Volume 27, Number 3—March 2021
Synopsis
Genomic Evidence of In-Flight Transmission of SARS-CoV-2 Despite Predeparture Testing
Table 1
Detailed information for 7 passengers with SARS-CoV-2 infection detected after being on flight EK448, Dubai, United Arab Emirates, to Auckland, New Zealand, September 29, 2020*
Variable | Passenger |
|||||||
---|---|---|---|---|---|---|---|---|
A | B | C | D | E | F | G |
||
Genome |
Identical |
Identical |
Identical† |
1 additional mutation |
Identical |
Identical |
Identical |
|
Genome ID (GISAID accession no.) (5) |
20CV0408 (EPI_ISL_
582019) |
20CV0409 (EPI_ISL_
582020) |
20CV0410 (EPI_ISL_
582021) |
20CV0401 (EPI_ISL_
582018) |
20CV0398 (EPI_ISL_
582017) |
20CV0414 (EPI_ISL_
582022) |
20CV0415 (EPI_ISL_
582023) |
|
Preflight testing result (date)‡ |
Negative
(Sep 24) |
Negative
(Sep 24) |
Negative
(Sep 25) |
Negative
(Sep 24) |
Not tested |
Negative
(Sep 25) |
Not tested |
|
Symptom onset date |
Oct 1 |
Oct 2 |
Asymptomatic |
Oct 4 |
Asymptomatic |
Oct 3 |
Oct 9 |
|
Date tested positive |
Oct 2 |
Oct 2 |
Oct 2 |
Oct 7 |
Oct 6 |
Oct 8 |
Oct 8 |
|
Technology§ and Ct |
GeneXpert,
E-gene Ct 14.3, N2-gene Ct 16.4 |
GeneXpert, E-gene Ct 27, N2-gene Ct 29.3 |
GeneXpert, E-gene Ct 33.3, N2-gene Ct 36.8 |
GeneXpert, E-gene Ct 18.5 N2-gene Ct 20.4 |
GeneXpert, E-gene Ct 18.5, N2 gene Ct 22.3 |
BD Max,
N1-gene Ct 22.0 N2-gene Ct 22.3 |
BD Max,
N1-gene Ct 22.1, N2-gene Ct 19.1 |
|
Country of origin |
Switzerland |
Switzerland |
Ukraine |
Ireland |
India |
South Africa |
South Africa |
|
Layover time in Dubai |
9 h 27 min |
9 h 27 min |
11 h 30 min |
8 h 18 min |
70 h 54 min |
5 h 44 min |
5 h 44 min |
|
Seat no. on flight |
26G |
26D |
24C |
27D |
28G |
24D/E/F/G |
||
PPE worn on airplane and bus‡ |
Face mask
and gloves¶ |
Face mask and gloves¶ |
Not reported |
Face mask and gloves |
Not reported |
Face mask |
Face mask |
|
Bus from airport to MIQ# | Bus 1 | Bus 1 | Bus 1 briefly, transported on bus 2 | Bus 1 | Bus 3 | Bus 2 |
Bus 2 |
*GISAID, https://www.gisaid.org. Ct, cycle threshold; MIQ, managed isolation and quarantine; PPE, personal protective equipment. †Partial genome obtained (1 amplicon failed, resulting in 1,200 ambiguous nucleotide bases) but has the 5 defining mutations of the cluster. ‡Self-reported. §GeneXpert, https://www.cepheid.com; BD Max, https://www.bd.com. ¶Reportedly removed when sleeping and seated. #Social distancing and mandated mask wearing on all buses.
References
- Jefferies S, French N, Gilkison C, Graham G, Hope V, Marshall J, et al. COVID-19 in New Zealand and the impact of the national response: a descriptive epidemiological study. Lancet Public Health. 2020;5:e612–23. DOIPubMedGoogle Scholar
- International Air Transport Association. Low risk of transmission [cited 2020 Nov 1]. https://www.iata.org/en/youandiata/travelers/health/low-risk-transmission
- Freedman DO, Wilder-Smith A. In-flight transmission of SARS-CoV-2: a review of the attack rates and available data on the efficacy of face masks. J Travel Med. 2020;27:
taaa178 ; Epub ahead of print. DOIPubMedGoogle Scholar - Murphy N, Boland M, Bambury N, Fitzgerald M, Comerford L, Dever N, et al. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25:
200162 . DOIPubMedGoogle Scholar - Elbe S, Buckland-Merrett G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1:33–46. DOIPubMedGoogle Scholar
- Quick J. nCoV-2019 sequencing protocol V3 [cited 2020 Nov 1]. https://www.protocols.io/view/ncov-2019-sequencing-protocol-v3-locost-bh42j8y
- Freed NE, Vlková M, Faisal MB, Silander OK. Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biol Methods Protoc. 2020;5:bpaa014.
- Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. DOIPubMedGoogle Scholar
- Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. DOIPubMedGoogle Scholar
- Hasegawa M, Kishino H, Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22:160–74. DOIPubMedGoogle Scholar
- Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9. DOIPubMedGoogle Scholar
- Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol. 2018;35:518–22. DOIPubMedGoogle Scholar
- World Health Organization. Novel coronavirus situation report [cited 2020 Nov 1]. https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200121-sitrep-1-2019-ncov.pdf
- Byrne AW, McEvoy D, Collins AB, Hunt K, Casey M, Barber A, et al. Inferred duration of infectious period of SARS-CoV-2: rapid scoping review and analysis of available evidence for asymptomatic and symptomatic COVID-19 cases. BMJ Open. 2020;10:
e039856 . DOIPubMedGoogle Scholar - Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5:1403–7. DOIPubMedGoogle Scholar
- Choi EM, Chu DKW, Cheng PKC, Tsang DNC, Peiris M, Bausch DG, et al. In-flight transmission of SARS-CoV-2. Emerg Infect Dis. 2020;26:2713–6. DOIPubMedGoogle Scholar
- Speake H, Phillips A, Chong T, Sikazwe C, Levy A, Lang J, et al. Flight-associated transmission of severe acute respiratory syndrome coronavirus 2 corroborated by whole-genome sequencing. Emerg Infect Dis. 2020;26:2872–80. DOIPubMedGoogle Scholar
1These authors contributed equally to this article.