Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil

Abstract

Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves

“…Different sequencing efforts have been employed by Brazilian states thus resulting in differing numbers of available genomes for each state/region (totalizing n=113,681 complete genome sequences available as of 19 th February 2022), thus struggling our ability to describe in detail the progression of the epidemic in the country. Considering that since the beginning of the epidemic sustained lineage replacements over time have been observed ( Giovanetti et al, Oct 2021 , Giovanetti et al, Dec, 2021 ), our study reinforces how important it is to strengthen genomic monitoring in order to follow local time evolution of this viral pathogen.…”

“…The first wave from February 2020 to November 2020 was characterized by the co-circulation of different lineages because of multiple introduction events occurring through time ( Fig. 2 A ) ( Giovanetti et al, Oct 2021 ). The second epidemic wave (December 2020 up to December 2021) was fuelled by the emergence and circulation of several VUMs, such as P.2 (i.e., Zeta), and VOCs such as Gamma (i.e., P.1), which started to be detected from January 2021 ( Fig.…”

“…In Brazil, the COVID-19 epidemic had huge impact. According to the National health report Brazil reported more than 27 million confirmed cases and a death toll exceeding 640 thousand by the end of February of 2022, making it one of the countries hardest hit by COVID-19 pandemic ( World Health Organization 2022 , Giovanetti et al, Oct 2021 ).…”

Replacement of the Gamma by the Delta variant in Brazil: impact of lineage displacement on the ongoing pandemic

“…The first months of the Brazilian epidemic were fuelled by the circulation of multiple lineages, as a direct consequence of multiple viral independent introductions from overseas. As the epidemic progressed, the observed large-scale community transmission led to local emergence of VOCs and VUMs 23 . These variants dominated the end of the first and second epidemic wave in the country, resulting in an exponential increase in the number of daily cases and deaths, making Brazil one of the countries hardest hit by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic worldwide.…”

Genomic monitoring unveils a high prevalence of SARS-CoV-2 Omicron variant in vaccine breakthrough cases

“…( Table 1 ). The preparation of SARS-CoV-2 genomic libraries was performed using the nanopore sequencing technology 8 . The SuperScript IV Reverse Transcriptase kit (Invitrogen, USA) was initially used for cDNA synthesis, following the manufacturer’s instructions.…”