Fig. 1: Detection of SARS-CoV-2 nucleic acids in nasopharyngeal specimens collected in the first 10 weeks of 2020.
From: Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave
a Schematic representation of the study design. Nasopharyngeal swab specimens that tested negative for respiratory pathogens (RPN) were pooled. Each pool consisted of ten specimens from the same week from one of five hospital sites. Nucleic acid amplification testing (NAAT) was performed and RNA was processed for SARS-CoV-2 genome assembly. b Select events and responses to the evolving SARS-CoV-2 pandemic are annotated over the timeframe surveyed. Confirmed cases in NYC for the last 2 weeks are noted. Absolute counts of pools that tested positive or negative for RT-PCR targets (ORF1ab+E+ (magenta), ORF1ab+ (yellow), E+ (cyan), Negative (dark purple)) are depicted by week collected. c Distribution of pools with RT-PCR target results (ORF1ab+E+ (solid), ORF1ab+ (dotted), E+ (cross-hatched)) across the five different hospital sites in NYC (Hospital A, blue; B, red; C, green; D, purple; E, orange). d Distribution of SARS-CoV-2 sequences recovered by collection week and hospital site of RPN pools. Filled points reflect complete SARS-CoV-2 consensus genomes recovered and points with X’s reflect partial genomes recovered (e.g., incomplete genomes and those validated by SARS-CoV-2 reads). Colors denote hospital sites as indicated by the legend in (c).
