Your browser doesn't support javascript.
Analysis and forecasting of global real time RT-PCR primers and probes for SARS-CoV-2.
Nayar, Gowri; Seabolt, Edward E; Kunitomi, Mark; Agarwal, Akshay; Beck, Kristen L; Mukherjee, Vandana; Kaufman, James H.
  • Nayar G; IBM Research, San Jose, 95120, USA. Gowri.Nayar@ibm.com.
  • Seabolt EE; IBM Research, San Jose, 95120, USA.
  • Kunitomi M; IBM Research, San Jose, 95120, USA.
  • Agarwal A; IBM Research, San Jose, 95120, USA.
  • Beck KL; IBM Research, San Jose, 95120, USA.
  • Mukherjee V; IBM Research, San Jose, 95120, USA.
  • Kaufman JH; IBM Research, San Jose, 95120, USA.
Sci Rep ; 11(1): 8988, 2021 04 26.
Article in English | MEDLINE | ID: covidwho-1203449
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
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.
Subject(s)

Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA Probes / DNA Primers / Reverse Transcriptase Polymerase Chain Reaction / SARS-CoV-2 Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-88532-w

Similar

MEDLINE

...
LILACS

LIS


Full text: Available Collection: International databases Database: MEDLINE Main subject: DNA Probes / DNA Primers / Reverse Transcriptase Polymerase Chain Reaction / SARS-CoV-2 Language: English Journal: Sci Rep Year: 2021 Document Type: Article Affiliation country: S41598-021-88532-w