Temporal Detection and Phylogenetic Assessment of SARS-CoV-2 in Municipal Wastewater.
Artem Nemudryi,Anna Nemudraia,Tanner Wiegand,Kevin Surya,Murat Buyukyoruk,Calvin Cicha,Karl K Vanderwood,Royce A. Wilkinson,Blake Wiedenheft +8 more
- Vol. 1, Iss: 6, pp 100098
TLDR
It is shown that changes in SARS-CoV-2 RNA concentrations follow symptom onset gathered by retrospective interview of patients but precedes clinical test results, and how genome sequencing can be used for genotyping viral strains circulating in a community.Abstract:
SARS-CoV-2 has recently been detected in feces, which indicates that wastewater may be used to monitor viral prevalence in the community. Here, we use RT-qPCR to monitor wastewater for SARS-CoV-2 RNA over a 74-day time course. We show that changes in SARS-CoV-2 RNA concentrations follow symptom onset gathered by retrospective interview of patients but precedes clinical test results. In addition, we determine a nearly complete (98.5%) SARS-CoV-2 genome sequence from wastewater and use phylogenetic analysis to infer viral ancestry. Collectively, this work demonstrates how wastewater can be used as a proxy to monitor viral prevalence in the community and how genome sequencing can be used for genotyping viral strains circulating in a community.read more
Citations
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh,Heiko A. Schmidt,Olga Chernomor,Dominik Schrempf,Dominik Schrempf,Michael D. Woodhams,Arndt von Haeseler,Arndt von Haeseler,Robert Lanfear +8 more
TL;DR: Some notable features of IQ-TREE version 2 are described and the key advantages over other software are highlighted.
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ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.
Emmanuel Paradis,Klaus Schliep +1 more
TL;DR: Efforts have been put to improve efficiency, flexibility, support for 'big data' (R's long vectors), ease of use and quality check before a new release of ape.
Journal ArticleDOI
SARS-CoV-2 in wastewater: State of the knowledge and research needs.
Masaaki Kitajima,Warish Ahmed,Kyle Bibby,Annalaura Carducci,Charles P. Gerba,Kerry A. Hamilton,Eiji Haramoto,Joan B. Rose +7 more
TL;DR: There is an urgent need for further research to establish methodologies for wastewater surveillance and understand the implications of the presence of SARS-CoV-2 in wastewater.
Journal ArticleDOI
Comparison of virus concentration methods for the RT-qPCR-based recovery of murine hepatitis virus, a surrogate for SARS-CoV-2 from untreated wastewater.
Warish Ahmed,Paul M. Bertsch,Aaron Bivins,Kyle Bibby,Kata Farkas,Amy Gathercole,Eiji Haramoto,Pradip Gyawali,Asja Korajkic,Brian R. McMinn,Jochen F. Mueller,Stuart L. Simpson,Wendy Smith,Erin M. Symonds,Kevin V. Thomas,Rory Verhagen,Masaaki Kitajima +16 more
TL;DR: The results suggest that absorption-extraction methods with minimal pretreatment or without manipulation can provide suitably rapid, cost-effective and relatively straightforward recovery of enveloped viruses in wastewater.
Journal ArticleDOI
First proof of the capability of wastewater surveillance for COVID-19 in India through detection of genetic material of SARS-CoV-2.
Manish Kumar,Arbind Kumar Patel,Anil V. Shah,Janvi Raval,Neha Rajpara,Madhvi Joshi,Chaitanya G. Joshi +6 more
TL;DR: The first ever successful effort in India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of wastewater-based epidemiology (WBE) surveillance in India makes a strong case for the environmental surveillance of the COVID-19 pandemic.
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