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

Hammerling, M. J.; Kang, S. C.; Ward, W.; Escapa, I. F.; Bugga, P.; Del Castillo, C.; Hopkins, M.; Chase, S.; Rey, S.; Law, D.; Carpio, A.; Nelson, K.; Chhabria, S.; Gupta, S.; Rivera, T.; Laurent, J. M.; Hao, H.; Lee, H. H.

2022-05-27 infectious diseases
10.1101/2022.05.25.22273991 medRxiv
Show 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.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.