Nucleotide Sequence Sharing between the Human Genome and Primers for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Detection

Abstract

This study shows that oligonucleotide sequences are shared between the human genome and primers that have been proposed/used for SARS-CoV-2 detection by polymerase chain reaction (PCR). The high level of sharing (namely, up to 19mer with a maximum number of gaps equal to 2) might bear implications for the diagnostic validity of SARS-CoV-2 detection by PCR.

Keywords

PCR primers - SARS-CoV-2 detection - false positives

Publication History

Received: 29 November 2021

Accepted: 29 December 2021

Article published online:
08 March 2022

• References

• 1 Kanduc D. Rare human codons and HCMV translational regulation. J Mol Microbiol Biotechnol 2017; 27 (04) 213-216
• 2 Kanduc D. Human codon usage: the genetic basis of pathogen latency. Glob Med Genet 2021; 8 (03) 109-115
• 3 Keita AK, Koundouno FR, Faye M. et al. Resurgence of Ebola virus in 2021 in guinea suggests a new paradigm for outbreaks. Nature 2021; 597 (7877): 539-543
• 4 Dayama P, Sampath K. Dengue disease outbreak detection. Stud Health Technol Inform 2014; 205: 1105-1109
• 5 Wu D, Wu T, Liu Q, Yang Z. The SARS-CoV-2 outbreak: what we know. Int J Infect Dis 2020; 94: 44-48
• 6 Patriquin G, Davidson RJ, Hatchette TF. et al. Generation of false-positive SARS-CoV-2 antigen results with testing conditions outside manufacturer recommendations: a scientific approach to pandemic misinformation. Microbiol Spectr 2021; 9 (02) e0068321
• 7 Benoit J, Benoit SW, Lippi G, Henry BM. False negative RT-PCR or false positive serological testing in SARS-CoV-2 diagnostics? Navigating between Scylla and Charybdis to prevent misclassification bias in COVID-19 clinical investigations. Diagnosis (Berl) 2020; 7 (04) 405-407
• 8 Verna R, Alallon W, Murakami M. et al. Analytical performance of COVID-19 detection methods (RT-PCR): scientific and societal concerns. Life (Basel) 2021; 11 (07) 660
• 9 Corman VM, Landt O, Kaiser M. et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveill 2020; 25 (03) 2000045
• 10 Surkova E, Nikolayevskyy V, Drobniewski F. False-positive COVID-19 results: hidden problems and costs. Lancet Respir Med 2020; 8 (12) 1167-1168
• 11 Eurosurveillance Editorial Team. Response to retraction request and allegations of misconduct and scientific flaws. Euro Surveill 2021; 26 (05) 2102041
• 12 Kanduc D. From anti-severe acute respiratory syndrome coronavirus 2 immune response to cancer onset via molecular mimicry and cross-reactivity. Glob Med Genet 2021; 8 (04) 176-182
• 13 Kanduc D. Thromboses and hemostasis disorders associated with coronavirus disease 2019: the possible causal role of cross-reactivity and immunological imprinting. Glob Med Genet 2021; 8 (04) 162-170
• 14 Kanduc D. From anti-SARS-CoV-2 immune responses to COVID-19 via molecular mimicry. Antibodies (Basel) 2020; 9 (03) 33
• 15 Kanduc D. From anti-SARS-CoV-2 immune response to the cytokine storm via molecular mimicry. Antibodies (Basel) 2021; 10 (04) 36
• 16 Altschul SF, Madden TL, Schäffer AA. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25 (17) 3389-3402
• 17 Boratyn GM, Thierry-Mieg J, Thierry-Mieg D, Busby B, Madden TL. Magic-BLAST, an accurate RNA-seq aligner for long and short reads. BMC Bioinformatics 2019; 20 (01) 405
• 18 Gadkar VJ, Goldfarb DM, Young V. et al. Development and validation of a new triplex real-time quantitative reverse Transcriptase-PCR assay for the clinical detection of SARS-CoV-2. Mol Cell Probes 2021; 58: 101744
• 19 Qasem A, Shaw AM, Elkamel E, Naser SA. Coronavirus disease 2019 (COVID-19) diagnostic tools: a focus on detection technologies and limitations. Curr Issues Mol Biol 2021; 43 (02) 728-748
• 20 Uniprot. Accessed November 2021 at: https://www.uniprot.org/uniprot/?query=proteome:UP000464024&sort=score