Objectives. This study aimed to evaluate the prevalence and distribution of dengue virus genotype V serotype 1 (DENV-1) and cosmopolitan genotype serotype 2 (DENV-2) in Peru between 2019 and 2022. Materials and methods. The envelope (E) gene region was amplified from 79 serum samples by polymerase chain reaction (PCR) and sequenced by next-generation sequencing (NGS) technology. The obtained sequences were subsequently analyzed with bioinformatics tools. Results. The study generated envelope gene sequences of DENV-1 and DENV-2 serotypes. Our study revealed a rapid dispersal and wide distribution of the cosmopolitan DENV-2 genotype in several regions of Peru in 2022, as well as the spread of DENV-1 genotype V to new Peruvian regions, along with the cosmopolitan DENV-2 genotype. Conclusions. Our findings suggest the urgent need to strengthen epidemiological and genomic surveillance systems to understand and control the spread of circulating DENV genotypes in Peru. This will allow a more rapid response, as well as the monitoring of its potential dissemination to other countries in the Americas.

Background: Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru. Methods: We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections. Results: There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases. Conclusions: We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru’s second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America. We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections.

Presentamos una descripción completa de la implementación de la vigilancia genómica del SARS-CoV-2 durante la pandemia por COVID-19 en el Perú, y el impacto que tuvo al aplicar esta tecnología en otros patógenos importantes para la salud pública del país. Con el objetivo de resaltar los logros, desafíos y lecciones aprendidas que permitan fortalecer la respuesta ante los retos sanitarios presentes y futuros a nivel nacional, así como las decisiones en salud pública. Con la iniciativa de vigilancia genómica liderada por el Instituto Nacional de Salud se ha logrado secuenciar 48 691 genomas de SARS-CoV-2 procedentes de todas las regiones del país desde el año 2020 al 2024, logrando la identificación de ocho variantes del virus y la designación de 25 linajes nuevos dentro de las variantes Gamma, Delta y Ómicron. La vigilancia genómica de SARS-CoV-2 ha permitido identificar oportunamente variantes de interés epidemiológico, monitorizar la evolución del virus en tiempo real y utilizar esta información como herramienta para la toma de decisiones en salud pública. Esta experiencia posteriormente brindó las bases para vigilar otros patógenos que han causado emergencias sanitarias en el Perú y el mundo, como el dengue, influenza y viruela símica.

Acute respiratory infections (ARIs) are diseases that significantly impact public health, traditional PCR panels often fail to detect acute respiratory infections (ARIs) due to unmonitored viruses, primer mismatches, or geographically isolated variants. To overcome these diagnostic limitations, the primary purpose of this study is to uncover hidden viral etiologies through a stringent mNGS bioinformatic algorithm. By applying untargeted metagenomic sequencing to 300 previously test-negative nasopharyngeal samples across diverse cohorts in Peru, this research aims to characterize undetected pathogens and support national genomic surveillance. Genomic material was amplified via sequence-independent single-primer amplification (SISPA) and sequenced using the Illumina platform. Following quality filtering and human read depletion, taxonomic identification was performed using Kraken2. A stringent custom filtration algorithm based on taxon-specific reads per million ratios (RPMr), SMNR and MAPQ thresholds. Unbiased mNGS of 300 test-negative respiratory samples revealed a viral landscape dominated by Coronaviridae (67.2%; predominantly SARS-CoV-2), followed by Picornaviridae (13.6%), Orthoherpesviridae (12.0%), Paramyxoviridae (5.6%), Anelloviridae (0.8%), and Adenoviridae (0.8%). Agnostic mNGS bypasses targeted assay limitations, revealing that 35.66% of previously negative samples contained hidden pathogens. This approach proves pivotal for respiratory virus surveillance, enhancing pathogen tracking and outbreak detection.