Dengue virus (DENV) is estimated to cause 390 million infections per year worldwide. A quarter of these infections manifest clinically and are associated with a morbidity and mortality that put a significant burden on the affected regions. Reports of increased frequency, intensity, and extended geographical range of outbreaks highlight the virus’s ongoing global spread. Persistent transmission in endemic areas and the emergence in territories formerly devoid of transmission have shaped DENV’s current genetic diversity and divergence. This genetic layout is hierarchically organized in serotypes, genotypes, and sub-genotypic clades. While serotypes are well defined, the genotype nomenclature and classification system lack consistency, which complicates a broader analysis of their clinical and epidemiological characteristics. We identify five key challenges: (1) Currently, there is no formal definition of a DENV genotype; (2) Two different nomenclature systems are used in parallel, which causes significant confusion; (3) A standardized classification procedure is lacking so far; (4) No formal definition of sub-genotypic clades is in place; (5) There is no consensus on how to report antigenic diversity. Therefore, we believe that the time is right to re-evaluate DENV genetic diversity in an essential effort to provide harmonization across DENV studies.

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

Dengue is an emerging public health threat in the United States, and currently, no FDA-approved rapid diagnostic test (RDT) is available. A reliable RDT could support timely clinical management and outbreak response. We evaluated nine commercially available dengue RDTs using 197 stored serum samples: 99 from acute laboratory-confirmed dengue cases, 88 negative by RT-PCR, IgM ELISA, and NS1 ELISA, and 10 from acute confirmed Zika cases. Test performance varied, with sensitivity ranging from 36%–82% and specificity from 78%–100%. The CTK Biotech and Artron tests showed the highest sensitivity (80% and 82%, respectively), but only CTK Biotech maintained high specificity (98%). Cross-reactivity with Zika virus was low (0%–20%). These findings suggest that RDTs could enhance dengue detection in clinical settings, though further validation under field conditions is warranted, and some of these tests may be suitable for regulatory approval, which could lead to broader availability and use.

The representativeness and timeliness of sentinel surveillance for endemic and emerging arboviral and respiratory diseases in low-resource settings are understudied. We compared laboratory-confirmed epidemic dengue, non-epidemic dengue, Zika, chikungunya, and COVID-19 (pre-Omicron and Omicron periods) cases reported in Puerto Rico’s Sentinel Enhanced Dengue Surveillance System (SEDSS) with island-wide trends reported by the Department of Health’s passive disease surveillance system (PADSS). We plotted trends over time to assess representativeness and used lagged cross-correlations to determine whether SEDSS reporting preceded PADSS. SEDSS trends were representative of island-wide trends for all pathogens. SEDSS preceded reporting in PADSS by up to three, eight, and two weeks for epidemic dengue, Zika, and pre-Omicron COVID-19, respectively. Increasing case trends for non- epidemic dengue and chikungunya occurred simultaneously in both systems. In Puerto Rico, sentinel surveillance was representative of island-wide trends and could provide early warning for dengue epidemics and emerging diseases, such as Zika, and COVID-19.

The representativeness and timeliness of sentinel surveillance for endemic and emerging arboviral and respiratory diseases in low-resource settings are understudied. We compared laboratory-confirmed epidemic dengue, non-epidemic dengue, Zika, chikungunya, and COVID-19 (pre-Omicron and Omicron periods) cases reported in Puerto Rico’s Sentinel Enhanced Dengue Surveillance System (SEDSS) with island-wide trends reported by the Department of Health’s passive disease surveillance system (PADSS). We plotted trends over time to assess representativeness and used lagged cross-correlations to determine whether SEDSS reporting preceded PADSS. SEDSS trends were representative of island-wide trends for all pathogens. SEDSS preceded reporting in PADSS by up to three, eight, and two weeks for epidemic dengue, Zika, and pre-Omicron COVID-19, respectively. Increasing case trends for chikungunya occurred at broadly similar times in both systems, while temporal concordance was lower for non-epidemic dengue. In Puerto Rico, sentinel surveillance was representative of island-wide trends and could provide early warning for dengue epidemics and emerging diseases, such as Zika and COVID-19.