Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru
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...
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| Lenguaje: | inglés |
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2026
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| _version_ | 1881700521016819712 |
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| author | Íris Terezinha Santos de Santana Silva Víctor Jimenez‐Vasquez Nancy Rojas Priscila Lope‐Pari Luis Barcena Omar Cáceres Maribel Huaringa Janet Otárola Johana Balbuena Pool Marcos-Carbajal Sila Ruiton Enrique Mamani Carlos Padilla |
| author_browse | Carlos Padilla Enrique Mamani Janet Otárola Johana Balbuena Luis Barcena Maribel Huaringa Nancy Rojas Omar Cáceres Pool Marcos-Carbajal Priscila Lope‐Pari Sila Ruiton Víctor Jimenez‐Vasquez Íris Terezinha Santos de Santana Silva |
| author_facet | Íris Terezinha Santos de Santana Silva Víctor Jimenez‐Vasquez Nancy Rojas Priscila Lope‐Pari Luis Barcena Omar Cáceres Maribel Huaringa Janet Otárola Johana Balbuena Pool Marcos-Carbajal Sila Ruiton Enrique Mamani Carlos Padilla |
| author_sort | Íris Terezinha Santos de Santana Silva |
| collection | Producción científica |
| description | 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. |
| format | Article |
| id | openalex:W7212807534 |
| institution | UPeU |
| language | English |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| record_format | dspace |
| spelling | openalex:W7212807534Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in PeruÍris Terezinha Santos de Santana SilvaVíctor Jimenez‐VasquezNancy RojasPriscila Lope‐PariLuis BarcenaOmar CáceresMaribel HuaringaJanet OtárolaJohana BalbuenaPool Marcos-CarbajalSila RuitonEnrique MamaniCarlos Padillaacute respiratory infectionsmetagenomic next-generation sequencingviral etiologySARS-CoV-2CoronaviridaepicornavirusParamyxoviridaeAnelloviridaeAdenoviridaeviral surveillancePeruoutbreak detectionRespiratory viral infections researchGenomics and Phylogenetic StudiesBacterial Identification and Susceptibility TestingAcute 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.Articlehttps://doi.org/10.3390/microbiolres17090178W7212807534enMicrobiology Research2036-74812036-74732026-09-14 |
| spellingShingle | acute respiratory infections metagenomic next-generation sequencing viral etiology SARS-CoV-2 Coronaviridae picornavirus Paramyxoviridae Anelloviridae Adenoviridae viral surveillance Peru outbreak detection Respiratory viral infections research Genomics and Phylogenetic Studies Bacterial Identification and Susceptibility Testing Íris Terezinha Santos de Santana Silva Víctor Jimenez‐Vasquez Nancy Rojas Priscila Lope‐Pari Luis Barcena Omar Cáceres Maribel Huaringa Janet Otárola Johana Balbuena Pool Marcos-Carbajal Sila Ruiton Enrique Mamani Carlos Padilla Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru |
| title | Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru |
| title_full | Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru |
| title_fullStr | Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru |
| title_full_unstemmed | Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru |
| title_short | Metagenomic Approach Reveals the Circulation of Pathogenic Viruses Associated with Respiratory Infections in Peru |
| title_sort | metagenomic approach reveals the circulation of pathogenic viruses associated with respiratory infections in peru |
| topic | acute respiratory infections metagenomic next-generation sequencing viral etiology SARS-CoV-2 Coronaviridae picornavirus Paramyxoviridae Anelloviridae Adenoviridae viral surveillance Peru outbreak detection Respiratory viral infections research Genomics and Phylogenetic Studies Bacterial Identification and Susceptibility Testing |
| topic_facet | acute respiratory infections metagenomic next-generation sequencing viral etiology SARS-CoV-2 Coronaviridae picornavirus Paramyxoviridae Anelloviridae Adenoviridae viral surveillance Peru outbreak detection Respiratory viral infections research Genomics and Phylogenetic Studies Bacterial Identification and Susceptibility Testing |
| url | https://doi.org/10.3390/microbiolres17090178 |
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