARS-CoV-2 re-infections on immune response milieu, laboratory tests and control measures against COVID-19

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