Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020.
Wastewater-Based Epidemiology and Long-Read Sequencing to Identify Enterovirus Circulation in Three Municipalities in Maricopa County, Arizona, Southwest United States between June and October 2020.
复制标题
基于废水的流行病学和长读长测序，以识别 2020 年 6 月至 10 月美国西南部亚利桑那州马里科帕县三个城市的肠道病毒循环。
DOI：
10.3390/v13091803
复制
发表时间：
2021-09-10
期刊：
影响因子：
--
通讯作者：
Scotch M
中科院分区：
文献类型：
--
作者：
Faleye TOC;Bowes DA;Driver EM;Adhikari S;Adams D;Varsani A;Halden RU;Scotch M
我们使用基于废水的流行病学和基于扩增子的长读长高通量测序来监测美国西南部亚利桑那州马里科帕县的肠道病毒 (EV)。 2020 年 6 月 18 日至 10 月 1 日期间，我们从三个城市的 13 个地点收集了 48 个样本，进行过滤（每个样本 175 mL；孔径 0.45 µm），并从过滤器截留的固体中提取 RNA。 RNA 被转换为 cDNA，并通过两个工作流程（桑格测序 (SSW) 和长读长 Illumina 测序 (LRISW)）进行处理，每个工作流程都包括嵌套聚合酶链反应 (nPCR) 测定。我们对来自 SSW 的约 350 bp 扩增子进行了 Sanger 测序，对来自 LRISW 的约 1900–2400 bp 扩增子进行了 Illumina 测序。我们从 13 个位点中的 11 个位点和 41.67% (20/48) 的筛选样本中鉴定出 EV 重叠群。使用 LRISW，我们检测到来自 3 个物种的 9 种 EV 基因型（肠道病毒 A（CVA4、EV-A76、EV-A90）、肠道病毒 B（E14）和肠道病毒 C（CVA1、CVA11、CVA13、CVA19 和 CVA24）），其中肠道病毒 C 代表大约 90% 的变种。然而，SSW 仅检测到五种肠道病毒 C 型。相似性和系统发育分析表明，尽管 SARS-CoV-2 大流行并且采取了非药物公共卫生措施来遏制传播，但在该季节，多种肠道病毒 C 谱系仍在人群中循环、共同感染和重组。
We used wastewater-based epidemiology and amplicon-based long-read high-throughput sequencing for surveillance of enteroviruses (EVs) in Maricopa County, Arizona, Southwest United States. We collected 48 samples from 13 sites in three municipalities between 18 June and 1 October 2020, and filtered (175 mL each; 0.45 µm pore size) and extracted RNA from the filter-trapped solids. The RNA was converted to cDNA and processed through two workflows (Sanger sequencing (SSW) and long-read Illumina sequencing (LRISW)) each including a nested polymerase chain reaction (nPCR) assay. We subjected the ~350 bp amplicon from SSW to Sanger sequencing and the ~1900–2400 bp amplicon from LRISW to Illumina sequencing. We identified EV contigs from 11 of the 13 sites and 41.67% (20/48) of screened samples. Using the LRISW, we detected nine EV genotypes from three species (Enterovirus A (CVA4, EV-A76, EV-A90), Enterovirus B (E14) and Enterovirus C (CVA1, CVA11, CVA13, CVA19 and CVA24)) with Enterovirus C representing approximately 90% of the variants. However, the SSW only detected the five Enterovirus C types. Similarity and phylogenetic analysis showed that multiple Enterovirus C lineages were circulating, co-infecting and recombining in the population during the season despite the SARS-CoV-2 pandemic and the non-pharmaceutical public health measures taken to curb transmission.
登录
查看更多内容
影响因子：
4.6
作者：
Fernandez-Garcia MD;Kebe O;Fall AD;Ndiaye K
通讯作者：
Ndiaye K
影响因子：
12.8
作者：
Bisseux, Maxime;Debroas, Didier;Henquell, Cecile
通讯作者：
Henquell, Cecile
具有合成长读数的超精确微生物扩增子测序。
影响因子：
15.5
作者：
Callahan BJ;Grinevich D;Thakur S;Balamotis MA;Yehezkel TB
通讯作者：
Yehezkel TB
影响因子：
11.8
作者：
Kuo SC;Tsou HH;Wu HY;Hsu YT;Lee FJ;Shih SM;Hsiung CA;Chen WJ
通讯作者：
Chen WJ
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.