Earliest Detection to Date of SARS-CoV-2 in Florida: Identification Together With Influenza Virus on the Main Entry Door of a University Building, February 2020

Abstract

BackgroundQuestions persist about patterns of initial dissemination of SARS-CoV-2 in the United States in early 2020.MethodsIn February and March, 2020, environmental surface swab samples were collected from the handle of the main entry door of a major university building in Florida, as part of a pilot surveillance project screening for influenza. Samples were taken at the end of regular classroom hours, between the dates of February 1-5 and February 19-March 4, 2020. ResultsInfluenza H1N1pdm09 was isolated from the door handle on four of the 19 days sampled. Both SARS-CoV-2 and influenza virus were detected in the sample collected on February 21, 2020. Based on sequence analysis, the Florida SARS-CoV-2 strain (designated UF-11) was identical to strains being identified in Washington state during the same time period, while the earliest similar sequences were sampled in China/Hubei between Dec 30th 2019 and Jan 5th 2020. The first human case of COVID-19 was not officially reported in Florida until March 1st. In an analysis of sequences from COVID-19 patients in this region of Florida, there was only limited evidence of subsequent dissemination of the UF-11 strain. Identical or highly similar strains, possibly related through a common transmission chain, were detected with increasing frequency in Washington state between end of February and beginning of March. ConclusionsOur data provide further documentation of the rapid early spread of SARS-CoV-2, and underscore the likelihood that closely related strains were cryptically circulating in multiple U.S. communities before the first “official” cases were recognized.

In-Frame 12-Nucleotide Deletion within Open Reading Frame 3a in a SARS-CoV-2 Strain Isolated from a Patient Hospitalized with COVID-19

“…from the NP swab to confirm the 12-nt deletion. Phylogenetic analyses performed as previously described (2) revealed that UF-8 was closely related to early SARS-CoV-2 strains that circulated locally, but we did not see evidence of dissemination based on sequence analyses of subsequent strains from our institution (Fig. 1a).…”

Role of hospital environmental surfaces in the transmission of the severe acute respiratory syndrome - Coronavirus-2

“…The systematic review included 37 eligible studies and the authors reported that contamination of the surfaces with SARS-CoV-2 RNA was detected on a wide range of surfaces with the highest contamination rates were detected in healthcare facilities where 17.7% and 10.1% of the samples that were taken from hospital settings and non-hospital settings were positive, respectively. Furthermore, in their systematic review, they found that only six [22,24,[26][27][28][29] out of the 37 eligible studies have tested the viability/infectivity of the detected SARS-CoV-2 RNA from 242 positive surface samples but the viral viability was not confirmed. Although studies of SARS-CoV-2 viability on surfaces are scarce, surface transmission may be possible [30].…”

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics

“…Phylodynamic tools, such as NextStrain [6] and BEAST [23,1], are now routinely utilized to monitor evolution and population dynamics of epidemics based on real-time deposition of pathogen sequences in databases (e.g. Gen-Bank, HIVdatabases, GISAID) [22,14,12,10,15,13,24]. Not unlike traditional epidemiological analysis, however, these methods can significantly be affected by sampling bias [7], and sampling during outbreaks are rarely performed randomly from a representative, stratified population [21].…”