Travel-associated SARS-CoV-2 transmission documented with whole genome sequencing following a long-haul international flight

Abstract

Background: Multiple instances of flight-associated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission during long-haul flights have been reported during the COVID-19 pandemic. However, comprehensive investigations of passenger risk behaviours, before, during and after the flight, are scarce.

Methods: To investigate suspected SARS-CoV-2 transmission during a flight from United Arab Emirates to Australia in July 2020, systematic, repeated polymerase chain reaction (PCR) testing of passengers in hotel quarantine was linked to whole genome sequencing. Epidemiological analyses of in-depth interviews covering behaviours during the flight and activities pre- and post-boarding were used to identify risk factors for infection.

Results: Seventeen of the 95 passengers from four different travel origins had PCR-confirmed infection yielding indistinguishable genomic sequences. Two of the 17 passengers were symptomatic within 2 days of the flight, and classified as co-primary cases. Seven secondary cases were seated within two rows of the co-primary cases, but five economy passengers seated further away and three business class passengers were also infected (attack rate = 16% [15/93]). In multivariable analysis, being seated within two rows of a primary case [odds ratio (OR) 7.16; 95% confidence interval (CI) 1.66-30.85] and spending more than an hour in the arrival airport (OR 4.96; 95% CI 1.04-23.60) were independent predictors of secondary infection, suggesting travel-associated SARS-CoV-2 transmission likely occurred both during and after the flight. Self-reported increased hand hygiene, frequent aisle walking and using the bathroom on the plane did not independently affect the risk of SARS-CoV-2 acquisition.

Conclusions: This investigation identified substantial in-flight transmission among passengers seated both within and beyond two rows of the primary cases. Infection of passengers in separate cabin classes also suggests transmission occurred outside the cabin environment, likely at the arrival airport. Recognizing that transmission may occur pre- and post-boarding may inform contact tracing advice and improve efforts to prevent future travel-associated outbreaks.

Keywords: COVID-19; SARS-CoV-2; air travel; disease outbreaks; pandemics.

Figure 1

Epidemiologic and clinical timeline for passengers on flight from Dubai to Perth, 1 July 2020. SARS-CoV-2 lineage determined by WGS.

Figure 2

A global maximum likelihood phylogenetic tree* including the B.1.480 lineage from genomes submitted to GISAID as of 13 December 2021. *All branch lengths are drawn to a scale of nucleotide substitutions per site and the tree is rooted to the prototype strain of SARS-CoV-2 (NC_045512.2).

Figure 3

Seating location of passengers on flight from Dubai to Perth, 1 July 2020.