Genetic Diversity Among SARS-CoV2 Strains in South America may Impact Performance of Molecular Detection

Pathogens
Juan David RamirezA. Paniz-Mondolfi

Abstract

Since its emergence in Wuhan (China) on December 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide. After its arrival in South America in February 2020, the virus has expanded throughout the region, infecting over 900,000 individuals with approximately 41,000 reported deaths to date. In response to the rapidly growing number of cases, a number of different primer-probe sets have been developed. However, despite being highly specific, most of these primer-probe sets are known to exhibit variable sensitivity. Currently, there are more than 300 SARS-CoV2 whole genome sequences deposited in databases from Brazil, Chile, Ecuador, Colombia, Uruguay, Peru, and Argentina. To test how regional viral diversity may impact oligo binding sites and affect test performance, we reviewed all available primer-probe sets targeting the E, N, and RdRp genes against available South American SARS-CoV-2 genomes checking for nucleotide variations in annealing sites. Results from this in silico analysis showed no nucleotide variations on the E-gene target region, in contrast to the N and RdRp genes which showed massive nucleotide variations within oligo binding sites. In lines with previous data, our res...Continue Reading

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Citations

Dec 23, 2020·Meta Gene·Manisha RayVinaykumar Hallur
Jan 29, 2021·Journal of Medical Virology·Juan D RamírezAlberto Paniz-Mondolfi
Dec 12, 2020·Emerging Microbes & Infections·Victoria ElizondoRalf Duerr
Dec 3, 2020·Revista Da Sociedade Brasileira De Medicina Tropical·Renan da Silva SantosKaio Cesar Simiano Tavares
Feb 23, 2021·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Marina MuñozJuan David Ramírez
Apr 30, 2021·Journal of Medical Virology·Carolina HernándezJuan David Ramírez
Apr 1, 2021·Genome Génome / Conseil National De Recherches Canada·Jayanta Kumar Das, Swarup Roy
Jul 3, 2021·International Journal of Molecular Sciences·Tapan BehlSimona Gabriela Bungau
Jul 1, 2021·Revista Do Instituto De Medicina Tropical De São Paulo·Karoline Rodrigues CamposAdele Caterino-de-Araujo
Jul 27, 2021·Computational and Structural Biotechnology Journal·Daniele MercatelliPietro Hiram Guzzi
Aug 29, 2021·Vaccines·Sergio CastañedaJuan David Ramírez

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Methods Mentioned

BETA
PCR
nucleic acid amplification

Software Mentioned

DnaSP
NexStrain
FastTree
MAFFT
IQtree
GISAID
Tree Of Life

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