Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil

Abstract

The emergence and widespread circulation of SARS-CoV-2 variants of concern (VOC) or interest (VOI) imposes an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates this variant has circulated locally since the first weeks of 2021 and only seven weeks were necessary for it to achieve a frequency above 70%, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates VOC Gamma spread throughout Brazil between December 2020 and January 2021, and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of RT-qPCR cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95% CI = ±0.7). This analysis corroborates the previously proposed mechanistic basis for this variant enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.

Delta Variant of SARS-CoV-2 Replacement in Brazil: A National Epidemiologic Surveillance Program

“…The pipeline for sequencing data processing was performed as previously described [ 17 ], which includes: (i) Filtering and trimming reads and adapters using fastp v.0.20.1 [ 20 ]; (ii) mapping the sequences with the reference genome (NCBI RefSeq SARS-CoV-2; accession number: NC_045512) with Bowtie2 v2.4.2 [ 21 ]; (iii) sorting and indexing the mapped files with SAMtools v1.12 [ 22 ]; (iv) variant calling and consensus genome inference using the BCFtools v1.12; and (v) mask sites with depth less than 10× with BEDtools v2.30.0. Sequences with less than 70% coverage were removed from the analysis [ 23 ].…”

“…These initiatives allowed the establishment of specific SARS-CoV-2 databases [ 13 ] that accelerated vaccine development [ 14 ]. Several regional initiatives have also emerged in Brazil to collect information associated with the COVID-19 pandemic [ 10 , 15 , 16 , 17 ]. However, due to its enormous territorial extension, a national unified genomic surveillance system is urgent to expand and connect the regional data in real-time.…”

Molecular dynamics of the COVID-19 pandemic in Espirito Santo (Brazil) and border States

“…In Brazil, the Zeta lineage was identified for the first time in July 2020 in RJ 23 , and it became predominant in this State from December 2020 until January 2021. This pattern changed after the emergence of the P.1 lineage, after its first detection 19 . As in RJ, in ES there was cocirculation of important lineages together with the Zeta lineage, such as B.1.1.33, B.1.1.28, Alpha and Gamma .…”

“…Lineages B.1.1.28 and B.1.1.33 had the highest percentages in the country (n=156, 31.01%, and 26.04%, respectively). In Rio de Janeiro, a study conducted with samples collected on December 1, 2020 and May 12, 2021 19 identified lineages P.2 (43.44%), P.1 (36.47), B.1.1 (5.73%), B .1 (3.69%), B.1.1.28 (3.28%), P.1.2 (3.28%), B.1.1.33 (1.23%), B.1.1.7 (1.23%), P.4 (0.82%, B.1,407 (0.41%) and N.9 (0.41%). The predominant lineage in Rio de Janeiro was Zeta , which occurred between December 2020 and January 2021, followed by P. 1, which was detected in the sixth week of 2021.…”

A SARS-CoV-2 negative antigen rapid diagnostic in RT-qPCR positive samples correlates with a low likelihood of infectious viruses in the nasopharynx

“…Illumina sequencing proceeded using two distinct protocols for library construction, as described in Orf et al (2021) and Moreira et al (2021). Briefly, viral RNA was converted to cDNA with SuperScript IV (ThermoFisher, USA) and whole genome amplification was performed with the ARTIC SARS-CoV-2 V3 primer panel and the Q5 hotstart polymerase (NewEnglandBiolabs, USA).…”