Genomic surveillance of SARS-CoV-2 in Puerto Rico enabled early detection and tracking of variants

Abstract

Background Puerto Rico has experienced the full impact of the COVID-19 pandemic. Since SARS-CoV-2, the virus that causes COVID-19, was first detected on the island in March of 2020, it spread rapidly though the island’s population and became a critical threat to public health. Methods We conducted a genomic surveillance study through a partnership with health agencies and academic institutions to understand the emergence and molecular epidemiology of the virus on the island. We sampled COVID-19 cases monthly over 19 months and sequenced a total of 753 SARS-CoV-2 genomes between March 2020 and September 2021 to reconstruct the local epidemic in a regional context using phylogenetic inference. Results Our analyses reveal that multiple importation events propelled the emergence and spread of the virus throughout the study period, including the introduction and spread of most SARS-CoV-2 variants detected world-wide. Lineage turnover cycles through various phases of the local epidemic were observed, where the predominant lineage was replaced by the next competing lineage or variant after ~4 months of circulation locally. We also identified the emergence of lineage B.1.588, an autochthonous lineage that predominated in Puerto Rico from September to December 2020 and subsequently spread to the United States. Conclusions The results of this collaborative approach highlight the importance of timely collection and analysis of SARS-CoV-2 genomic surveillance data to inform public health responses.

SARS-CoV-2 Omicron Replacement of Delta as Predominant Variant, Puerto Rico

“…S ince the arrival of SARS-CoV-2 in Puerto Rico in March 2020, epidemic waves of COVID-19 have occurred on the island during the emergence of several variants of concern. Genomic surveillance conducted by partnered public health and academic groups reported an epidemic wave caused by the Alpha variant in April 2021, which coincided with the vaccination campaign for adults (1). Despite the detection of other variants of interest or concern, circulation of most of those variants was limited.…”

“…To elucidate the emergence of the Omicron variant and subsequent replacement of Delta as the predominant variant, we used a phylogenetic approach to reconstruct the SARS-CoV-2 epidemic in Puerto Rico (Figure). We sequenced 2,377 SARS-CoV-2 complete genomes directly from reverse transcription PCRpositive diagnostic samples collected in Puerto Rico during the study period (1). We conducted time-calibrated phylogenetic analyses locally using the ncov augur/auspice pipeline (https://docs.nextstrain.…”

Routes of importation and spatial dynamics of SARS-CoV-2 variants during localised interventions in Chile

“…Similarly, in South Africa epidemic waves were driven by emerging and imported VOCs; starting with Beta, followed by Delta and finally Omicron (6,7). Given the high connectivity of various South American countries with European countries and US states (18,31,46,47), SARS-CoV-2 lineages that were dominant in the northern hemisphere heavily influenced the viral lineage composition of the region during the early epidemic waves (48)(49)(50)(51)(52)(53)(54)(55)(56)(57). Nonetheless, locally emerging variants played an important role in the viral dynamics of the continent, as exemplified by the emergence and spread of Gamma (5,58).…”

Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic

“…Especially in island nation settings, the clinical and epidemiological relevance of these new genetic combinations is substantial, since they may provoke the emergence of autochthonous variants ( 15 , 16 ). With continuing high global transmission rates, inequitable vaccine access and coverage and numerous long-term infections in immunosuppressed hosts present high risks for emerging SARS-CoV-2 variants.…”