National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Disease, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China.
Sierra Leone-China Friendship Biological Safety Laboratory, Freetown, Sierra Leone.
Virol J. 2024 Aug 27;21(1):201. doi: 10.1186/s12985-024-02466-z.
The COVID-19 pandemic has underscored the critical role of sequencing technology in disease control and outbreak response. However, resource limitations and challenging environments often impede such efforts in low and middle-income countries. This study aimed to investigate the spectrum of viral co-infections, particularly with human viral pathogens, in SARS-CoV-2 positive individuals in Sierra Leone using metagenomic sequencing, evaluating the feasibility of utilizing this technology for epidemiological and evolutionary surveillance of pathogens related to public health in low-income environments.
We retrospectively collected and analyzed 98 nasopharyngeal swab specimens from SARS-CoV-2 positive individuals in Sierra Leone. Samples were pre-processed locally and transferred to China via FTA cards for metagenomic sequencing, which was performed using the Novaseq platform. The study focused on the identification of nasopharyngeal viruses co-infecting with SARS-CoV-2, with a deeper analysis of significant human viral pathogens such as HPV.
The study identified 22 viral taxa from 20 families, including 4 human viruses. Notably, 19.4% of samples showed HPV co-infection with 34 distinct types, predominantly beta and gamma HPVs. Multiple HPV types were found in individual samples, indicating a high complexity of viral co-infections.
The identification of a wide range of co-infecting viruses, particularly multiple HPV genotypes, highlights the complexity of viral interactions and their potential implications for public health. These findings enhance our understanding of viral co-infections and provide valuable insights for public health interventions in Sierra Leone. Further research is needed to explore the clinical significance of these findings and their impact on disease outcomes.
COVID-19 大流行突显了测序技术在疾病控制和疫情应对中的关键作用。然而，资源限制和挑战性的环境常常阻碍了中低收入国家的这些努力。本研究旨在通过宏基因组测序调查塞拉利昂 SARS-CoV-2 阳性个体中病毒合并感染的谱，特别是人类病毒病原体，评估利用该技术对低收入环境中与公共卫生相关的病原体进行流行病学和进化监测的可行性。
我们回顾性收集并分析了塞拉利昂 98 例 SARS-CoV-2 阳性个体的鼻咽拭子标本。样本在当地进行预处理，然后通过 FTA 卡转移到中国进行宏基因组测序，使用 Novaseq 平台进行。该研究重点关注与 SARS-CoV-2 合并感染的鼻咽病毒，对 HPV 等重要人类病毒病原体进行了更深入的分析。
研究从 20 个科的 22 个病毒分类群中鉴定出 4 种人类病毒。值得注意的是，19.4%的样本存在 HPV 合并感染，有 34 种不同的类型，主要是 beta 和 gamma HPV 型。在单个样本中发现了多种 HPV 类型，表明病毒合并感染的复杂性很高。
鉴定出广泛的合并感染病毒，特别是多种 HPV 基因型，突出了病毒相互作用的复杂性及其对公共卫生的潜在影响。这些发现增进了我们对病毒合并感染的理解，并为塞拉利昂的公共卫生干预措施提供了有价值的见解。需要进一步研究以探讨这些发现的临床意义及其对疾病结果的影响。
