Cancela Florencia, Lizasoain Andrés, Panzera Yanina, Fernández-López Elena, Lozano Joaquín, Calleros Lucia, Grecco Sofia, Marandino Ana Eugenia, Cortinas María Noel, Masachessi Gisela, Nates Silvia, Icasuriaga Romina, Colina Rodney, Mirazo Santiago
Laboratorio de Ecología Viral y Virus Zoonóticos, Unidad Académica de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, 11600, Montevideo, Uruguay.
Laboratorio de Virología Molecular, Departamento de Ciencias Biológicas, Centro Universitario Regional Litoral Norte, Universidad de la República, 50000, Salto, Uruguay.
Food Environ Virol. 2025 Jan 9;17(1):14. doi: 10.1007/s12560-024-09629-9.
Human respiratory and enteric viruses are responsible for substantial morbidity and mortality worldwide. Wastewater-based epidemiology utilizing next-generation sequencing serves as an effective tool for monitoring viral circulation dynamics at the community level. However, these complex environmental samples are often laden with other microorganisms and host genomic material, which can hinder the sensitivity of viral detection. To address this limitation, targeted enrichment sequencing is emerging as a preferred strategy, facilitating the acquisition of a more comprehensive understanding of specific pathogens. In this study, we evaluated the performance of a targeted enrichment sequencing panel for 42 excreted respiratory viruses (including Picornaviridae, Adenoviridae, Coronaviridae, Paramyxoviridae, Orthomyxoviridae, Orthoherpesviridae, Pneumoviridae, and Parvoviridae families), known as the Respiratory Pathogen ID/AMR enrichment panel (RPIP), coupled with Explify bioinformatics analysis in 3 sewage samples from Uruguay. RPIP panel successfully identified sequences from frequently circulating viruses, along with some that had not been documented previously. We identified and characterized various viruses, including human Enterovirus (Coxsackievirus A1 and A19), Influenza A-H1N1, and full-length sequences of SARS-CoV-2. Additionally, several other viral pathogens were detected, such as human Bocavirus, human Parechovirus, Enterovirus A71, and Enterovirus D68; however, for these viruses further analysis was limited due to the small genomic regions or low-read coverage obtained. While the RPIP panel necessitates substantial sequencing depth and may introduce bias towards the more predominant strains present in the samples, this approach suggests its viability as a genomic epidemiological tool for assessing respiratory and enteric viruses in wastewater.
人类呼吸道和肠道病毒在全球范围内导致了大量发病和死亡。利用下一代测序技术的污水流行病学是监测社区层面病毒传播动态的有效工具。然而，这些复杂的环境样本往往含有其他微生物和宿主基因组物质，这可能会阻碍病毒检测的灵敏度。为了解决这一局限性，靶向富集测序正成为一种首选策略，有助于更全面地了解特定病原体。在本研究中，我们评估了一种针对42种排泄性呼吸道病毒（包括小RNA病毒科、腺病毒科、冠状病毒科、副粘病毒科、正粘病毒科、正疱疹病毒科、肺病毒科和细小病毒科）的靶向富集测序 panel，即呼吸道病原体ID/AMR富集 panel（RPIP），并结合Explify生物信息学分析，对来自乌拉圭的3份污水样本进行了检测。RPIP panel成功鉴定出了常见循环病毒的序列，以及一些先前未记录的序列。我们鉴定并表征了多种病毒，包括人肠道病毒（柯萨奇病毒A1和A19）、甲型H1N1流感病毒以及严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的全长序列。此外，还检测到了其他几种病毒病原体，如人博卡病毒、人帕里病毒、肠道病毒A71和肠道病毒D68；然而，由于获得的基因组区域较小或读数覆盖率较低，对这些病毒的进一步分析受到限制。虽然RPIP panel需要大量的测序深度，并且可能会对样本中更占优势的菌株产生偏差，但这种方法表明了其作为评估污水中呼吸道和肠道病毒的基因组流行病学工具的可行性。
