Development and scaling of a sequencing pipeline for genomic surveillance of SARS-CoV-2 in New York City

Abstract

In the ongoing COVID-19 pandemic, detecting the appearance and spread of variants of concern (VOC) is a critical capability in the fight to quell the virus and return to normalcy. Genomic surveillance of the emergence, propagation, and geographical spread of VOCs is thus an important tool for public health officials and government leaders to make policy decisions and advise the public. As part of our role as a major SARS-CoV-2 diagnostic testing facility in New York City, the Pandemic Response Lab (PRL) has been performing genomic surveillance on the large number of positive samples processed by the facility on a daily basis from throughout the New York metropolitan area. Here we describe the development and optimization of a high-throughput SARS-CoV-2 genome sequencing facility at PRL serving New York City.

Comparative hospitalization risk for SARS‐CoV‐2 Omicron and Delta variant infections, by variant predominance periods and patient‐level sequencing results, New York City, August 2021–January 2022

“…Clinical and commercial laboratories are required to report SARS‐CoV‐2 test results for New York State residents through the New York State Electronic Clinical Laboratory Reporting System (ECLRS). 26 For some SARS‐CoV‐2 infections diagnosed among NYC residents, WGS is performed by the NYC Department of Health and Mental Hygiene (DOHMH) Public Health Laboratory, the Pandemic Response Laboratory, 27 and other laboratories reporting through ECLRS. 28 The Pandemic Response Laboratory reported most sequencing results during the study period, including 85% of sequencing results among patients tested during January 2022.…”

Assessment of COVID-19 hospitalization risk during SARS-CoV-2 Omicron relative to Delta variant predominance, New York City, August 2021–January 2022

“…Clinical and commercial laboratories are required to report SARS-CoV-2 test results for New York State residents through the New York State Electronic Clinical Laboratory Reporting System (ECLRS). 24 For some SARS-CoV-2 infections diagnosed among NYC residents, WGS is performed by the NYC Department of Health and Mental Hygiene (DOHMH) Public Health Laboratory, the Pandemic Response Laboratory, 25 and other laboratories reporting through ECLRS. 26 The Pandemic Response Laboratory reported most sequencing results during the study period, including 85% of sequencing results Using an observational cohort design, we defined a cohort of patients presumed infected with Delta as testing positive by laboratory-based molecular or antigen testing and diagnosed during August-November 2021 (≥98% of sequencing results were Delta during each week ending August 7-November 27, 2021).…”