key: cord-0917485-eoxrh2sl authors: Mizumoto, Kenji; Chowell, Gerardo title: Transmission potential of the novel coronavirus (COVID-19) onboard the Diamond Princess Cruises Ship, 2020 date: 2020-02-27 journal: nan DOI: 10.1101/2020.02.24.20027649 sha: d7701711485f822c0f43df58b48faf6a433028c4 doc_id: 917485 cord_uid: eoxrh2sl An outbreak of COVID-19 developed aboard the Princess Cruises Ship during January-February 2020. Using mathematical modeling and time-series incidence data describing the trajectory of the outbreak among passengers and crew members, we characterize how the transmission potential varied over the course of the outbreak. Our estimate of the mean reproduction number in the confined setting reached values as high as ~11, which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore (approximate range: 1.1-7). Our findings suggest that Rt decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control. Most recent estimates of Rt reached values largely below the epidemic threshold, indicating that a secondary outbreak of the novel coronavirus was unlikely to occur aboard the Diamond Princess Ship. While the novel coronavirus (Covid-19) spread rapidly throughout China for several weeks since December 2019, the virus had not taken off outside China in part due to the unprecedented social distancing measures that the Chinese government put in place. One exception is the outbreak of COVID-19 that developed aboard the Diamond Princess Ship which was detected in early February when one of its passengers, a traveler from Hong Kong, tested positive for the novel coronavirus. The number of cases in the Diamond Princess Ship quickly jumped to 454 confirmed cases by February 18, 2020. In contrast, the total number of cases in Singapore, one of the countries with the highest number of COVID-19 cases after China, was only 77 at the time [1] . Accumulating evidence indicates that the novel coronavirus can spread widely in confined settings including hospitals [2] , cruise ships [3], prisons, and churches [4] [5] . In Wuhan City, China, outbreaks inside health care settings led to the infection of hundreds of health professionals [2] . In Tokyo, Japan, most of the reported infections have been linked to a party inside a traditional wooden ship, called Yakatabune [6] while most of the infections in Korea have affected members of one church and one hospital. . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org /10.1101 /10. /2020 Tracking the evolution of the transmission potential of COVID-19 in different confined settings and how it compares with that of other respiratory diseases such influenza has public health implications. When outbreaks occur in confined settings, it is useful to investigate how the effective reproduction number changes as a result of interventions strategies such as the quarantine that the Japanese government imposed on travelers and crew members aboard the Diamond Princess Ship. In this study we sought to characterize the temporal variation in the transmission potential of the COVID-19 outbreak aboard the Princess Cruises Ship using mathematical modeling and time-series incidence data by dates of symptoms onset describing the trajectory of the outbreak among passengers and crew members. In Yokohama, Japan, an outbreak of COVID-19 has been unfolding on board the Princess Cruise Ship, which has been under quarantine orders since February 5, 2020, after a former passenger of the Diamond Princess Ship tested positive for the virus after disembarking in Hong Kong [3,7]. As of February 22, 2020, two days after the scheduled two-week quarantine came to an end, a total of 621 symptomatic and . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint We connected the daily incidence series with a discrete-time integral equation to describe the epidemic dynamics aboard the Diamond Princess Ship. Specifically, let f s denote the probability mass function of the serial interval of COVID-19, where the serial interval is defined as the time from illness onset in the primary case to time of illness onset in the secondary case. Then f s , of length s days, is given by For s>0, F(s) represents the cumulative distribution function of the gamma distribution. We characterized the expected number of new incident cases E[c i,t ] in type i at symptom onset week t as follows, where r ij denotes the average number of cases of type i infected by a single individual of type j. Here we assume that the incidence, c i,t , follows a Poisson sampling process with The reproduction matrix for each type is given by . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint This matrix is referred to as a next-generation matrix (NGM) in a fully susceptible population [8] . Using this matrix, we derive the instantaneous time-dependent effective reproduction number, R t , for the entire transmission dynamics from the largest eigenvalue of the NGM. Under the assumption that the per-contact infection probability and the generation interval are consistent over time regardless of the type of infection, the NGM quantifies the within type and inter-type patterns of transmission [9] . The sum of the value in column j is the reproduction number for a specific type j. Serial interval estimates of COVID-19 were derived from previous studies of COVID-19, indicating that it follows a gamma distribution with the mean and SD at 7.5 and 3.4 days, respectively, based on ref. [10] . . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint A summary of the COVID-19 confirmed cases by age group and symptom status onboard the Princess Cruises Ship is illustrated in Table 2 CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint of the 95%CrI of estimated data for observed data, the number of days where the model 95% CrI overlapped with the observed data, is 54% (15/28) for all, and 50% (14/28) and 43% (12/28) for passenger and crew, respectively. The time-dependent reproduction number for all and by type are presented in Distributions of median R t for entire study period for overall, for type and by each transmission type are shown in Figure 3 . Median R t are 5.8 (95%CrI: 0.6-11.0), 6.1 (95%CrI: 0.5, 11.8), 0.9 (95%CrI: 0.3, 1.5) for overall and by type (passenger, crew). Examining inter-type and within-type transmission, R t estimates greatly vary across transmission types: 5.6 (95%CrI: 0.3, 10.9) for passenger to passenger, 0.6 (95%CrI: 0.1, 1.1) for passenger to crew, 0.5 (95%CrI: 0.2, 0.8) for crew to passenger, 0.5 (95%CrI: 0.3, 0.8) for crew to crew. Although vaccines are still in early development stages as of February 2020, based on our findings, the corresponding target vaccination coverage to contain the outbreak in this confined setting were estimated at 91% and . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint 94% from the maximum value of the 50 percentile distribution and the 97.5 percentile distribution, respectively. Our latest estimate of the overall R t is 0.35 (95%CrI: 0.02, 2.19), with only 2% of R t estimates lying above the epidemic threshold of 1.0. Passenger and crew also have total (within-type and inter-type) R t values largely below the epidemic threshold, with only small percentages at 0% and 9% above the epidemic threshold, respectively (Table 3 ). This is the first study to assess the transmission potential of the COVID-19 outbreak that unfolded aboard the Diamond Princess Ship, January-February 2020. The overall mean reproduction number in the confined setting reached values as high as ~11, which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore in the range 1.1-7 [10] [11] [12] [13] [14] [15] [16] . However, following the implementation of the quarantine period, the overall R t decreased substantially compared to values estimated during the early stage, but it exhibited fluctuations around the epidemic threshold, which likely prolonged the outbreak. . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. As for the crude asymptomatic ratios by age groups, they show significant differences across age groups. However, these crude ratios are severely influenced by the timing of specimen collection relative to the infection time [19] . Hence, these ratios could be better ascertained if additional data with the timing of specimen collection becomes available. . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint The overall effective reproduction number were calculated from the dominant eigenvalue of next-generation matrix. Light and dark indicates 95% and 50% credible intervals for posterior estimates, respectively. Day 1 on horizontal axis corresponds to January 20, 2020. Horizontal grey dashed line shows the reproduction number at 1.0 for reference, below which incidence declines. Vertical dashed line indicates the day when quarantine was implemented (February 5, 2020). Proportion of asymptomatic cases among all the cases. CI: Confidence Interval (CI) is based on binomial distribution * Symptom status is based on the information at the time of specimen collection. There is a possibility that a fraction of asymptomatic cases develop symptom. . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint Total transmission includes within-type and inter-type transmission . CC-BY-NC-ND 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity. is the (which was not peer-reviewed) The copyright holder for this preprint . https://doi.org/10.1101/2020.02.24.20027649 doi: medRxiv preprint Situation Report -29 Over 1,700 frontline medics infected with coronavirus in China, presenting new crisis for the government It's ruining everyone': eerie quiet reigns in coronavirus-hit South Korean city The construction of next-generation matrices for compartmental epidemic models Euro Surveill. 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