Collection of SARS-CoV-2 Virus from the Air of a Clinic Within a University Student Health Care Center and Analyses of the Viral Genomic Sequence

Abstract

The progression of COVID-19 worldwide can be tracked by identifying mutations within the genomic sequence of SARS-CoV-2 that occur as a function of time. Such efforts currently rely on sequencing the genome of SARS-CoV-2 in patient specimens (direct sequencing) or of virus isolated from patient specimens in cell cultures. A pilot SARS-CoV-2 air sampling study conducted at a clinic within a university student health care center detected the virus vRNA, with an estimated concentration of 0.87 virus genomes L^-1 air. To determine whether the virus detected was viable ('live'), attempts were made to isolate the virus in cell cultures. Virus-induced cytopathic effects (CPE) were observed within two days post-inoculation of Vero E6 cells with collection media from air samples; however, rtRT-PCR tests for SARS-CoV-2 vRNA from cell culture were negative. Instead, three other fast-growing human respiratory viruses were isolated and subsequently identified, illustrating the challenge in isolating SARS-CoV-2 when multiple viruses are present in a test sample. The complete SAR-CoV-2 genomic sequence was nevertheless determined by Sanger sequencing and most closely resembles SARS-CoV-2 genomes previously described in Georgia, USA. Results of this study illustrate the feasibility of tracking progression of the COVID-19 pandemic using environmental aerosol samples instead of human specimens. Collection of a positive sample from a distance more than 2 m away from the nearest patient traffic implies the virus was in an aerosol.

Keywords: COVID-19; aerosol; air sampling.

Figure 1.

[A] Mock-infected Vero E6 cells. [B] Vero E6 cells inoculated with material collected from air sample 1. [C]. Vero E6 cells inoculated with material from air sample 2. Images A- C photographed at an original magnification of 200X. [D]. Close-up view (400x) of Vero E6 cells inoculated with material collected from air sample 1.

Figure 2.

Biofire RVP test results for viruses isolated after inoculation of Vero E6 cells with sample 1. Human coronavirus OC43, and Influenza A H1N1 and H3N2 viruses were identified.

Figure 3.

Maximum likelihood subtree of SARS-CoV-2. Phylogeny of subtree SARS-CoV-2_air_sampler_USA_UF-3_2020-03-25 clusters. Diamonds at nodes indicate ultrafast bootstrap (BB) support >90%.