Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing

Abstract

To investigate potential transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a domestic flight within Australia, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed SARS-CoV-2 infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified SARS-CoV-2 outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had culture-positive A2-RP virus strain. This investigation provides evidence of flight-associated SARS-CoV-2 transmission.

Keywords: 2019 novel coronavirus disease; COVID-19; SARS-CoV-2; aircraft; airport; coronavirus disease; cruise; flight-associated; in-flight; outbreak; respiratory infections; severe acute respiratory syndrome coronavirus 2; transmission; viruses; whole-genome sequencing; zoonoses.

Figure 1

Distribution of SARS-CoV-2 infection cases among passengers on a flight from Sydney to Perth, Australia, on March 19, 2020. Far right column shows passenger identification numbers and SARS-CoV-2 lineage determined by whole-genome sequencing (A.2, B.1, not determined).

Figure 2

Theoretical maximum incubation (exposure), infectious period, and symptomatic period until time of resolution of illness in passengers on flight from Sydney to Perth, Australia, on March 19, 2020, with primary and secondary SARS-CoV-2 cases, by place of journey origin. Passenger identification numbers and SARS-CoV-2 lineage determined by whole-genome sequencing (A.2, B.1, not determined) indicated to right of bars. NSW, New South Wales, Australia; 1I, primary case, infectious; 1N, primary case, noninfectious; 2F, secondary case, flight associated; 2P, secondary case, possibly flight associated.

Figure 3

Phylogenetic tree generated in MEGA version 7.0.14 (8) for all SARS-CoV-2 whole-genome sequences with >80% genome coverage. Colors indicate samples from 458 persons with cases linked to cluster on flight from Sydney to Perth, Australia, on March 19, 2020. Scale bar indicates nucleotide substitutions per site.

Figure 4

Spatial distribution of primary (infectious and noninfectious) and secondary (flight-associated and possibly flight-associated) cases of SARS-CoV-2 aboard flight from Sydney to Perth, Australia, on March 19, 2020. Passengers are identified by place of origin and SARS-CoV-2 lineage as determined by whole-genome sequencing. 1I, primary case, infectious; 1N, primary case, noninfectious; 2F, secondary case, flight associated; 2P, secondary case, possibly flight associated.