scholarly journals Transmissibility of coronavirus disease 2019 (COVID-19) in Chinese cities with different transmission dynamics of imported cases

2020 ◽  
Author(s):  
Ka Chun Chong ◽  
Wei Cheng ◽  
Shi Zhao ◽  
Feng Ling ◽  
Kirran N. Mohammad ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Likelihood Function ◽  
Transmission Dynamics ◽  
Time Varying ◽  
Outbreak Response ◽  
Chinese Cities ◽  
Imported Cases ◽  
Response Measures ◽  
Local Transmission

AbstractBackgroundMonitoring the time-varying reproduction number (Rt) of the disease is useful in determining whether there is sustained transmission in a population. In this study, we examined Rt of COVID-19 and compared its transmissibility between different intervention periods in Hangzhou and Shenzhen.MethodsDaily aggregated counts of confirmed imported and local cases between January 1, 2020 and March 13, 2020 were analysed. A likelihood function was constructed to estimate Rt, accounting for imported cases.ResultsAlthough Hangzhou had fewer number of cases than Shenzhen, Shenzhen had higher proportion of imported cases than Hangzhou (83% vs 29%). Since the epidemic of COVID-19 in Shenzhen was dominated by imported cases, Rt was kept below unity through time. On the contrary, Rt was greater than unity in Hangzhou from 16 January to 7 February due to the surge in local cases. Credits to the Wuhan lockdown and outbreak response measures following the local lockdown, Rt decreased steadily and dropped below unity in mid-February.ConclusionThe lockdown measures and local outbreak responses helped reduce the potential of local transmission in Hangzhou and Shenzhen. Meanwhile, cities with similar epidemic trend could have different transmission dynamics given the variation in imported cases.

scholarly journals Transmissibility of coronavirus disease 2019 in Chinese cities with different dynamics of imported cases

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10350 ◽  
Author(s):  
Ka Chun Chong ◽  
Wei Cheng ◽  
Shi Zhao ◽  
Feng Ling ◽  
Kirran N. Mohammad ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Transmission Dynamics ◽  
Outbreak Response ◽  
Chinese Cities ◽  
Before And After ◽  
Imported Cases ◽  
Response Measures ◽  
The City ◽  
Local Transmission

Background Monitoring the reproduction number (Rt) of the disease could help determine whether there is sustained transmission in a population, but areas with similar epidemic trends could have different transmission dynamics given the risk from imported cases varied across regions. In this study, we examined the Rt of coronavirus disease 2019 (COVID-19) by taking different dynamics of imported cases into account and compared the transmissibility of COVID-19 at different intervention periods in Hangzhou and Shenzhen. Methods We obtained the daily aggregated counts of laboratory-confirmed imported and local cases of COVID-19 infections in Hangzhou and Shenzhen from January 1 to March 13, 2020. Daily Rt and piecewise Rt before and after Wuhan lockdown were estimated, accounting for imported cases. Results Since the epidemic of COVID-19 in Shenzhen was dominated by imported cases, Rt was around 0.1 to 0.7 before the Wuhan lockdown. After the lockdown of Wuhan and the initialization of measures in response to the outbreak, local transmission was well-controlled as indicated by a low estimated value of piecewise Rt, 0.15 (95% CI [0.09–0.21]). On the contrary, Rt obtained for Hangzhou ranged from 1.2 to 4.9 with a piecewise Rt of 2.55 (95% CI [2.13–2.97]) before the lockdown of Wuhan due to the surge in local cases. Because of the Wuhan lockdown and other outbreak response measures, Rt dropped below unity in mid-February. Conclusions Even though Shenzhen had more cases than Hangzhou, local transmission did not sustain probably due to limited transmission from imported cases owing to the reduction in local susceptibles as residents left the city during Chunyun. The lockdown measures and local outbreak responses helped reduce the local transmissibility.

scholarly journals Accounting for imported cases in estimating the time-varying reproductive number of COVID-19

2021 ◽  
Author(s):  
Tim K. Tsang ◽  
Peng Wu ◽  
Eric H. Y. Lau ◽  
Benjamin J. Cowling
Keyword(s):  
Public Health ◽  
Control Measures ◽  
Transmission Dynamics ◽  
Reproductive Number ◽  
Considerable Proportion ◽  
Time Varying ◽  
Health Measures ◽  
Imported Cases ◽  
The Impact ◽  
Local Transmission

ABSTRACTBackgroundEstimating the time-varying reproductive number, Rt, is critical for monitoring transmissibility of an emerging infectious disease during outbreaks. When local transmission is effectively suppressed, imported cases could substantially impact transmission dynamics.MethodsWe developed methodology to estimate separately the Rt for local cases and imported cases, since certain public health measures aim only to reduce onwards transmission from imported cases. We applied the framework to data on COVID-19 outbreaks in Hong Kong.ResultsWe estimated that the Rt for local cases decreased from above one in the early phase of outbreak to below one after tightening of public health measures. Assuming the same infectiousness of local and imported cases underestimated Rt for local cases due to control measures targeting travelers.ConclusionsWhen a considerable proportion of all cases are imported, the impact of imported cases in estimating Rt is critical. The methodology described here can allow for differential infectiousness of local imported cases.

scholarly journals Development of the reproduction number from coronavirus SARS-CoV-2 case data in Germany and implications for political measures

BMC Medicine ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Sahamoddin Khailaie ◽  
Tanmay Mitra ◽  
Arnab Bandyopadhyay ◽  
Marta Schips ◽  
Pietro Mascheroni ◽  
...  
Keyword(s):  
Structural Changes ◽  
Reproduction Number ◽  
National Level ◽  
Transmission Dynamics ◽  
Federal State ◽  
Parameter Estimates ◽  
Time Varying ◽  
Short Term ◽  
Robert Koch Institute ◽  
Federal States

Abstract Background SARS-CoV-2 has induced a worldwide pandemic and subsequent non-pharmaceutical interventions (NPIs) to control the spread of the virus. As in many countries, the SARS-CoV-2 pandemic in Germany has led to a consecutive roll-out of different NPIs. As these NPIs have (largely unknown) adverse effects, targeting them precisely and monitoring their effectiveness are essential. We developed a compartmental infection dynamics model with specific features of SARS-CoV-2 that allows daily estimation of a time-varying reproduction number and published this information openly since the beginning of April 2020. Here, we present the transmission dynamics in Germany over time to understand the effect of NPIs and allow adaptive forecasts of the epidemic progression. Methods We used a data-driven estimation of the evolution of the reproduction number for viral spreading in Germany as well as in all its federal states using our model. Using parameter estimates from literature and, alternatively, with parameters derived from a fit to the initial phase of COVID-19 spread in different regions of Italy, the model was optimized to fit data from the Robert Koch Institute. Results The time-varying reproduction number (Rt) in Germany decreased to <1 in early April 2020, 2–3 weeks after the implementation of NPIs. Partial release of NPIs both nationally and on federal state level correlated with moderate increases in Rt until August 2020. Implications of state-specific Rt on other states and on national level are characterized. Retrospective evaluation of the model shows excellent agreement with the data and usage of inpatient facilities well within the healthcare limit. While short-term predictions may work for a few weeks, long-term projections are complicated by unpredictable structural changes. Conclusions The estimated fraction of immunized population by August 2020 warns of a renewed outbreak upon release of measures. A low detection rate prolongs the delay reaching a low case incidence number upon release, showing the importance of an effective testing-quarantine strategy. We show that real-time monitoring of transmission dynamics is important to evaluate the extent of the outbreak, short-term projections for the burden on the healthcare system, and their response to policy changes.

scholarly journals Tracking progress towards malaria elimination in China: estimates of reproduction numbers and their spatiotemporal variation

2019 ◽  
Author(s):  
Isobel Routledge ◽  
Shengjie Lai ◽  
Katherine E Battle ◽  
Azra C Ghani ◽  
Manuel Gomez-Rodriguez ◽  
...  
Keyword(s):  
Yunnan Province ◽  
Reproduction Number ◽  
Individual Level ◽  
Reproduction Numbers ◽  
Imported Cases ◽  
Geostatistical Models ◽  
Sources Of Infection ◽  
Spatio Temporal ◽  
The Relationship ◽  
Local Transmission

AbstractChina reported zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we jointly estimate the case reproduction number, Rc, and the number of unobserved sources of infection. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean Rc of 0.005 projected for the year 2019, locally-acquired cases are possible due to high levels of importation.

scholarly journals Reduction of Human Mobility Matters during Early COVID-19 Outbreaks: Evidence from India, Japan and China

2021 ◽  
Vol 18 (6) ◽  
pp. 2826
Author(s):  
Zhehao Ren ◽  
Ruiyun Li ◽  
Tao Zhang ◽  
Bin Chen ◽  
Che Wang ◽  
...  
Keyword(s):  
Human Mobility ◽  
Critical Time ◽  
Reproductive Number ◽  
Time Varying ◽  
Virus Spread ◽  
Illness Onset ◽  
Global Pandemic ◽  
Imported Cases ◽  
Local Transmission ◽  
Japan And China

Mobility restrictions have been a heated topic during the global pandemic of coronavirus disease 2019 (COVID-19). However, multiple recent findings have verified its importance in blocking virus spread. Evidence on the association between mobility, cases imported from abroad and local medical resource supplies is limited. To reveal the association, this study quantified the importance of inter- and intra-country mobility in containing virus spread and avoiding hospitalizations during early stages of COVID-19 outbreaks in India, Japan, and China. We calculated the time-varying reproductive number (Rt) and duration from illness onset to diagnosis confirmation (Doc), to represent conditions of virus spread and hospital bed shortages, respectively. Results showed that inter-country mobility fluctuation could explain 80%, 35%, and 12% of the variance in imported cases and could prevent 20 million, 5 million, and 40 million imported cases in India, Japan and China, respectively. The critical time for screening and monitoring of imported cases is 2 weeks at minimum and 4 weeks at maximum, according to the time when the Pearson’s Rs between Rt and imported cases reaches a peak (>0.8). We also found that if local transmission is initiated, a 1% increase in intra-country mobility would result in 1430 (±501), 109 (±181), and 10 (±1) additional bed shortages, as estimated using the Doc in India, Japan, and China, respectively. Our findings provide vital reference for governments to tailor their pre-vaccination policies regarding mobility, especially during future epidemic waves of COVID-19 or similar severe epidemic outbreaks.

scholarly journals Estimation of local time-varying reproduction numbers in noisy surveillance data

2021 ◽  
Author(s):  
Wenrui Li ◽  
Katia Bulekova ◽  
Brian Gregor ◽  
Laura F. White ◽  
Eric D. Kolaczyk
Keyword(s):  
Local Time ◽  
Reproduction Number ◽  
Infected Individual ◽  
Accurate Estimation ◽  
Time Varying ◽  
Simulation Studies ◽  
Expected Number ◽  
Reproduction Numbers ◽  
Practical Performance ◽  
Local Transmission

AbstractA valuable metric in understanding infectious disease local dynamics is the local time-varying reproduction number, i.e. the expected number of secondary local cases caused by each infected individual. Accurate estimation of this quantity requires distinguishing cases arising from local transmission from those imported from elsewhere. Realistically, we can expect identification of cases as local or imported to be imperfect. We study the propagation of such errors in estimation of the local time-varying reproduction number. In addition, we propose a Bayesian framework for estimation of the true local time-varying reproduction number when identification errors exist. And we illustrate the practical performance of our estimator through simulation studies and with outbreaks of COVID-19 in Hong Kong and Victoria, Australia.

scholarly journals Measuring Time-Varying Effective Reproduction (Rt) Numbers for COVID-19 and Their Relationship with Movement Control Order (MCO) in Malaysia

2021 ◽  
Author(s):  
Musa Kamarul Imran ◽  
Wan Nor Ariffin ◽  
Mohd Mohd Hafiz ◽  
Subhi Jamiluddin ◽  
Noor Atinah Ahmad ◽  
...  
Keyword(s):  
Reproduction Number ◽  
Movement Control ◽  
Systems Science ◽  
Time Varying ◽  
Science And Engineering ◽  
University Center ◽  
Incidence Data ◽  
Johns Hopkins University ◽  
Control Order ◽  
Local Transmission

To quantify the time-varying reproduction number (Rt) for Malaysia using the COVID-19 incidence data., we used data the from the Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus repository. Day 1 was taken from the first assumed local transmission of COVID-19. Data was split into four intervals: a) Interval 1: from Day 1 to Day 10 MCO 1, b) Interval 2: from Day 1 to Day 10 MCO 2, c) Interval 3: from Day 1 to Day 10 MCO 3 and d) Interval 4: from Day 1 to Day 10 MCO 4. We estimated the Rt using the EpiEstim package. The means for Rt at Day 1, Day 5 and Day 10 for all MCOs ranged between 0.665 to 1.147. The average Rt gradually decreased in MCO 1 and MCO 2. However, Rt increased in MCO 3 before stabilized around 0.8 in MCO 4. MCO 1 and MCO 2 which were stricter coincide with the gradual reduction of Rt. However, the more relaxed MCO 3 and MCO 4 correspond to a slight increase in the Rt before it stabilized.

scholarly journals Serial interval and generation interval for respectively the imported and local infectors estimated using reported contact-tracing data of COVID-19 in China

2020 ◽  
Author(s):  
Menghui Li ◽  
Kai Liu ◽  
Yukun Song ◽  
Ming Wang ◽  
Jinshan Wu
Keyword(s):  
Reproduction Number ◽  
Contact Tracing ◽  
Time Varying ◽  
Generation Interval ◽  
2Nd Generation ◽  
Serial Interval ◽  
Interval Censored ◽  
Imported Cases ◽  
Emerging Virus ◽  
Censored Likelihood

AbstractBackgroundsThe emerging virus, COVID-19, has caused a massive out-break worldwide. Based on the publicly available contact-tracing data, we identified 337 transmission chains from 10 provinces in China and estimated the serial interval (SI) and generation interval (GI) of COVID-19 in China.MethodsInspired by possibly different values of the time-varying reproduction number for the imported cases and the local cases in China, we divided all transmission events into three subsets: imported (the zeroth generation) infecting 1st-generation locals, 1st-generation locals infecting 2nd-generation locals, and others transmissions among 2+ generations. The corresponding SI (GI) is respec-tively denoted as , and . A Bayesian approach with doubly interval-censored likelihood is employed to fit the lognormal, gamma, and Weibull distribution function of the SI and GI using the identified 337 transmission chains.FindingsIt is found that the estimated , and , thus overall both SI and GI decrease when generation increases.

scholarly journals Impact of physical distancing policy on reducing transmission of SARS-CoV-2 globally: Perspective from government’s response and residents’ compliance

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255873
Author(s):  
Ping-Chen Chung ◽  
Ta-Chien Chan
Keyword(s):  
South Korea ◽  
Reproduction Number ◽  
Human Mobility ◽  
International Travel ◽  
World Health ◽  
Contact Tracing ◽  
Time Varying ◽  
Lag Effects ◽  
Local Transmission ◽  
At Home

Background COVID-19 was declared a public health emergency by the World Health Organization (WHO) in January 2020. Various physical distancing interventions were introduced to flatten the epidemic curve and reduce the disease burden. We evaluated the impacts of policy stringency and residents’ compliance on time-varying reproduction number in 17 countries. Methods Data were from WHO reports of local transmission (February 28 to April 8, 2020) in Australia, Canada, Finland, France, Germany, Greece, Italy, Spain, Sweden, Thailand, the UK, US and Vietnam. Earlier local transmission data where available from press releases were added for Japan, South Korea, Singapore and Taiwan starting January 28, 2020. COVID-19 policy responses were from the Oxford Covid-19 Government Response Tracker with 17 indicators. Changes in people’s behaviors were from Google’s COVID-19 community mobility reports and Apple Maps’ mobility trends reports. We estimated the daily time-varying reproduction number (Rt) by country. 0-, 7- and 14-day lagged effects of non-pharmaceutical interventions and changes in human mobility on Rt were estimated by linear mixed-effects models. Results Rt initially surged rapidly, then declined gradually depending on policy stringency. The highest mean policy stringency scores were for Italy (69.97) and South Korea (61.00). Variations in stringency scores were higher in Europe, the US and Australia than in Asia. The human mobility reduction was greater in countries with strict policies (median stringency score > = 50). In terms of immediate (0-day lag) effects, Rt reductions were found for workplace-closure, limited-gathering, and stay-at-home policies. At a 7-day lag, Rt reductions were found for workplace closure, restrictions on gatherings, stay-at-home requirements, international travel controls, contact tracing and reducing walking around. At a 14-day lag, Rt reductions were found for restrictions on gatherings, less visiting and staying in parks, and reduced walking around. Conclusion The findings show physical distancing policies and residents’ compliance can slow transmission, with the lag-to-effect time varying by policy.

scholarly journals Time-varying transmission dynamics of Novel Coronavirus Pneumonia in China

2020 ◽  
Author(s):  
Tao Liu ◽  
Jianxiong Hu ◽  
Jianpeng Xiao ◽  
Guanhao He ◽  
Min Kang ◽  
...  
Keyword(s):  
Hong Kong ◽  
Doubling Time ◽  
Reproduction Number ◽  
Control Measures ◽  
Transmission Dynamics ◽  
Time Varying ◽  
Basic Production ◽  
The Subject ◽  
Novel Virus ◽  
Novel Coronavirus

ABSTRACTRationaleSeveral studies have estimated basic production number of novel coronavirus pneumonia (NCP). However, the time-varying transmission dynamics of NCP during the outbreak remain unclear.ObjectivesWe aimed to estimate the basic and time-varying transmission dynamics of NCP across China, and compared them with SARS.MethodsData on NCP cases by February 7, 2020 were collected from epidemiological investigations or official websites. Data on severe acute respiratory syndrome (SARS) cases in Guangdong Province, Beijing and Hong Kong during 2002-2003 were also obtained. We estimated the doubling time, basic reproduction number (R0) and time-varying reproduction number (Rt) of NCP and SARS.Measurements and main resultsAs of February 7, 2020, 34,598 NCP cases were identified in China, and daily confirmed cases decreased after February 4. The doubling time of NCP nationwide was 2.4 days which was shorter than that of SARS in Guangdong (14.3 days), Hong Kong (5.7 days) and Beijing (12.4 days). The R0 of NCP cases nationwide and in Wuhan were 4.5 and 4.4 respectively, which were higher than R0 of SARS in Guangdong (R0=2.3), Hongkong (R0=2.3), and Beijing (R0=2.6). The Rt for NCP continuously decreased especially after January 16 nationwide and in Wuhan. The R0 for secondary NCP cases in Guangdong was 0.6, and the Rt values were less than 1 during the epidemic.ConclusionsNCP may have a higher transmissibility than SARS, and the efforts of containing the outbreak are effective. However, the efforts are needed to persist in for reducing time-varying reproduction number below one.At a Glance CommentaryScientific Knowledge on the SubjectSince December 29, 2019, pneumonia infection with 2019-nCoV, now named as Novel Coronavirus Pneumonia (NCP), occurred in Wuhan, Hubei Province, China. The disease has rapidly spread from Wuhan to other areas. As a novel virus, the time-varying transmission dynamics of NCP remain unclear, and it is also important to compare it with SARS.What This Study Adds to the FieldWe compared the transmission dynamics of NCP with SARS, and found that NCP has a higher transmissibility than SARS. Time-varying production number indicates that rigorous control measures taken by governments are effective across China, and persistent efforts are needed to be taken for reducing instantaneous reproduction number below one.

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