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The serial interval distribution is used to approximate the generation time distribution, an essential parameter to infer the transmissibility (${R}_t$) of an epidemic. However, serial interval distributions may change as an epidemic progresses. We examined detailed contact tracing data on laboratory-confirmed cases of COVID-19 in Hong Kong during the five waves from January 2020 to July 2022. We reconstructed the transmission pairs and estimated time-varying effective serial interval distributions and factors associated with longer or shorter intervals. Finally, we assessed the biases in estimating transmissibility using constant serial interval distributions. We found clear temporal changes in mean serial interval estimates within each epidemic wave studied and across waves, with mean serial intervals ranged from 5.5 days (95% CrI: 4.4, 6.6) to 2.7 (95% CrI: 2.2, 3.2) days. The mean serial intervals shortened or lengthened over time, which were found to be closely associated with the temporal variation in COVID-19 case profiles and public health and social measures and could lead to the biases in predicting ${R}_t$. Accounting for the impact of these factors, the time-varying quantification of serial interval distributions could lead to improved estimation of ${R}_t$, and provide additional insights into the impact of public health measures on transmission.
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INTRODUCTION: The association between COVID-19 vaccination and length of hospital stay may provide further insight into vaccination benefits, but few studies have investigated such associations in detail. We aimed to investigate the association between COVID-19 vaccination and length of hospital stay in COVID-19 patients during Omicron waves in Hong Kong, and explore potential predictors. METHODS: This retrospective cohort study was conducted on local patients aged ≥60 years who were admitted due to COVID-19 infection in Hong Kong in 2022, from 1 February to 22 November, and with 28 days of follow-up since admission. The exposure was either not vaccinated; or having received 2/3/4 doses of CoronaVac (Sinovac); or 2/3/4 doses of BNT162b2 (BioNTech/Fosun Pharma/Pfizer). Length of stay in hospital was the main outcome. Accelerated failure time models were used to quantify variation in hospital stay for vaccinated compared with unvaccinated patients, accounting for age, sex, comorbidity, type of vaccine and number of doses received, care home residence and admission timing; stratified by age groups and epidemic waves. RESULTS: This study included 32,398 patients aged 60 years and above for main analysis, their median (IQR) age was 79 (71-87) years, 53% were men, and 40% were unvaccinated. The patients were stratified by confirmation prior to or since 23 May 2022, resulting in a sample size of 15,803 and 16,595 in those two waves respectively. Vaccinated patients were found to have 13-39% shorter hospital stay compared to unvaccinated patients. More vaccine doses received were associated with shorter hospital stay, and BNT162b2 recipients had slightly shorter hospital stays than CoronaVac recipients. CONCLUSION: Vaccination was associated with reduced hospital stay in breakthrough infections. Increased vaccination uptake in older adults may improve hospital bed turnover and public health outcomes especially during large community epidemics.
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Vacina BNT162 , COVID-19 , Masculino , Humanos , Idoso , Feminino , Hong Kong/epidemiologia , Vacinas contra COVID-19 , Estudos Retrospectivos , COVID-19/epidemiologia , COVID-19/prevenção & controle , Hospitalização , VacinaçãoRESUMO
Background: Hong Kong contained COVID-19 for two years but experienced a large epidemic of Omicron BA.2 in early 2022 and endemic transmission of Omicron subvariants thereafter. We reflected on pandemic preparedness and responses by assessing COVID-19 transmission and associated disease burden in the context of implementation of various public health and social measures (PHSMs). Methods: We examined the use and impact of pandemic controls in Hong Kong by analysing data on more than 1.7 million confirmed COVID-19 cases and characterizing the temporal changes non-pharmaceutical and pharmaceutical interventions implemented from January 2020 through to 30 December 2022. We estimated the daily effective reproductive number (Rt) to track changes in transmissibility and effectiveness of community-based measures against infection over time. We examined the temporal changes of pharmaceutical interventions, mortality rate and case-fatality risks (CFRs), particularly among older adults. Findings: Hong Kong experienced four local epidemic waves predominated by the ancestral strain in 2020 and early 2021 and prevented multiple SARS-CoV-2 variants from spreading in the community before 2022. Strict travel-related, case-based, and community-based measures were increasingly tightened in Hong Kong over the first two years of the pandemic. However, even very stringent measures were unable to contain the spread of Omicron BA.2 in Hong Kong. Despite high overall vaccination uptake (>70% with at least two doses), high mortality was observed during the Omicron BA.2 wave due to lower vaccine coverage (42%) among adults ≥65 years of age. Increases in antiviral usage and vaccination uptake over time through 2022 was associated with decreased case fatality risks. Interpretation: Integrated strict measures were able to reduce importation risks and interrupt local transmission to contain COVID-19 transmission and disease burden while awaiting vaccine development and rollout. Increasing coverage of pharmaceutical interventions among high-risk groups reduced infection-related mortality and mitigated the adverse health impact of the pandemic. Funding: Health and Medical Research Fund.
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BACKGROUND: Assessment of viral kinetics of SARS-CoV-2 can inform on host immune responses to the virus and on the viral transmission potential. We aimed to characterise viral shedding kinetics by age, virus type, and clinical outcome, and to examine the potential effect of vaccination on viral shedding. METHODS: In this retrospective observational study, we analysed longitudinal data on cycle threshold (Ct) values of reverse-transcription quantitative PCR (RT-qPCR) assays of upper respiratory tract samples from symptomatic patients with COVID-19. Patients who were confirmed with COVID-19 with at least one Ct value of the RT-qPCR test available within 28 days after symptom onset, and discharged or died at the time of the analysis, were included in the study. Patients were isolated in hospitals in Hong Kong during three major epidemic waves dominated by the ancestral strain or omicron BA.2. We modelled the temporal trajectories of viral burden in these patients. Electronic medical records of the patients with COVID-19 were retrieved and linked to the patients' epidemiological information obtained from contact tracing. Patients who were infected outside Hong Kong, infected with variants other than the ancestral strain or omicron BA.2, not reporting any COVID-19 related symptoms, still hospitalised at the time of analysis, missing information on age, time of symptom onset, infection severity, vaccination or clinical outcome, infected more than once, or treated with nirmatrelvir-ritonavir or molnupiravir were excluded from analysis. The main outcome of this study is the temporal change of SARS-CoV-2 viral burden measured by Ct values of RT-qPCR tests in symptomatic patients with COVID-19. FINDINGS: Among 22â461 symptomatic patients with COVID-19 confirmed from July 1, 2020, to May 22, 2022, the estimated viral burden from a random-effects model indicated a longer duration of viral shedding in patients with more severe outcomes of infection (mean difference 13·1 days, 95% CI 12·9-13·3, for fatal vs mild-to-moderate) and in older patients (5·2, 5·0-5·5, for age ≥80 years vs 0-18 years). Vaccinated individuals with a breakthrough infection with the omicron BA.2 variant had a generally lower viral burden and shorter durations of viral shedding (mean difference of 2-4 days) over 4 weeks after onset than unvaccinated individuals infected with omicron BA.2, particularly in patients whose last dose of COVID-19 vaccine was received ≤90 days before symptom onset. Marginal differences in viral burden following symptom onset and the duration of viral shedding were observed between unvaccinated individuals infected with the ancestral strain and omicron BA.2. INTERPRETATION: The viral kinetics since symptom onset characterised for symptomatic patients with COVID-19 in our study show that previously vaccinated or younger individuals, or those with a milder infection, shed fewer viruses in a shorter period, implying possible transmission dynamics of SARS-CoV-2 and protective mechanisms of vaccination against infection and severe outcomes. FUNDING: Hong Kong Health and Medical Research Fund and Hong Kong Collaborative Research Fund.
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COVID-19 , SARS-CoV-2 , Humanos , Idoso , Idoso de 80 Anos ou mais , SARS-CoV-2/genética , COVID-19/epidemiologia , Vacinas contra COVID-19/uso terapêutico , Hong Kong/epidemiologia , CinéticaRESUMO
Social distancing measures (SDMs) are community-level interventions that aim to reduce person-to-person contacts in the community. SDMs were a major part of the responses first to contain, then to mitigate, the spread of SARS-CoV-2 in the community. Common SDMs included limiting the size of gatherings, closing schools and/or workplaces, implementing work-from-home arrangements, or more stringent restrictions such as lockdowns. This systematic review summarized the evidence for the effectiveness of nine SDMs. Almost all of the studies included were observational in nature, which meant that there were intrinsic risks of bias that could have been avoided were conditions randomly assigned to study participants. There were no instances where only one form of SDM had been in place in a particular setting during the study period, making it challenging to estimate the separate effect of each intervention. The more stringent SDMs such as stay-at-home orders, restrictions on mass gatherings and closures were estimated to be most effective at reducing SARS-CoV-2 transmission. Most studies included in this review suggested that combinations of SDMs successfully slowed or even stopped SARS-CoV-2 transmission in the community. However, individual effects and optimal combinations of interventions, as well as the optimal timing for particular measures, require further investigation. This article is part of the theme issue 'The effectiveness of non-pharmaceutical interventions on the COVID-19 pandemic: the evidence'.
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COVID-19 , Humanos , COVID-19/epidemiologia , COVID-19/prevenção & controle , SARS-CoV-2 , Pandemias/prevenção & controle , Distanciamento Físico , Controle de Doenças TransmissíveisRESUMO
BACKGROUND: Understanding severity of infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants is crucial to inform public health measures. Here we used coronavirus disease 2019 (COVID-19) patient data from Hong Kong to characterize the severity profile of COVID-19. METHODS: Time-varying and age-specific effective severity measured by case hospitalization risk and hospitalization fatality risk was estimated with all individual COVID-19 case data collected in Hong Kong from 23 January 2020 through 26 October 2022 over 6 epidemic waves. The intrinsic severity of Omicron BA.2 was compared with the estimate for the ancestral strain with the data from unvaccinated patients without previous infections. RESULTS: With 32 222 COVID-19 hospitalizations and 9669 deaths confirmed over 6 epidemic waves, the time-varying hospitalization fatality risk dramatically increased from <10% before the largest fifth wave of Omicron BA.2 to 41% during the peak of the fifth wave when hospital resources were severely constrained. The age-specific fatality risk in unvaccinated hospitalized Omicron cases was comparable to the estimates for unvaccinated cases with the ancestral strain. During epidemics predominated by Omicron BA.2, fatality risk was highest among older unvaccinated patients. CONCLUSIONS: Omicron has comparable intrinsic severity to the ancestral Wuhan strain, although the effective severity is substantially lower in Omicron cases due to vaccination.
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COVID-19 , Epidemias , Humanos , SARS-CoV-2/genética , Hong Kong/epidemiologia , HospitalizaçãoRESUMO
We described the frequency of residential case clusters and the efficiency of compulsory testing in identifying cases using buildings targeted in compulsory testing and locally infected coronavirus disease 2019 (COVID-19) cases matched by residence in Hong Kong. Most of the buildings (4246 of 7688, 55.2%) with COVID-19 cases identified had only 1 reported case, and 13% of the daily reported cases were detected through compulsory testing. Compulsory testing notices could be essential in attempting to eliminate infections ("zero COVID") and have an impact early in an epidemic, but they appear to be relatively inefficient in response to sustained community transmission.
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COVID-19 , Epidemias , Humanos , COVID-19/epidemiologia , Hong Kong/epidemiologia , SARS-CoV-2RESUMO
PURPOSE OF REVIEW: Initial response strategies to the COVID-19 pandemic were heavily reliant on nonpharmaceutical interventions (NPIs), a set of measures implemented to slow or even stop the spread of infection. Here, we reviewed key measures used during the COVID-19 pandemic. RECENT FINDINGS: Some NPIs were successful in reducing the transmission of SARS-CoV-2. Personal protective measures such as face masks were widely used, and likely had some effect on transmission. The development and production of rapid antigen tests allowed self-diagnosis in the community, informing isolation and quarantine measures. Community-wide measures such as school closures, workplace closures and complete stay-at-home orders were able to reduce contacts and prevent transmission. They were widely used in the pandemic and contributed to reduce transmission in the community; however, there were also negative unintended consequences in the society and economy. SUMMARY: NPIs slowed the spread of SARS-CoV-2 and are essential for pandemic preparedness and response. Understanding which measures are more effective at reducing transmission with lower costs is imperative.
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COVID-19 , SARS-CoV-2 , Humanos , COVID-19/epidemiologia , COVID-19/prevenção & controle , Pandemias/prevenção & controle , Quarentena , Teste para COVID-19RESUMO
Background: Hong Kong followed a strict COVID-19 elimination strategy in 2020. We estimated the impact of the COVID-19 pandemic responses on all-cause and cause-specific hospitalizations and deaths in 2020. Methods: Interrupted time-series analysis using negative binomial regression accounting for seasonality and long-term trend was used on weekly 2010-2020 data to estimate the change in hospitalization risk and excess mortality occurring both within and out of hospitals. Findings: In 2020, as compared to a 2010-2019 baseline, we observed an overall reduction in all-cause hospitalizations, and a concurrent increase in deaths. The overall hospitalization reduction (per 100,000 population) was 4809 (95% CI: 4692, 4926) in 2020, with respiratory diseases (632, 95% CI: 607, 658) and cardiovascular diseases (275, 95% CI: 264, 286) contributing most. The overall excess mortality (per 100,000 population) was 25 (95% CI: 23, 27) in 2020, mostly among individuals with pre-existing cardiovascular diseases (12, 95% CI: 11, 13). A reduction in excess in-hospital mortality (-10 per 100,000, 95% CI: -12, -8) was accompanied by an increase in excess out-of-hospital mortality (32, 95% CI: 29, 34). Interpretation: The COVID-19 pandemic might have caused indirect impact on population morbidity and mortality likely through changed healthcare seeking particularly in youngest and oldest individuals and those with cardiovascular diseases. Better healthcare planning is needed during public health emergencies with disruptions in healthcare services. Funding: Health and Medical Research Fund, Collaborative Research Fund, AIR@InnoHK and RGC Senior Research Fellow Scheme, Hong Kong.
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Our analysis of data collected from multiple epidemics in Hong Kong indicated a shorter serial interval and generation time of infections with the SARS-CoV-2 Omicron variant. The age-specific case-fatality risk for Omicron BA.2.2 case-patients without complete primary vaccination was comparable to that of persons infected with ancestral strains in earlier waves.
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COVID-19 , SARS-CoV-2 , COVID-19/epidemiologia , Surtos de Doenças , Hong Kong/epidemiologia , HumanosRESUMO
BACKGROUND: Hong Kong maintained low circulation of SARS-CoV-2 until a major community epidemic of the omicron (B.1.1.529) sublineage BA.2 began in January, 2022. Both mRNA (BNT162b2 [Fosun Pharma-BioNTech]) and inactivated CoronaVac (Sinovac, Beijing, China) vaccines are widely available; however, vaccination coverage has been low, particularly in older adults aged 70 years or older. We aimed to assess vaccine effectiveness in this predominantly infection-naive population. METHODS: In this observational study, we used individual-level case data on mild or moderate, severe or fatal, and fatal disease in patients hospitalised with COVID-19 along with census information and coverage data of BNT162b2 and CoronaVac. We used a negative binomial model, adjusting for age, sex, and calendar day to estimate vaccine effectiveness of one, two, and three doses of both BNT162b2 and CoronaVac vaccines, and relative effectiveness by number of doses and vaccine type. FINDINGS: Between Dec 31, 2020, and March 16, 2022, 13·2 million vaccine doses were administered in Hong Kong's 7·4-million population. We analysed data from confirmed cases with mild or moderate (n=5566), severe or fatal (n=8875), and fatal (n=6866) COVID-19. Two doses of either vaccine protected against severe disease and death within 28 days of a positive test, with higher effectiveness among adults aged 60 years or older with BNT162b2 (vaccine effectiveness 89·3% [95% CI 86·6-91·6]) compared with CoronaVac (69·9% [64·4-74·6]). Three doses of either vaccine offered very high levels of protection against severe or fatal outcomes (97·9% [97·3-98·4]). INTERPRETATION: Third doses of either BNT162b2 or CoronaVac provide substantial additional protection against severe COVID-19 and should be prioritised, particularly in older adults older than 60 years and others in high-risk populations who received CoronaVac primary schedules. Longer follow-up is needed to assess duration of protection across different vaccine platforms and schedules. FUNDING: COVID-19 Vaccines Evaluation Program, Chinese Center for Disease Control and Prevention.
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Vacinas contra COVID-19 , COVID-19 , Idoso , Vacina BNT162 , COVID-19/prevenção & controle , Hong Kong/epidemiologia , Humanos , SARS-CoV-2 , Eficácia de VacinasRESUMO
Influenza virus infections can lead to a number of secondary complications, including sepsis. We applied linear regression models to mortality and hospital admission data coded for septicaemia from 1998 to 2019 in Hong Kong, and estimated that septicaemia was associated with an annual average excess mortality rate of 0.23 (95% CI 0.04-0.40) per 100 000 persons per year and an excess septicaemia hospitalisation rate of 1.73 (95% CI 0.94-2.50) per 100 000 persons per year. The highest excess morbidity and mortality was found in older adults and young children, and during influenza A(H3N2) epidemics.
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Influenza Humana , Sepse , Idoso , Criança , Pré-Escolar , Hong Kong/epidemiologia , Hospitalização , Humanos , Vírus da Influenza A Subtipo H3N2 , Sepse/epidemiologiaRESUMO
For >70 years, a 4-fold or greater rise in antibody titer has been used to confirm influenza virus infections in paired sera, despite recognition that this heuristic can lack sensitivity. Here we analyze with a novel Bayesian model a large cohort of 2353 individuals followed for up to 5 years in Hong Kong to characterize influenza antibody dynamics and develop an algorithm to improve the identification of influenza virus infections. After infection, we estimate that hemagglutination-inhibiting (HAI) titers were boosted by 16-fold on average and subsequently decrease by 14% per year. In six epidemics, the infection risks for adults were 3%-19% while the infection risks for children were 1.6-4.4 times higher than that of younger adults. Every two-fold increase in pre-epidemic HAI titer was associated with 19%-58% protection against infection. Our inferential framework clarifies the contributions of age and pre-epidemic HAI titers to characterize individual infection risk.
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Doenças Transmissíveis , Vacinas contra Influenza , Influenza Humana , Orthomyxoviridae , Adulto , Anticorpos Antivirais , Teorema de Bayes , Criança , Suscetibilidade a Doenças , Testes de Inibição da Hemaglutinação , HumanosRESUMO
Many locations around the world have used real-time estimates of the time-varying effective reproductive number ([Formula: see text]) of COVID-19 to provide evidence of transmission intensity to inform control strategies. Estimates of [Formula: see text] are typically based on statistical models applied to case counts and typically suffer lags of more than a week because of the latent period and reporting delays. Noting that viral loads tend to decline over time since illness onset, analysis of the distribution of viral loads among confirmed cases can provide insights into epidemic trajectory. Here, we analyzed viral load data on confirmed cases during two local epidemics in Hong Kong, identifying a strong correlation between temporal changes in the distribution of viral loads (measured by RT-qPCR cycle threshold values) and estimates of [Formula: see text] based on case counts. We demonstrate that cycle threshold values could be used to improve real-time [Formula: see text] estimation, enabling more timely tracking of epidemic dynamics.
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COVID-19/transmissão , Modelos Epidemiológicos , SARS-CoV-2 , Carga Viral , Número Básico de Reprodução/estatística & dados numéricos , COVID-19/epidemiologia , COVID-19/virologia , Simulação por Computador , Sistemas Computacionais , Epidemias , Hong Kong/epidemiologia , Humanos , Modelos Estatísticos , Pandemias , Carga Viral/estatística & dados numéricosRESUMO
Controlling transmission in restaurants is an important component of public health and social measures for coronavirus disease. We examined the effects of restaurant measures in Hong Kong. Our findings indicate that shortening operating hours did not have an effect on time-varying effective reproduction number when capacity was already reduced.
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COVID-19 , Número Básico de Reprodução , COVID-19/prevenção & controle , Hong Kong/epidemiologia , Humanos , Restaurantes , SARS-CoV-2RESUMO
BACKGROUND: Influenza is the most common vaccine-preventable disease in Australia, causing significant morbidity and mortality. We assessed the burden of influenza across all ages in terms of influenza-associated mortality and hospitalizations using national mortality, hospital-discharge and influenza surveillance data. METHODS: Influenza-associated excess respiratory mortality and hospitalization rates from 2007 to 2015 were estimated using generalized additive models with a proxy of influenza activity based on syndromic and laboratory surveillance data. Estimates were made for each age group and year. RESULTS: The estimated mean annual influenza-associated excess respiratory mortality was 2.6 per 100 000 population [95% confidence interval (CI): 1.8, 3.4 per 100 000 population]. The excess annual respiratory hospitalization rate was 57.4 per 100 000 population (95% CI: 32.5, 82.2 per 100 000 population). The highest mortality rates were observed among those aged ≥75 years (35.11 per 100 000 population; 95% CI: 19.93, 50.29 per 100 000 population) and hospitalization rates were also highest among older adults aged ≥75 years (302.95 per 100 000 population; 95% CI: 144.71, 461.19 per 100 000 population), as well as children aged <6 months (164.02 per 100 000 population; 95% CI: -34.84, 362.88 per 100 000 population). Annual variation was apparent, ranging from 1.0 to 3.9 per 100 000 population for mortality and 24.2 to 94.28 per 100 000 population for hospitalizations. Influenza A contributed to almost 80% of the average excess respiratory hospitalizations and 60% of the average excess respiratory deaths. CONCLUSIONS: Influenza causes considerable burden to all Australians. Expected variation was observed among age groups, years and influenza type, with the greatest burden falling to older adults and young children. Understanding the current burden is useful for understanding the potential impact of mitigation strategies, such as vaccination.
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Vacinas contra Influenza , Influenza Humana , Idoso , Austrália/epidemiologia , Hospitalização , Humanos , Lactente , Influenza Humana/complicações , VacinaçãoRESUMO
BACKGROUND: Testing of an entire community has been used as an approach to control coronavirus disease 2019 (COVID-19). In Hong Kong, a universal community testing program (UCTP) was implemented at the fadeout phase of a community epidemic in July to September 2020. We described the utility of the UCTP in finding unrecognized infections and analyzed data from the UCTP and other sources to characterize transmission dynamics. METHODS: We described the characteristics of people participating in the UCTP and compared the clinical and epidemiological characteristics of COVID-19 cases detected by the UCTP versus those detected by clinical diagnosis and public health surveillance (CDPHS). We developed a Bayesian model to estimate the age-specific incidence of infection and the proportion of cases detected by CDPHS. RESULTS: In total, 1.77 million people, 24% of the Hong Kong population, participated in the UCTP from 1 to 14 September 2020. The UCTP identified 32 new infections (1.8 per 100000 samples tested), consisting of 29% of all local cases reported during the two-week UCTP period. Compared with the CDPHS, the UCTP detected a higher proportion of sporadic cases (62% vs 27%, P<.01) and identified 6 (out of 18) additional clusters during that period. We estimated that 27% (95% credible interval: 22%, 34%) of all infections were detected by the CDPHS in the third wave. CONCLUSIONS: We reported empirical evidence of the utility of population-wide COVID-19 testing in detecting unrecognized infections and clusters. Around three quarters of infections have not been identified through existing surveillance approaches including contact tracing.
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COVID-19 , Ácidos Nucleicos , Teorema de Bayes , COVID-19/diagnóstico , COVID-19/epidemiologia , Teste para COVID-19 , Estudos Transversais , Hong Kong/epidemiologia , Humanos , SARS-CoV-2RESUMO
BACKGROUND: Influenza epidemics occur during winter in temperate zones, but have less regular seasonality in the subtropics and tropics. Here we quantified the role of environmental drivers of influenza seasonality in temperate and subtropical China. METHODS: We used weekly surveillance data on influenza virus activity in mainland China and Hong Kong from 2005 through 2016. We estimated the transmissibility via the instantaneous reproduction number (Rt), a real-time measure of transmissibility, and examined its relationship with different climactic drivers and allowed for the timing of school holidays and the decline in susceptibility in the population as an epidemic progressed. We developed a multivariable regression model for Rt to quantify the contribution of various potential environmental drivers of transmission. FINDINGS: We found that absolute humidity is a potential driver of influenza seasonality and had a U-shaped association with transmissibility and hence can predict the pattern of influenza virus transmission across different climate zones. Absolute humidity was able to explain up to 15% of the variance in Rt, and was a stronger predictor of Rt across the latitudes. Other climatic drivers including mean daily temperature explained up to 13% of variance in Rt and limited to the locations where the indoor measures of these factors have better indicators of outdoor measures. The non-climatic driver, holiday-related school closures could explain up to 7% of variance in Rt. INTERPRETATION: A U-shaped association of absolute humidity with influenza transmissibility was able to predict seasonal patterns of influenza virus epidemics in temperate and subtropical locations.
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Epidemias , Influenza Humana , China/epidemiologia , Hong Kong/epidemiologia , Humanos , Influenza Humana/epidemiologia , Estações do AnoRESUMO
BACKGROUND: Coronavirus disease 2019 (COVID-19) has caused a heavy disease burden globally. The impact of process and timing of data collection on the accuracy of estimation of key epidemiological distributions are unclear. Because infection times are typically unobserved, there are relatively few estimates of generation time distribution. METHODS: We developed a statistical framework to jointly estimate generation time and incubation period from human-to-human transmission pairs, accounting for sampling biases. We applied the framework on 80 laboratory-confirmed human-to-human transmission pairs in China. We further inferred the infectiousness profile, serial interval distribution, proportions of presymptomatic transmission, and basic reproduction number (R0) for COVID-19. RESULTS: The estimated mean incubation period was 4.8 days (95% confidence interval [CI], 4.1-5.6), and mean generation time was 5.7 days (95% CI, 4.8-6.5). The estimated R0 based on the estimated generation time was 2.2 (95% CI, 1.9-2.4). A simulation study suggested that our approach could provide unbiased estimates, insensitive to the width of exposure windows. CONCLUSIONS: Properly accounting for the timing and process of data collection is critical to have correct estimates of generation time and incubation period. R0 can be biased when it is derived based on serial interval as the proxy of generation time.