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

Juan David Ramírez,Esther C Barros,Carolina Hernández,Sergio Gomez,Alberto E Paniz-Mondolfi,Lisseth Pardo,Angelica Rico,Marina Muñoz,Carolina Flórez

doi:10.3390/pathogens9070580

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 results suggest that the 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.

Highlights

The Coronaviridae comprises a large family of pathogenic viruses that are generally transmitted person-to-person through respiratory secretions or the fecal-oral route, but may spread through zoonotic transmission [1]
Current classification by the Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTVs’) recognizes 39 species in 27 genera within the Coronaviridae family in the Nidovirales order which are known to infect a variety of vertebrates, including humans [4,5]
Verification of redundant sequences showed a total of 373 different genome sequences from the following seven South America countries: Argentina (n = 29), Brazil (n = 95), Colombia (n = 88), Ecuador (n = 4), Peru (n = 2), and Uruguay (n = 11)

Summary

Introduction

The Coronaviridae comprises a large family of pathogenic viruses that are generally transmitted person-to-person through respiratory secretions or the fecal-oral route, but may spread through zoonotic transmission [1]. Seven coronaviruses are known to infect humans—HKU1, NL63, OC43, and 229E, which have been associated to mild respiratory and gastrointestinal symptoms, as well as SARS-CoV, MERS-CoV, and the novel emerging SARS-CoV-2, which share similar zoonotic features and are linked to severe disease outcomes, often in the context of epidemic and pandemic settings [6]. The latter three, aside from sharing their host-switching capacity and zoonotic origin, have shown a propensity for increased pathogenicity. In the last two decades, the spillover of SARS-Coronavirus (SARS-CoV) in China (2002–2003), and MERS-Coronavirus (MERS-CoV) in the Middle East (2012–2016)

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Conclusion