Lab Matters Summer 2021 | Page 14

ENVIRONMENTAL HEALTH

CDC and NCBI Coordinate Wastewater-based Genomic Surveillance Data

by Mia Catharine Mattioli , PhD , National Wastewater Surveillance System , Waterborne Disease Prevention Branch , Centers for Disease Control and Prevention and Ilene Karsch Mizrachi , PhD , Intramural Research Program , Information Engineering Branch , National Center for Biotechnology Information , National Library of Medicine , National Institutes of Health .

In September 2020 , the US Centers for Disease Control and Prevention ( CDC ) launched the National Wastewater Surveillance System ( NWSS ) to provide national coordination and support to public health departments implementing this new surveillance tool . Wastewater surveillance is supporting the COVID-19 pandemic response by serving as an early indicator of community infection trends in advance of reported cases and hospitalizations .

Benefits of Wastewater Sequencing

Since wastewater is essentially a pooled community sample , one of the most promising applications of wastewater surveillance is community-level variant tracking . Variant tracking in wastewater is currently done using two different approaches : by targeting known mutations through reverse transcriptase polymerase chain reaction-based

National Center for Biotechnology Information ( NCBI ) to develop metadata requirements (“ data package ”) that must accompany the submission of any disease surveillanceassociated wastewater sequencing data .

Coordinating Wastewater Sequencing Data Submission

In response to the COVID-19 pandemic , NCBI streamlined SARS-CoV-2 genome sequence submission processes to GenBank ^® and the Sequence Read Archive publicly available , which allows for increased global coordination of SARS-CoV-2 wastewater data .

For wastewater surveillance data , CDC and NCBI collaborated to develop a BioSample package specific for wastewater samples sequenced for disease surveillance . The goal of this standardized data submission process was to : 1 . Create a centralized , internationally available repository of wastewaterderived pathogen genomic data for disease surveillance .

2 . Standardize wastewater metadata and ensure it is consistent with other clinical and environmental sequence databases globally . ¹

Metadata for Wastewater Surveillance BioSample package

Mandatory

• Collection date

• Location

• Wastewater sample matrix ** and collection methods

• Population represented by the wastewater sample

• Wastewater surveillance target .

** Defined as the wastewater matrix that was sampled . Response options include raw wastewater , sewer pipeline sediments , post grit removal , primary sludge , primary effluent , secondary sludge , secondary effluent , other , restricted access , not applicable , not collected , not provided and / or missing .

Suggested but optional

• Sequencing purpose

• Sampling site total daily flow , and

• Levels of human fecal content in the sample .

12 LAB MATTERS Summer 2021

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