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Abstract
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). RT-PCR uses reverse transcription of RNA into complementary DNA (cDNA) and amplification of specific DNA (primer and probe) targets using polymerase chain reaction (PCR). The technology makes rapid and specific identification of the virus possible based on sequence homology of nucleic acid sequence and is much faster than tissue culture or animal cell models. However the technique can lose sensitivity over time as the virus evolves and the target sequences diverge from the selective primer sequences. Different primer sequences have been adopted in different geographic regions. As we rely on these existing RT-PCR primers to track and manage the spread of the Coronavirus, it is imperative to understand how SARS-CoV-2 mutations, over time and geographically, diverge from existing primers used today. In this study, we analyze the performance of the SARS-CoV-2 primers in use today by measuring the number of mismatches between primer sequence and genome targets over time and spatially. We find that there is a growing number of mismatches, an increase by 2% per month, as well as a high specificity of virus based on geographic location.
Highlights
Rapid tests for active SARS-CoV-2 infections are based on reverse transcription polymerase chain reaction (RT-PCR)
This study investigates the effectivity of current SARS-CoV-2 PCR tests over the development of the virus in space and time, and projects how the performance of each may change as the virus undergoes mutation
Using the methods described below, we observed high sequence homology for at least 95% of all genomes for most of the PCRs, showing that each primer is able to detect most of the SARS-CoV-2 genomes sequenced at the time of this report
Summary
Rapid tests for active SARS-CoV-2 infections rely on reverse transcription polymerase chain reaction (RT-PCR). Rapid tests for active SARS-CoV-2 infections are based on reverse transcription polymerase chain reaction (RT-PCR). These tests consist of a forward primer, reverse primer, and probe that together are used to amplify the signal from the targeted virus within a sample. By analyzing the number of mismatches of the PCR primers with respect to the sequenced SARS-CoV-2 genomes, we can measure how the targeted proteins are mutating. This provides an understanding of possible shortcomings of current tests, and suggests how often we may need to update those tests in the future. The SARS-CoV E protein forms a Ca2+ permeable ion channel that alters homeostasis within cells which leads to the overproduction of IL-1beta[10,11]
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