Environmental Surveillance of Coronavirus in Malawi

由于SARS-CoV-2在感染期间和感染后早期和长期的胃肠道脱落，无论症状如何，环境监测为在没有临床测试的情况下估计社区中正在传播的新冠肺炎提供了一个有希望的监测工具。然而，目前从废水中浓缩病毒的方法(超滤法、聚乙二醇法和电负膜吸附)可以很容易地共净化污染物，这些污染物既阻碍了通过聚合酶链式反应检测病毒RNA，也不允许对培养物中的病毒进行后续处理来确定病毒的活力和感染性。一个有吸引力的解决方案是构建高亲和力结合试剂，专门从大量废水中浓缩完整的病毒。我们建议使用SARS-CoV-2进入受体ACE-2与标签(组氨酸和链霉亲和素)融合，使用磁珠从废水中纯化完整的可通过PCR检测的SARS-CoV-2。马拉维最近的一项临床监测研究表明，SARS-CoV2在人群中存在高流行率(13.3%)(未发表)。然而，马拉维目前只有19个新冠肺炎试验点，因此促进大规模临床监测的能力有限。在马拉维-利物浦欢迎信托基金内，早在2020年5月就已利用先前建立的伤寒环境监测系统监测废水中的新冠肺炎。初步数据显示，使用CDC N1分析方法在19%的样本中检测到SARS-CoV-2。这一有限的数据集突显了大规模SARS-CoV-2环境监测的潜力，以了解马拉维的传播热点和监测干预策略。该项目将确定标记的ACE-2是否可以用于从废水中提纯完整的病毒并扩大规模，以便在LMIC中适当使用，随后将确定纯化病毒的感染性，并对NGS进行基因组分析。

With early and prolonged gastrointestinal shedding of SARS-CoV-2 during and after infectionregardless of presentation of symptoms, environmental surveillance provides a promisingmonitoring tool for estimating circulating COVID-19 in a community, in the absence of clinicaltesting. However, current methods of concentrating virus from wastewater (ultrafiltration, PEGprecipitation, and electronegative membrane adsorption) can readily co-purify contaminants that,both hinder detection of virus RNA by PCR and, and also do not allow for subsequent processing ofvirus in culture to determine viral viability and thus infectiousness. An attractive solution is toconstruct high affinity binding reagents which specifically enrich for intact virus from large volumesof wastewater. We propose the use of the SARS-CoV-2 entry receptor ACE-2 fused to tags (histidineand streptavidin) for the purification of intact PCR detectable SARS-CoV-2 from wastewater usingmagnetic beads.A recent clinical surveillance study in Malawi illustrated a high prevalence (13.3%) of SARS-CoV2present within the population (unpublished). However, currently only having 19 COVID-19 testingsites, Malawi thus has limited capacity to facilitate large scale clinical surveillance. Within theMalawi-Liverpool Welcome Trust previously established environmental surveillance systems inplace for typhoid have been utilized to monitor COVID-19 in wastewater from as early as May 2020.Preliminary data shows that SARS-CoV-2 was detected in 19% of samples using the CDC N1 assay.This limited dataset highlights the potential for large scale environmental surveillance of SARS-CoV-2 to understand transmission hotspots and monitor intervention strategies in Malawi. This project will establish if tagged ACE-2 can be used to purify intact virus from wastewater and scaled up forappropriate use in LMIC's, followed by establishing infectivity of purified virus and genomic analysisfollowing NGS.