Viral emissions into the air and environment after SARS-CoV-2 human challenge: a phase 1, open label, first-in-human study

Abstract

Background: Effectively implementing strategies to curb SARS-CoV-2 transmission requires understanding who is contagious and when. Although viral load on upper respiratory swabs has commonly been used to infer contagiousness, measuring viral emissions might be more accurate to indicate the chance of onward transmission and identify likely routes. We aimed to correlate viral emissions, viral load in the upper respiratory tract, and symptoms, longitudinally, in participants who were experimentally infected with SARS-CoV-2.

Methods: In this phase 1, open label, first-in-human SARS-CoV-2 experimental infection study at quarantine unit at the Royal Free London NHS Foundation Trust, London, UK, healthy adults aged 18-30 years who were unvaccinated for SARS-CoV-2, not previously known to have been infected with SARS-CoV-2, and seronegative at screening were recruited. Participants were inoculated with 10 50% tissue culture infectious dose of pre-alpha wild-type SARS-CoV-2 (Asp614Gly) by intranasal drops and remained in individual negative pressure rooms for a minimum of 14 days. Nose and throat swabs were collected daily. Emissions were collected daily from the air (using a Coriolis μ air sampler and directly into facemasks) and the surrounding environment (via surface and hand swabs). All samples were collected by researchers, and tested by using PCR, plaque assay, or lateral flow antigen test. Symptom scores were collected using self-reported symptom diaries three times daily. The study is registered with ClinicalTrials.gov, NCT04865237.

Findings: Between March 6 and July 8, 2021, 36 participants (ten female and 26 male) were recruited and 18 (53%) of 34 participants became infected, resulting in protracted high viral loads in the nose and throat following a short incubation period, with mild-to-moderate symptoms. Two participants were excluded from the per-protocol analysis owing to seroconversion between screening and inoculation, identified post hoc. Viral RNA was detected in 63 (25%) of 252 Coriolis air samples from 16 participants, 109 (43%) of 252 mask samples from 17 participants, 67 (27%) of 252 hand swabs from 16 participants, and 371 (29%) of 1260 surface swabs from 18 participants. Viable SARS-CoV-2 was collected from breath captured in 16 masks and from 13 surfaces, including four small frequently touched surfaces and nine larger surfaces where airborne virus could deposit. Viral emissions correlated more strongly with viral load in nasal swabs than throat swabs. Two individuals emitted 86% of airborne virus, and the majority of airborne virus collected was released on 3 days. Individuals who reported the highest total symptom scores were not those who emitted most virus. Very few emissions occurred before the first reported symptom (7%) and hardly any before the first positive lateral flow antigen test (2%).

Interpretation: After controlled experimental inoculation, the timing, extent, and routes of viral emissions was heterogeneous. We observed that a minority of participants were high airborne virus emitters, giving support to the notion of superspreading individuals or events. Our data implicates the nose as the most important source of emissions. Frequent self-testing coupled with isolation upon awareness of first symptoms could reduce onward transmissions.

Funding: UK Vaccine Taskforce of the Department for Business, Energy and Industrial Strategy of Her Majesty's Government.

Figure 1

Schematic of air and environment sampling in participants’ rooms Environmental surface swabs were collected from overbed table (A), bed frame (B), bedside table (C), television remote control (D), and bathroom handles (door metal handles [inside and outside], flush metal handles, and sink metal handles; E). A Coriolis μ air sampler (Bertin Technologies, France) was placed on the bedside table, about 1 m distance to the participant's head.

Figure 2

Longitudinal viral emissions into the air and environment from SARS-CoV-2 infected participants (n=18) Sampling masks, Coriolis air samples, hand swabs, and environmental surface swabs were collected daily, and E gene copies were quantified by RT-qPCR (left y axis). Culture-positive mask and surface swabs are indicated. Nose and throat swabs were collected daily and infectious virus was quantified by plaque assay (right y axis). Total symptom score was calculated using self-reported symptom diaries three times daily. The total symptom scores are displayed in the upper heatmap under each plot, ranging from green (no symptom) to red (highest symptom score). Lateral flow diagnosis from combined nose and throat swabs is shown in the lower heatmap under each plot. Participants are numbered in line with Killingley and colleagues. PFU=plaque forming units.

Figure 3

Correlation between viral load in the upper respiratory tract, viral emissions into the air and environment, and symptoms Heatmap matrix between systemic and respiratory symptom scores, viral load in nose and throat swabs (PCR and plaque assay), viral emissions in sampling masks (PCR), Coriolis air samples (PCR), hand swabs (PCR), and environmental surfaces (PCR) are shown.

Figure 4

Heterogeneity in virus emissions after SARS-CoV-2 human challenge (A) The sum of E gene copies in air samples (quantified by RT-qPCR) from each infected participant were ranked from highest to lowest (left y axis). (B) E gene copies in each positive air sample were ranked from highest to lowest (left y axis). In A and B, percentage of the cumulative total virus emissions are represented by the red curved line (right y axis) and the dashed line represents the 80% level of cumulative curve. (C) Heatmap matrix between the sum of E gene copies in air samples, sampling masks, hands, surfaces, 18S rRNA in air samples, BMI, FEV₁, FVC, and PEF are shown. Spearman correlation coefficients were calculated to assess correlations between pairs of variables. p values are shown in each cell. (D) Heatmap of the ranks of each variable of cumulative viral loads in nose and throat, air, sampling masks, hands, surfaces, total symptoms, human housekeeping genes are visualised in the heatmap, ranging from yellow (highest rank) to blue (lowest rank), except BMI, which is ranked from the lowest value to the highest value. BMI=body-mass index. FEV₁=forced expiratory volume in 1 s. FVC=forced vital capacity. PEF=peak expiratory flow.

Figure 5

Virus emissions in relation to timing of symptoms and diagnosis on lateral flow antigen tests Proportion of viral RNA detected from air, sampling masks, hands, and on surfaces before WHO SARS-CoV-2 symptom criteria (A), before fever (B), before any symptom (C), before first lateral flow antigen diagnosis (D), and before two consecutive negative lateral flow antigen tests (E), from combined nose and throat swabs. Each row of the heat map represents a participant, which is separated by a dotted line (indicating when criteria are met). The cumulative total virus emissions are represented by the curved line.