Genomic and epidemiological surveillance of SARS-COV-2 variants during
the pre-mass vaccination period in Botucatu, Brazil
Abstract
The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) has
caused an unprecedented pandemic in human history. To date, more than
6.5 million lives have been lost to COVID-19 (coronavirus disease 2019).
Following widespread efforts for COVID-19 vaccination in Brazil, there
has been a drastic reduction in COVID-19 deaths, which was particularly
evident in the city of Botucatu, SP, Brazil, after a campaign to a mass
vaccination. Our objective was to assess the temporal and
epidemiological spread of Variants of Concern (VOC) of SARS-CoV-2 in the
four weeks preceding the massive vaccination campaign in the
municipality. After randomizing 400 samples, Next-Generation Sequencing
was used to produce sequences and determine the variants. Among
high-quality sequences, 98.4% belonged to the VOC Gamma, with P.1 and
P.1.14 being the most prevalent lineages. P.1 was more frequent in both
men and women, and in younger individuals and adults (0-59 years)
compared to P.1.14. There was no correlation between the variants and
the presence of comorbidities or between them and moderate to severe
clinical cases of COVID-19 or death. However, P.1 was more frequent than
P.1.14 in people with mild forms of the disease and in those who
exhibited symptoms. In the phylogenetic analyses, a small cluster of 9
P.1.14 samples containing mutations in ORF1a: M584V and A3620V was
observed, which had not been found in any Gamma sequences to date. The
importance of genomic surveillance of SARS-CoV-2 is evident in assisting
public health decision-making and the management of COVID-19 and other
diseases.