Harnessing testing strategies and public health measures to avert COVID-19 outbreaks during ocean cruises.

To ensure the safe operation of schools, workplaces, nursing homes, and other businesses during COVID-19 pandemic there is an urgent need to develop cost-effective public health strategies. Here we focus on the cruise industry which was hit early by the COVID-19 pandemic, with more than 40 cruise ships reporting COVID-19 infections. We apply mathematical modeling to assess the impact of testing strategies together with social distancing protocols on the spread of the novel coronavirus during ocean cruises using an individual-level stochastic model of the transmission dynamics of COVID-19. We model the contact network, the potential importation of cases arising during shore excursions, the temporal course of infectivity at the individual level, the effects of social distancing strategies, different testing scenarios characterized by the test's sensitivity profile, and testing frequency. Our findings indicate that PCR testing at embarkation and daily testing of all individuals aboard, together with increased social distancing and other public health measures, should allow for rapid detection and isolation of COVID-19 infections and dramatically reducing the probability of onboard COVID-19 community spread. In contrast, relying only on PCR testing at embarkation would not be sufficient to avert outbreaks, even when implementing substantial levels of social distancing measures.

Estimation of the Actual Incidence of Coronavirus Disease (COVID-19) in Emergent Hotspots: The Example of Hokkaido, Japan during February-March 2020.

Following the first report of the coronavirus disease 2019 (COVID-19) in Sapporo city, Hokkaido Prefecture, Japan, on 14 February 2020, a surge of cases was observed in Hokkaido during February and March. As of 6 March, 90 cases were diagnosed in Hokkaido. Unfortunately, many infected persons may not have been recognized due to having mild or no symptoms during the initial months of the outbreak. We therefore aimed to predict the actual number of COVID-19 cases in (i) Hokkaido Prefecture and (ii) Sapporo city using data on cases diagnosed outside these areas. Two statistical frameworks involving a balance equation and an extrapolated linear regression model with a negative binomial link were used for deriving both estimates, respectively. The estimated cumulative incidence in Hokkaido as of 27 February was 2,297 cases (95% confidence interval (CI): 382-7091) based on data on travelers outbound from Hokkaido. The cumulative incidence in Sapporo city as of 28 February was estimated at 2233 cases (95% CI: 0-4893) based on the count of confirmed cases within Hokkaido. Both approaches resulted in similar estimates, indicating a higher incidence of infections in Hokkaido than were detected by the surveillance system. This quantification of the gap between detected and estimated cases helped to inform the public health response at the beginning of the pandemic and provided insight into the possible scope of undetected transmission for future assessments.

Characterizing all-cause excess mortality patterns during COVID-19 pandemic in Mexico.

BACKGROUND: Low testing rates and delays in reporting hinder the estimation of the mortality burden associated with the COVID-19 pandemic. During a public health emergency, estimating all cause excess deaths above an expected level of death can provide a more reliable picture of the mortality burden. Here, we aim to estimate the absolute and relative mortality impact of COVID-19 pandemic in Mexico. METHODS: We obtained weekly mortality time series due to all causes for Mexico, and by gender, and geographic region from 2015 to 2020. We also compiled surveillance data on COVID-19 cases and deaths to assess the timing and intensity of the pandemic and assembled weekly series of the proportion of tweets about 'death' from Mexico to assess the correlation between people's media interaction about 'death' and the rise in pandemic deaths. We estimated all-cause excess mortality rates and mortality rate ratio increase over baseline by fitting Serfling regression models and forecasted the total excess deaths for Mexico for the first 4 weeks of 2021 using the generalized logistic growth model. RESULTS: We estimated the all-cause excess mortality rate associated with the COVID-19 pandemic in Mexico in 2020 at 26.10 per 10,000 population, which corresponds to 333,538 excess deaths. Males had about 2-fold higher excess mortality rate (33.99) compared to females (18.53). Mexico City reported the highest excess death rate (63.54) and RR (2.09) compared to rest of the country (excess rate = 23.25, RR = 1.62). While COVID-19 deaths accounted for only 38.64% of total excess deaths in Mexico, our forecast estimate that Mexico has accumulated a total of ~ 61,610 [95% PI: 60,003, 63,216] excess deaths in the first 4 weeks of 2021. Proportion of tweets was significantly correlated with the excess mortality (ρ = 0.508 [95% CI: 0.245, 0.701], p-value = 0.0004). CONCLUSION: The COVID-19 pandemic has heavily affected Mexico. The lab-confirmed COVID-19 deaths accounted for only 38.64% of total all cause excess deaths (333,538) in Mexico in 2020. This reflects either the effect of low testing rates in Mexico, or the surge in number of deaths due to other causes during the pandemic. A model-based forecast indicates that an average of 61,610 excess deaths have occurred in January 2021.

COVID-19 case fatality risk by age and gender in a high testing setting in Latin America: Chile, March-August 2020.

BACKGROUND: Early severity estimates of coronavirus disease 2019 (COVID-19) are critically needed to assess the potential impact of the ongoing pandemic in different demographic groups. Here we estimate the real-time delay-adjusted case fatality rate across nine age groups by gender in Chile, the country with the highest testing rate for COVID-19 in Latin America. METHODS: We used a publicly available real-time daily series of age-stratified COVID-19 cases and deaths reported by the Ministry of Health in Chile from the beginning of the epidemic in March through August 31, 2020. We used a robust likelihood function and a delay distribution to estimate real-time delay-adjusted case-fatality risk and estimate model parameters using a Monte Carlo Markov Chain in a Bayesian framework. RESULTS: As of August 31, 2020, our estimates of the time-delay adjusted case fatality rate (CFR) for men and women are 4.16% [95% Credible Interval (CrI): 4.09-4.24%] and 3.26% (95% CrI: 3.19-3.34%), respectively, while the overall estimate is 3.72% (95% CrI: 3.67-3.78%). Seniors aged 80 years and over have an adjusted CFR of 56.82% (95% CrI: 55.25-58.34%) for men and 41.10% (95% CrI: 40.02-42.26%) for women. Results showed a peak in estimated CFR during the June peak of the epidemic. The peak possibly reflects insufficient laboratory capacity, as illustrated by high test positivity rates (33% positive 7-day average nationally in June), which may have resulted in lower reporting rates. CONCLUSIONS: Severity estimates from COVID-19 in Chile suggest that male seniors, especially among those aged ≥ 70 years, are being disproportionately affected by the pandemic, a finding consistent with other regions. The ongoing pandemic is imposing a high death toll in South America, and Chile has one of the highest reported mortality rates globally thus far. These real-time estimates may help inform public health officials' decisions in the region and underscore the need to implement more effective measures to ameliorate fatality.

Risk of death by age and gender from CoVID-19 in Peru, March-May, 2020.

Peru implemented strict social distancing measures during the early phase of the epidemic and is now experiencing one of the largest CoVID-19 epidemics in Latin America. Estimates of disease severity are an essential indicator to inform policy decisions about the intensity and duration of interventions needed to mitigate the outbreak. Here we derive delay-adjusted case fatality risks (aCFR) of CoVID-19 in a middle-income country in South America.We utilize government-reported time series of CoVID-19 cases and deaths in Peru stratified by age group and gender.As of May 25, 2020, we estimate the aCFR for men and women at 10.8% (95%CrI: 10.5-11.1%) and 6.5% (95%CrI: 6.2-6.8%), respectively, whereas the overall aCFR was estimated at 9.1% (95%CrI: 8.9-9.3%). Our results show that senior individuals have been the most severely affected by CoVID-19, particularly men, with an aCFR of nearly 60% for those aged 80- years. We also found that men have a significantly higher cumulative morbidity ratio across most age groups (proportion test, p-value< 0.001), with the exception of those aged 0-9 years.The ongoing CoVID-19 pandemic is generating a substantial mortality burden in Peru. Senior individuals, especially those older than 70 years, are being disproportionately affected by the CoVID-19 pandemic.

Early epidemiological assessment of the transmission potential and virulence of coronavirus disease 2019 (COVID-19) in Wuhan City, China, January-February, 2020.

BACKGROUND: Since the first cluster of cases was identified in Wuhan City, China, in December 2019, coronavirus disease 2019 (COVID-19) rapidly spreads globally. Scientists have made strides in estimating key transmission and epidemiological parameters. In particular, accumulating evidence points to a substantial fraction of asymptomatic or subclinical infections, which influences our understanding of the transmission potential and severity of this emerging disease. In this study, we derive estimates of the transmissibility and virulence of COVID-19 in Wuhan City, China, by reconstructing the underlying transmission dynamics using multiple data sources. METHODS: We employ statistical methods and publicly available epidemiological datasets to jointly derive estimates of transmissibility and severity associated with the novel coronavirus. For this purpose, the daily series of laboratory-confirmed COVID-19 cases and deaths in Wuhan City together with epidemiological data of Japanese repatriated from Wuhan City on board government-chartered flights were integrated into our analysis. RESULTS: Our posterior estimates of basic reproduction number (R) in Wuhan City, China, in 2019-2020 reached values at 3.49 (95% CrI 3.39-3.62) with a mean serial interval of 6.0 days, and the enhanced public health intervention after January 23 in 2020 was associated with a significantly reduced R at 0.84 (95% CrI 0.81-0.88), with the total number of infections (i.e., cumulative infections) estimated at 1,906,634 (95% CrI 1,373,500-2,651,124) in Wuhan City, elevating the overall proportion of infected individuals to 19.1% (95% CrI 13.5-26.6%). We also estimated the most recent crude infection fatality ratio (IFR) and time-delay adjusted IFR at 0.04% (95% CrI 0.03-0.06%) and 0.12% (95% CrI 0.08-0.17%), respectively, estimates that are substantially smaller than the crude CFR estimated at 4.06%. CONCLUSIONS: We have estimated key epidemiological parameters of the transmissibility and virulence of COVID-19 in Wuhan, China, during January-February 2020 using an ecological modeling approach that is suitable to infer epidemiological parameters with quantified uncertainty from partial observations collected by surveillance systems. Our estimate of time-delay adjusted IFR falls in the range of the median IFR estimates based on multiple serological studies conducted in several areas of the world.

Estimating Risk for Death from Coronavirus Disease, China, January-February 2020.

Since December 2019, when the first case of coronavirus disease (COVID-19) was identified in the city of Wuhan in the Hubei Province of China, the epidemic has generated tens of thousands of cases throughout China. As of February 28, 2020, the cumulative number of reported deaths in China was 2,858. We estimated the time-delay adjusted risk for death from COVID-19 in Wuhan, as well as for China excluding Wuhan, to assess the severity of the epidemic in the country. Our estimates of the risk for death in Wuhan reached values as high as 12% in the epicenter of the epidemic and ≈1% in other, more mildly affected areas. The elevated death risk estimates are probably associated with a breakdown of the healthcare system, indicating that enhanced public health interventions, including social distancing and movement restrictions, should be implemented to bring the COVID-19 epidemic under control.

Effect of a wet market on coronavirus disease (COVID-19) transmission dynamics in China, 2019-2020.

OBJECTIVES: The novel coronavirus (SARS-CoV-2) originating from Wuhan spread rapidly throughout China. While its origin remains uncertain, accumulating evidence links a wet market with the early spread of SARS-CoV-2 in Wuhan. Similarly, the influence of the marketplace on the early transmission dynamics is yet to be investigated. METHODS: Using the daily series of COVID-19 incidence, stratified according to contact history with the market, we have conducted quantitative modeling analyses to estimate the reproduction numbers (R) for market-to-human and human-to-human transmission, the reporting probability, and the early effects of public health interventions. RESULTS: We estimated R at 0.24 (95% CrI: 0.01-1.38) for market-to-human transmission and 2.37 (95% CrI: 2.08-2.71) for human-to-human transmission during the early spread in China (2019-2020). Moreover, we estimated that the reporting rate for cases stemming from market-to-human transmission was 2-34 fold higher than that for cases stemming from human-to-human transmission, suggesting that contact history with the wet market played a key role in identifying COVID-19 cases. CONCLUSIONS: Our R estimate tied to market-to-human transmission had substantial uncertainty, but it was significantly lower compared with the reproduction number driving human-to-human transmission. Our results also suggest that asymptomatic and subclinical infections constitute a substantial component of the COVID-19 morbidity burden.

Estimating the Risk of COVID-19 Death During the Course of the Outbreak in Korea, February-May 2020.

BACKGROUND: In Korea, a total of 10,840 confirmed cases of COVID-19 including 256 deaths have been recorded as of May 9, 2020. The time-delay adjusted case fatality risk (CFR) of COVID-19 in Korea is yet to be estimated. METHODS: We obtained the daily series of confirmed cases and deaths in Korea reported prior to May 9, 2020. Using statistical methods, we estimated the time-delay adjusted risk for death from COVID-19 in Daegu, Gyeongsangbuk-do, other regions in Korea, as well as the entire country. RESULTS: Our model-based crude CFR fitted the observed data well throughout the course of the epidemic except for the very early stage in Gyeongsangbuk-do; this was partially due to the reporting delay. Our estimates of the risk of death in Gyeongsangbuk-do reached 25.9% (95% Credible Interval (CrI): 19.6%-33.6%), 20.8% (95% CrI: 18.1%-24.0%) in Daegu, and 1.7% (95% CrI: 1.1%-2.5%) in other regions, whereas the national estimate was 10.2% (95% CrI: 9.0%-11.5%). CONCLUSIONS: The latest estimates of CFR of COVID-19 in Korea are considerably high, even with the early implementation of public health interventions including widespread testing, social distancing, and delayed school openings. Geographic differences in the CFR are likely influenced by clusters tied to hospitals and nursing homes.

Ascertainment rate of novel coronavirus disease (COVID-19) in Japan.

OBJECTIVE: To estimate the ascertainment rate of novel coronavirus disease (COVID-19). METHODS: The epidemiological dataset of confirmed cases with COVID-19 in Japan as of February 28, 2020 was analyzed. A statistical model was constructed to describe the heterogeneity of the reporting rate by age and severity. We estimated the number of severe and non-severe cases, accounting for under-ascertainment. RESULTS: The ascertainment rate of non-severe cases was estimated at 0.44 (95% confidence interval 0.37-0.50), indicating that the unbiased number of non-severe cases would be more than twice the reported count. CONCLUSIONS: Severe cases are twice as likely to be diagnosed and reported when compared to other cases. Considering that reported cases are usually dominated by non-severe cases, the adjusted total number of cases is also approximately double the observed count. This finding is critical in interpreting the reported data, and it is advised that the mild case data for COVID-19 should always be interpreted as under-ascertained [Au?1].

Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020.

On 5 February 2020, in Yokohama, Japan, a cruise ship hosting 3,711 people underwent a 2-week quarantine after a former passenger was found with COVID-19 post-disembarking. As at 20 February, 634 persons on board tested positive for the causative virus. We conducted statistical modelling to derive the delay-adjusted asymptomatic proportion of infections, along with the infections' timeline. The estimated asymptomatic proportion was 17.9% (95% credible interval (CrI): 15.5-20.2%). Most infections occurred before the quarantine start.

Transmission potential of the novel coronavirus (COVID-19) onboard the diamond Princess Cruises Ship, 2020.

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 R t decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control. Most recent estimates of R t 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.