High Rate of Mutational Events in SARS-CoV-2 Genomes across Brazilian Geographical Regions, February 2020 to June 2021

Abstract

Brazil was considered one of the emerging epicenters of the coronavirus pandemic in 2021, experiencing over 3000 daily deaths caused by the virus at the peak of the second wave. In total, the country had more than 20.8 million confirmed cases of COVID-19, including over 582,764 fatalities. A set of emerging variants arose in the country, some of them posing new challenges for COVID-19 control. The goal of this study was to describe mutational events across samples from Brazilian SARS-CoV-2 sequences publicly obtainable on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) platform and to generate indexes of new mutations by each genome. A total of 16,953 SARS-CoV-2 genomes were obtained, which were not proportionally representative of the five Brazilian geographical regions. A comparative sequence analysis was conducted to identify common mutations located at 42 positions of the genome (38 were in coding regions, whereas two were in 5′ and two in 3′ UTR). Moreover, 11 were synonymous variants, 27 were missense variants, and more than 44.4% were located in the spike gene. Across the total of single nucleotide variations (SNVs) identified, 32 were found in genomes obtained from all five Brazilian regions. While a high genomic diversity has been reported in Europe given the large number of sequenced genomes, Africa has demonstrated high potential for new variants. In South America, Brazil, and Chile, rates have been similar to those found in South Africa and India, providing enough “space” for new mutations to arise. Genomic surveillance is the central key to identifying the emerging variants of SARS-CoV-2 in Brazil and has shown that the country is one of the “hotspots” in the generation of new variants.

Repurposing Antifungals for Host-Directed Antiviral Therapy?

“…The ongoing pandemic with high mortality and morbidity rates highlights the urgent need for safe and fast development of new pharmaceutics to combat newly emerging viral infections [2,3]. While the ultrafast development of vaccines to fight SARS-CoV-2 has been an unprecedented success story, the high mutation rates leading to rapidly changing viral genomes also require a continuous update of vaccines [4][5][6]. Moreover, antigenic shift, i.e., the recombination of viral genomes and the appearance of new viral subtypes, is a great public health concern [5,6].…”

“…While the ultrafast development of vaccines to fight SARS-CoV-2 has been an unprecedented success story, the high mutation rates leading to rapidly changing viral genomes also require a continuous update of vaccines [4][5][6]. Moreover, antigenic shift, i.e., the recombination of viral genomes and the appearance of new viral subtypes, is a great public health concern [5,6]. Thus, antiviral drugs are essential for the management and control of viral infections to fill the gap until virus-specific routine immunization strategies are available.…”

“…Viral replication depends on the synthesis of viral components using the existing or modified host cell organelles (4) and the release of the newly assembled virions from the host cell via either exocytosis of virion-containing vesicles (5a) or budding (5b). To support the viral replication, viruses modulate cellular signaling pathways, such as the Wnt, Shh, VEGF, and mTORC1 signal transduction pathways(6). Repurposed drugs might target (i) viral interaction with cellular membranes (during virus internalization, assembly, release), (ii) translation and modification of viral proteins, and (iii) cellular signaling pathways hijacked by the virus to suppress virus detection and…”

Research Article Optimization of Illumina AmpliSeq protocol for SARS-CoV-2 and detection of circulating variants in Goiás State, Brazil from November 2020 to July 2021

“…In Brazil, some studies of SARS-CoV-2 at the genomic level were performed aiming at identifying the circulating variants (Candido et al, 2020;Xavier et al, 2020;Botelho-Souza et al, 2021;de Souza et al, 2021;Faria et al, 2021;LaMarcus et al, 2022). In March and April 2020, about 500 samples, mostly from the states of Rio de Janeiro and São Paulo (southeast Brazil), were classified into three distinct clades; lineage B was predominant (Candido et al, 2020).…”

Special Issue “Viral Infections in Developing Countries”

“…Paiva et al [2] sequenced 101 strains of SARS-CoV-2 from patients presenting COVID-19 symptoms that reside in Pernambuco and showed multiple introductions followed by the ongoing community spread of SARS-CoV-2 at one of the largest metropolitan areas of Northeast Brazil. In another study, de Souza et al [3] described mutational events across samples from Brazilian SARS-CoV-2 sequences available on Global Initiative on Sharing Avian Influenza Data-EpiCoV (GISAID-EpiCoV) [4] and estimated the number of genomes necessary to report a new variant. The authors also reported that the virus genomic diversity detected in Brazil and Chile in South America was similar to that detected in South Africa and India, and all represent potential hotspots for the generation of new variants, especially when social restrictions are not strictly applied, leading to increased viral circulation.…”