Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

Abstract

Mitigation of SARS-CoV-2 transmission from international travel is a priority. We evaluated the effectiveness of travellers being required to quarantine for 14-days on return to England in Summer 2020. We identified 4,207 travel-related SARS-CoV-2 cases and their contacts, and identified 827 associated SARS-CoV-2 genomes. Overall, quarantine was associated with a lower rate of contacts, and the impact of quarantine was greatest in the 16-20 age-group. 186 SARS-CoV-2 genomes were sufficiently unique to identify travel-related clusters. Fewer genomically-linked cases were observed for index cases who returned from countries with quarantine requirement compared to countries with no quarantine requirement. This difference was explained by fewer importation events per identified genome for these cases, as opposed to fewer onward contacts per case. Overall, our study demonstrates that a 14-day quarantine period reduces, but does not completely eliminate, the onward transmission of imported cases, mainly by dissuading travel to countries with a quarantine requirement.

Fig. 1. Case ascertainment and distribution during the study period.

a Timeline of the study period (27 May 2020 to 13 September 2020) and associated policy changes on travel introduced in England. Travel-related quarantine measures were assigned on a country by country basis from 4 July 2020. Travellers returning from countries that were on the ‘closed travel corridors list were required to quarantine for 14 days (*reduced to 10 days on 15/12/20), or from the 15th December 2020, choose to self-isolate for 5 days and then pay for a SARS-CoV-2 diagnostic test (test and release). b Flow diagram and map of travel-related cases ascertained from Test and Trace data and subsequent genome availability. Cases were defined as ‘highly probable’ and ‘probable’. ‘Highly probable’ travel-related cases were defined as individuals who reported international travel as an activity in the two days before symptom onset/testing. On 12/08/2020 the additional facility to report international travel in the 7 days prior to symptom onset/testing became available, and also included in this study and defined as ‘probable’ travel-related cases. c Flow diagram relaying contacts ascertained of cases from Test and Trace data. d Countries where importations originated. Countries with less than five importations were excluded for confidentiality reasons. e Destinations of imported cases within England. Areas with less than three cases have been excluded. Q/C quality control.

Fig. 2. Frequency of importations overtime for the top 4 most common countries of travel reported by individuals testing positive for SARS-CoV-2 during the study period.

a–d SARS-CoV-2 case numbers in returning travellers by the four most popular countries of travel reported by cases representing 2379/4207 (56.5%) of known travel-related cases. The light-shaded areas represent the period of time when the countries had an open ‘travel-corridor’ so did not have mandatory 14-day quarantine on return in place.

Fig. 3. The effect of travel restriction (14-day quarantine) on contacts per imported case of SARS-CoV-2.

The estimated marginal mean number of contacts per imported case a overall, b by age-group and c by date of test comparing countries with travel restriction guidance (closed ‘travel-corridors’) in place and those without (open ‘travel-corridors’). All points are estimated marginal means and are provided with 95% confidence intervals.

Fig. 4. The effect of travel restrictions (14-day quarantine) on the subsequent spread of likely imported cases as determined by genomics.

a The proportion of imported cases with any matching genome detected over the four weeks following index test result. Error bars correspond to bootstrapped confidence intervals, n = 81 and 71. b The number of genomes matching the index case, with zeros excluded. The midline of the boxplot represents the median value; the lower limit of the box represents the first quartile (25th percentile), and the upper limit of the box represents the third quartile (75th percentile); the whiskers (upper and lower) extend to the largest and smallest value from the box, no further than 1.5*IQR from the box. a, b Compare countries with travel restriction guidance (closed ‘travel-corridors’) in place and those without (open ‘travel-corridors’). c The number of cases and number of importation events for each imported genome, stratified by whether the index case had returned from a country with a travel restriction in place.