Stay-At-Home Orders Are Associated With Emergence of Novel SARS-CoV-2 Variants

Abstract

Background While public health strategies to contain the current coronavirus disease 2019 (COVID-19) pandemic are primarily focused on social distancing and isolation, emerging evidence suggest that in some regions social isolation failed to lead to further decrease in the number of COVID-19 deaths in the long run. This apparent paradox was particularly observed in the northern region of Brazil, in the state of Amazonas. We hypothesized that the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations, leading to more transmissible and pathogenic variants, could explain the lack of further reductions in COVID-19 new cases and related deaths in some regions. Our objective is to determine if social isolation is associated with the emergence of new SARS-CoV-2 variants, particularly the P.1 lineage and E484K mutants, in Brazil and in the state of Amazonas. Materials and methods We assessed the prevailing SARS-CoV-2 genomes present in Brazil available on the GISAID (Global Initiative on Sharing All Influenza Data) database collected between June 1, 2020, and January 31, 2021. Data regarding demographics, lineage, and prevalence of P.1 lineage and E484K mutations were obtained. Social isolation was measured using the Social Isolation Index (SII), which quantifies the percentage of individuals that stayed within a distance of 450 meters from their homes on a given day, between February 1, 2020, and January 24, 2021. The number of daily COVID-19 deaths was obtained from the Brazilian Ministry of Health (OpenDataSUS, 2021) between March 12, 2020, and January 10, 2021. SII was correlated with the prevalence P.1 lineage and E484K mutations in the eight following weeks. All univariate associations were estimated using the Spearman Correlation Index. 3D surfaces were employed to reflect the relationship between time, social isolation, and prevalence of genomic variants simultaneously. Results A total of 773 and 77 samples were obtained in Brazil and in the Amazonas state, respectively. In the state of Amazonas, SII on a given week was positively, significantly, and moderately or strongly (r > 0.6) correlated with the prevalence of both P.1 lineage and other E484K variants in the six following weeks after the SII on a given week. Conversely, in overall Brazil, correlations between SII and P.1 lineage and E484K variants were weaker and shorter, or negative, respectively. When SII was below 40%, P.1 lineage or E484K variants were not detected in the following weeks. When SII was above 40%, apparently exponential positive correlations between SII and prevalence of both P.1 lineage and E484K variants were observed. Conclusion The results of this study indicate that SII above 40% is associated with the emergence of SARS-CoV-2 E484K variants and P.1 lineage in the state of Amazonas, which was not observed in overall Brazil.

Public Health and Health Systems Impacts of SARS-CoV-2 Variants of Concern: A Rapid Scoping Review

“…We identified 10 studies which contributed data relevant to modifying infection-control procedures which are summarized in Table 4. Of these 10 studies, 8 were modeling, 50, 59–62 lab-based 63, 64 or grey literature 65 and thus not critically appraised. Of the two that were appraised, one was high quality, 27 and the other was medium quality.…”

“…Somewhat supporting that household transmission may be a key feature to monitor in VOC outbreaks, a study conducted by Zimerman et al in Brazil, reported contrasting findings in terms of outbreak management. 62 In their study comparing prevalence of the P.1 variant with social isolation data, authors found that prevalence of P.1 actually increased when individuals remained within 450m of their home. This study therefore highlights the need to tailor public health measures to specific populations and that vigilance regarding household transmission is warranted.…”

Rapid SARS-CoV-2 variant monitoring using PCR confirmed by whole genome sequencing in a high-volume diagnostic laboratory

“…The Variant PCR incorrectly interpreted several other lineages to be either B.1.1.7 or B.1.351/P1. Interestingly, all these wrongly interpreted lineages had biologically important mutations and were in fact “variants of interest” [21] . Sixteen samples defined as potentially B.1.1.7 by Variant PCR were B.1.525, a variant of interest, lacking the N501Y spike mutation but possessing the biologically important E484K mutation.…”

Pharmacological Treatment of Patients with Mild to Moderate COVID-19: A Comprehensive Review

“…Early COVID-19 treatment may be especially effective in developing countries where mass vaccination is in progress, but only on a small scale. In such countries, non-pharmacological measures to curb the pandemic are difficult to deploy because of social inequalities and illiteracy, and these methods might be associated with the appearance of dangerous SARS-CoV-2 variants [ 44 ], themselves a potential worldwide threat. Furthermore, in such countries, epidemiological surveys suggest that early COVID-19 treatment may be associated with decreased mortality [ 45 ].…”