Genetic diversity among SARS-CoV2 strains in South America may impact performance of Molecular detection

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 700 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 results suggest that E-gene stands as the most conserved and reliable target when considering single-gene target testing for molecular diagnosis of SARS-CoV-2 in South America.

Saliva Sampling and Its Direct Lysis, an Excellent Option To Increase the Number of SARS-CoV-2 Diagnostic Tests in Settings with Supply Shortages

“…Samples were taken from ambulatory patients in the respiratory triage of the Tlaltenango health center in Cuernavaca, Morelos, Mexico. The RT-qPCR Berlin protocol was used to detect SARS-CoV-2, using only the primers and probe for gene E, since previous studies have shown a weak detection of viral RNA when the RNA-dependent RNA polymerase (RdRp) gene is probed (9,10). As an internal control of RNA content in the samples, the RNase P gene was detected.…”

Saliva sampling is an excellent option to increase the number of SARS CoV2 diagnostic tests in settings with supply shortages

“…Samples were taken from ambulatory patients in the respiratory triage of the Tlaltenango health center, in Cuernavaca, Morelos. The RT-qPCR Berlin protocol was used to detect SARS-CoV-2, using only the primers and probe for gene E, since previous studies have shown a weak detection of viral RNA when the RdRp gene is probed [10][11]. As an internal control of RNA content in the samples, the RNase P gene was detected.…”

Essential interpretations of bioinformatics in COVID-19 pandemic

“…have represented novel insights in case of SARS-CoV-2 experiments by accurately detect and quantify rare viral variants within the species ( Khailany et al, 2020 ; Ellinghaus et al, 2020 ; Aiewsakun et al, 2020 ; Ray et al, 2020a ) ( Table 4 ). In addition to the SNP analysis, the incorporation of haplotype diversity analysis with phylogenetic analysis has been frequently used in the SARS-CoV-2 research analyses to study the evolution and population demography of SARS-CoV-2 globally ( Ramírez et al, 2020 ; Fang et al, 2020 ). The molecular and evolutionary relationship with other coronavirus species, closely related species identification etc.…”

“…in drug discovery and development ( Song et al, 2009 ). Also, the additional benefits like cost-saving, time to market, in-sight knowledge of drug-receptor interaction, speed up in drug discovery and development increases its popularity in scientific researches ( Ramírez et al, 2020 ).…”