Case Details and Consent

In New Zealand, COVID-19 is a notifiable disease; all positive cases are reported to the national surveillance system, enabling further public health investigation. All persons with COVID-19 described in this article were contacted, and they provided written or verbal consent for their data to be used in this article. Case data were collected under the Ministry of Health contract for epidemic surveillance. The 7 persons with COVID-19 are denoted here as passengers A–G (Tables 1, 2).

Clinical Data and Sample Collection

Case details were sourced from the national notifiable diseases database, EpiSurv (https://surv.esr.cri.nz/episurv/index.php). While in MIQ, all 86 passengers on the flight underwent real-time reverse transcription PCR (rRT-PCR) diagnostic testing for SARS-CoV-2 on day 3 and again on day 12 if the previous test result was negative. Cabin crew members departed New Zealand soon after their arrival and were therefore not tested. Investigations used information from rRT-PCR testing by using the Cepheid GeneXpert system (https://www.cepheid.com) and BD Max (https://www.bd.com). We determined seating plans by consulting the flight manifest for the Boeing 777–300ER aircraft and confirmed them by administering a questionnaire to passengers, asking where they actually sat.

Genome Sequencing

Independent viral extracts were prepared by the Institute of Environmental Science and Research (Porirua, New Zealand) from the 7 positive respiratory tract samples in which SARS-CoV-2 was initially detected by rRT-PCR. We extracted RNA from SARS-CoV-2–positive samples and subjected it to whole-genome sequencing by following the 1,200-bp amplicon protocol (6) and Oxford Nanopore Rapid barcoding R9.0 sequencing (7). Genomic data are available on GISAID (5) (Table 1).

Phylogenetic Analysis of SARS-CoV-2 Genomes

The lineage of the genomes obtained from the 7 passengers was determined by using pangolin version 2.0.8 (https://pangolin.cog-uk.io) and compared with genomes from the same lineage available on GISAID (5). Genomes were aligned by using MAFFT version 7 (8) and using the FFT-NS-2 progressive alignment algorithm. We estimated a maximum-likelihood phylogenetic tree by using IQ-TREE version 1.6.8 (9) and the Hasegawa-Kishino-Yano nucleotide substitution model (10) with a gamma distributed rate variation among sites (HKY+Γ), the best-fit model as determined by ModelFinder (11), and branch support assessment by using the ultrafast bootstrap method (12).

Analysis of Disease Transmission Data

All times and dates reported here were converted to New Zealand daylight savings time (Greenwich mean time + 13 hours) (Table 2). The mean incubation period, defined as the duration between estimated dates of infection and reported symptom onset, has been reported as 5–6 days (range 1–14 days) (13). We assumed a 5-day incubation period for passengers A, B, D, E, F, and G, and a 3-day incubation period for passenger C. We considered the median presymptomatic infectious period to be <1–4 days unless a negative PCR result indicated otherwise (14).

The Flight

Flight EK448 from Dubai, UAE to Auckland, New Zealand, was an 18-hour, 2-minute flight on a Boeing 777–300ER aircraft. It departed Dubai on September 28, 2020, at 5:29 pm; arrived in Kuala Lumpur on September 29 at 12:11 am to refuel; and departed Kuala Lumpur on September 29 at 2:03 am. No passengers entered or exited the aircraft during the 2-hour refueling period in Kuala Lumpur. The flight arrived in Auckland on September 29 at 11:31 am. During the flight and before departure in Dubai airport, mask use was not mandatory; passengers A, B, D, F, and G self-reported mask and glove use while on the airplane but passengers C and E did not. In the days before the flight, these 7 passengers (other than the 2 travel groups, 1 of which comprised passengers A and B and the other passengers F and G) had been in different countries and did not have any form of contact (Figure 1). Similarly, none of the passengers reported having been in close contact at the Dubai airport. Passengers F and G were part of a family travel group of 4, all of whom reported having changed seats within their row during the flight.

All passengers, with the exception of passenger E, were transferred by bus to an MIQ facility in Rotorua, New Zealand. All passengers reported wearing masks during the bus journeys. Passengers A, B, and D were on bus 1; passengers F and G were on bus 2. Passenger C was initially seated on bus 1 but was transferred to bus 2 before transit. Both buses departed Auckland at 12:05 pm and arrived in Rotorua at 3:00 pm. Passenger E traveled on bus 3 to an MIQ facility in Auckland. Seating on all buses was physically distanced where possible, and mask use was mandated.

Testing and Disease Progression

Five passengers reported having received negative test results before departure (Table 1). A negative test result was mandatory according to airline regulations for passenger C, who traveled from Ukraine.

Figure 2

Figure 2. Timeline of likely incubation and infectious periods, indicating testing dates, for 7 passengers who tested positive for severe acute respiratory syndrome coronavirus 2 infection after traveling on the same flight...

The first 3 passengers to receive positive SARS-CoV-2 test results (passengers A, B, and C) were identified through routine surveillance testing on the third day of the quarantine period in New Zealand (Figure 2). Passengers A and B traveled together from Switzerland; both reported having had negative test results in their country of origin, <72 hours before boarding the flight. They departed Zurich, Switzerland, and arrived in Dubai on September 28, 2020, at 08:02 am. Passenger A reported symptom onset (general weakness and muscle pain) while in MIQ on October 1, and passenger B reported symptom onset (rhinorrhea, general weakness, cough, and muscle pain) on October 2. Test results for samples collected on October 2 from both persons were positive.

Test results for passenger C were also positive on October 2, but the passenger did not report symptoms at any time during the infection. This person had traveled from Kiev, Ukraine, and arrived in Dubai on September 28 at 5:59 am.

Test results for passenger D were negative on October 2, but the passenger reported symptoms on the fifth day after arrival in New Zealand. The symptoms progressively worsened, and another test on October 7 returned a positive result. Reported symptoms included coryza, headache, muscle pain, general weakness, irritability, confusion, and a head cold. This passenger had departed from Dublin, Ireland, and arrived in Dubai on September 28 at 9:05 am.

Test results for passenger E were negative on October 2, but the passenger was retested on October 6 as a potential close contact of those on the airplane and found to be positive for SARS-CoV-2. This passenger was not in the same MIQ facility (nor the same city) in New Zealand as the other passengers with reported cases and did not report symptoms during the infection. This passenger had departed from Kochi, India, and arrived in Dubai on September 25 at 6:35 pm.

Test results for passengers F and G (part of a group of 4 family members traveling together) were negative on October 2 in New Zealand. Passenger F became mildly symptomatic (coryza and a cough) on October 2 and self-reported having had a negative test result before leaving South Africa. The group was retested as potential contacts of those on the flight with positive results, and on October 8, results were positive for passengers F and G. Passenger G reported coryza and a sore throat on October 9. The 4-person travel group had departed from Johannesburg, South Africa, and arrived in Dubai on September 28 at 11:45 am. The 4 family members were seated in 4 adjacent seats in row 24 but interchanged seats within the row, such that no specific seat can be determined for each passenger (Figure 2). Test results were positive for only 2 of the 4 family members; after receiving the positive results, the persons were separated in the MIQ facility.

Timeline of Transmission Events

Figure 3

Figure 3. Seating arrangement (Boeing 777–300ER) for 7 passengers who tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on flight EK448 from Dubai, United Arab Emirates, to Auckland, New...

The first person to experience symptoms was passenger A on October 1, consistent with having been infectious while on flight EK448 2 days earlier (Figure 3). The second person to experience symptoms, on October 2, was passenger B, a travel companion of passenger A, which may represent shared exposure to a source A, such that passenger B’s infection is not considered a case of in-flight transmission. Passenger C was asymptomatic and received a positive test result on day 3. Symptom onset and positive test result dates for passengers D, E, and F were all consistent with in-flight transmission. Passenger G was a travel companion of passenger F, and their date of symptom onset was consistent with infection during their stay in an MIQ facility, where they resided in the same room. As such, passenger G’s infection was not considered a result of in-flight transmission.

Viral Genomic Data

Figure 4

Figure 4. Simplified maximum-likelihood phylogenetic tree of genomes from severe acute respiratory syndrome coronavirus 2 from 7 passengers who traveled on flight EK448 (Boeing 777–300ER) from Dubai, United Arab Emirates, to Auckland,...

Figure 5

Figure 5. Network of likely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission among 7 passengers who traveled on flight EK448 (Boeing 777–300ER) from Dubai, United Arab Emirates, to Auckland, New Zealand,...

All SARS-CoV-2 samples from the 7 passengers were subjected to whole-genome sequencing for surveillance purposes. The sequences obtained were assigned to lineage B.1 and were genetically identical, apart from 1 mutation for the sample from passenger D (Figure 4) (15). By comparing these 7 genomes to the international database (GISAID), we identified 6 additional identical genomes: 4 from Switzerland and 2 from the United Kingdom, sampled during September 2–23. These findings were consistent with virus introduction onto the airplane from Switzerland by passenger A, B, or both (Figure 5). Nevertheless, accurately identifying the source of this outbreak may be impeded by substantial biases and gaps in global sequencing data (J. Geoghegan, unpub. data, https://www.medrxiv.org/content/10.1101/2020.10.28.20221853v1); hence, we cannot explicitly exclude passenger C as the source.