Effect of wastewater collection and concentration methods on assessment of viral diversity
Effect of wastewater collection and concentration methods on assessment of viral diversity
复制标题
废水收集和浓缩方法对病毒多样性评估的影响
DOI：
10.1016/j.scitotenv.2023.168128
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发表时间：
2023
影响因子：
9.8
通讯作者：
Xagoraraki, Irene
中科院分区：
文献类型：
--
作者：
Li, Yabing;Miyani, Brijen;Childs, Kevin L.;Shiu, Shin-Han;Xagoraraki, Irene
监测废水中可能致病的人类病毒对于了解社区疾病趋势、预测潜在疫情以及提高公共卫生部门的防备和应对能力至关重要。高通量元基因组测序为扩大废水监测能力提供了机会。然而，在元基因组支持的废水监测中存在着主要的瓶颈，包括选择适当的采样和浓缩/病毒浓缩方法的复杂性，以及对低人类病毒浓度的复杂样本的生物信息学分析。为了评价两种常用的采样和浓缩方法在病毒鉴定中的能力，比较了病毒吸附-洗脱(VIRADEL)和聚乙二醇法(PEG)浓缩的病毒群落在3个截留点的能力。结果表明，VIRADEL浓缩法获得的病毒读数较多，样品中病毒读数为2.84±0.57%。聚乙二醇法浓缩的样本，病毒读数在样本中的平均比例为0.63%±0.19%。在所有的废水样品中，隶属于噬菌体家族的噬菌体是丰富的种群。与自定义的Swiss-Prot人类病毒数据库的比较表明，VIRADEL方法浓缩的样本中相对丰富的人类病毒(在人类病毒群落中的平均比例大于1.00%)是正痘病毒、流行性感冒病毒、副痘病毒、水痘病毒、肝炎病毒、单纯疱疹病毒、软体痘病毒、副冠状病毒、淋巴病毒和Spuma病毒。在用聚乙二醇法浓缩的样本中，发现较少的人类病毒相对丰富。它们是正痘病毒、流行性出血热病毒、水痘病毒、单纯疱疹病毒、软体水痘病毒、淋巴分泌病毒和贝塔冠状病毒。在VIRADEL和聚乙二醇样品中发现了含有SARS冠状病毒2(SARS-CoV-2)的BetacoronaVirus重叠群。我们的研究论证了在废水监测中使用元基因组学作为第一筛选工具的可行性，以及在分析废水样本的元基因组数据时选择合适的病毒浓缩方法和优化生物信息学方法的必要性。
Monitoring of potentially pathogenic human viruses in wastewater is of crucial importance to understand disease trends in communities, predict potential outbreaks, and boost preparedness and response by public health departments. High throughput metagenomic sequencing opens an opportunity to expand the capabilities of wastewater surveillance. However, there are major bottlenecks in the metagenomic enabled wastewater surveillance, including the complexities in selecting appropriate sampling and concentration/virus enrichment methods as well as in bioinformatic analysis of complex samples with low human virus concentrations. To evaluate the abilities of two commonly used sampling and concentration methods in virus identification, virus communities concentrated with Virus Adsorption-Elution (VIRADEL) and PolyEthylene Glycol (PEG) precipitation were compared for three interceptor sites. Results indicated that more viral reads were obtained by the VIRADEL concentration method, with 2.84 ± 0.57 % viral reads in the sample. For samples concentrated with PEG, the average proportion of viral reads in the sample was 0.63 ± 0.19 %. In all wastewater samples, bacteriophage affiliated with the familiesSiphoviridae,MyoviridaeandPodoviridaewere found to be the abundant populations. Comparison against a custom Swiss-Prot human virus database indicated that the relatively abundant human viruses (average proportions in human virus community greater than 1.00 %) in samples concentrated with the VIRADEL method wereOrthopoxvirus, Rhadinovirus,Parapoxvirus,Varicellovirus,Hepatovirus,Simplexvirus,Molluscipoxvirus,Parechovirus,Lymphocryptovirus, andSpumavirus. In samples concentrated with the PEG method, fewer human viruses were found to be relatively abundant. These wereOrthopoxvirus, Rhadinovirus,Varicellovirus,Simplexvirus,Molluscipoxvirus,Lymphocryptovirus, andBetacoronavirus. Contigs ofBetacoronavirus, which contains severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were identified in VIRADEL and PEG samples. Our study demonstrates the feasibility of using metagenomics in wastewater surveillance as a first screening tool and the need for selecting the appropriate virus concentration methods and optimizing bioinformatic approaches in analyzing metagenomic data of wastewater samples.