RESUMO
The epidemiological characteristics of SARS-CoV-2 transmission have changed over the pandemic due to emergence of new variants. A decrease in the generation or serial intervals would imply a shortened transmission timescale and, hence, outbreak response measures would need to expand at a faster rate. However, there are challenges in measuring these intervals. Alongside epidemiological changes, factors like varying delays in outbreak response, social contact patterns, dependence on the growth phase of an outbreak, and effects of exposure to multiple infectors can also influence measured generation or serial intervals. To guide real-time interpretation of variant data, we simulated concurrent changes in the aforementioned factors and estimated the statistical power to detect a change in the generation and serial interval. We compared our findings to the reported decrease or lack thereof in the generation and serial intervals of different SARS-CoV-2 variants. Our study helps to clarify contradictory outbreak observations and informs the required sample sizes under certain outbreak conditions to ensure that future studies of generation and serial intervals are adequately powered.
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COVID-19 , Humanos , COVID-19/epidemiologia , Surtos de Doenças , Pandemias , Previsões , BiologiaRESUMO
The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics-such as varying levels of immunity-can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform Coronavirus Disease 2019 (COVID-19) planning and response and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both interindividual variation in Ct values and complex host characteristics-such as vaccination status, exposure history, and age-we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least 5 prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs. Trial Registration: The Legacy study is a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening for SARS-CoV-2 at University College London Hospitals or at the Francis Crick Institute (NCT04750356) (22,23). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469) and is sponsored by University College London Hospitals. Written consent was given by all participants.
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COVID-19 , SARS-CoV-2 , Adulto , Humanos , SARS-CoV-2/genética , Teorema de Bayes , COVID-19/epidemiologia , Estudos ProspectivosRESUMO
Several XBB subvariants such as XBB.1.5, XBB.1.9, XBB.1.16 and XBB.2.3 co-circulate in Singapore. Despite the different viral properties of XBB.1.16 as compared to other XBB subvariants, comparison on their severity is limited. In this study, we investigate the outcomes of hospitalisation and severe COVID-19 infection in individuals infected with different XBB subvariants, adjusted for potential confounders such as age and vaccination history. Overall, our preliminary analysis showed that the risk of severe outcomes when infected with XBB.1.16 is higher than that of XBB.1.5 or XBB.1.9 but there is no difference in the risk of hospitalisation across different XBB subvariants.
RESUMO
The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.
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BACKGROUND: Understanding the overall effectiveness of non-pharmaceutical interventions to control the COVID-19 pandemic and reduce the burden of disease is crucial for future pandemic planning. However, quantifying the effectiveness of specific control measures and the extent of missed infections, in the absence of early large-scale serological surveys or random community testing, has remained challenging. METHODS: Combining data on notified local COVID-19 cases with known and unknown sources of infections in Singapore with a branching process model, we reconstructed the incidence of missed infections during the early phase of the wild-type SARS-CoV-2 and Delta variant transmission. We then estimated the relative effectiveness of border control measures, case finding and contact tracing when there was no or low vaccine coverage in the population. We compared the risk of ICU admission and death between the wild-type SARS-CoV-2 and the Delta variant in notified cases and all infections. RESULTS: We estimated strict border control measures were associated with 0.2 (95% credible intervals, CrI 0.04-0.8) missed imported infections per notified case between July and December 2020, a decline from around 1 missed imported infection per notified case in the early phases of the pandemic. Contact tracing was estimated to identify 78% (95% CrI 62-93%) of the secondary infections generated by notified cases before the partial lockdown in Apr 2020, but this declined to 63% (95% CrI 56-71%) during the lockdown and rebounded to 78% (95% CrI 58-94%) during reopening in Jul 2020. The contribution of contact tracing towards overall outbreak control also hinges on ability to find cases with unknown sources of infection: 42% (95% CrI 12-84%) of such cases were found prior to the lockdown; 10% (95% CrI 7-15%) during the lockdown; 47% (95% CrI 17-85%) during reopening, due to increased testing capacity and health-seeking behaviour. We estimated around 63% (95% CrI 49-78%) of the wild-type SARS-CoV-2 infections were undetected during 2020 and around 70% (95% CrI 49-91%) for the Delta variant in 2021. CONCLUSIONS: Combining models with case linkage data enables evaluation of the effectiveness of different components of outbreak control measures, and provides more reliable situational awareness when some cases are missed. Using such approaches for early identification of the weakest link in containment efforts could help policy makers to better redirect limited resources to strengthen outbreak control.
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COVID-19 , SARS-CoV-2 , Humanos , SARS-CoV-2/genética , COVID-19/diagnóstico , COVID-19/epidemiologia , COVID-19/prevenção & controle , Busca de Comunicante , Controle de Doenças Transmissíveis , Pandemias/prevenção & controleRESUMO
The emergence of highly transmissible SARS-CoV-2 variants has created a need to reassess the risk posed by increasing social contacts as countries resume pre-pandemic activities, particularly in the context of resuming large-scale events over multiple days. To examine how social contacts formed in different activity settings influences interventions required to control Delta variant outbreaks, we collected high-resolution data on contacts among passengers and crew on cruise ships and combined the data with network transmission models. We found passengers had a median of 20 (IQR 10-36) unique close contacts per day, and over 60% of their contact episodes were made in dining or sports areas where mask wearing is typically limited. In simulated outbreaks, we found that vaccination coverage and rapid antigen tests had a larger effect than mask mandates alone, indicating the importance of combined interventions against Delta to reduce event risk in the vaccine era.
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COVID-19 , SARS-CoV-2 , COVID-19/epidemiologia , COVID-19/prevenção & controle , Surtos de Doenças/prevenção & controle , Humanos , NaviosRESUMO
Starting with a handful of SARS-CoV-2 infections in dormitory residents in late March 2020, rapid transmission in their dense living environments ensued and by October 2020, more than 50,000 acute infections were identified across various dormitories in Singapore. The aim of the study is to identify combination of factors facilitating SARS-CoV-2 transmission and the impact of control measures in a dormitory through extensive epidemiological, serological and phylogenetic investigations, supported by simulation models. Our findings showed that asymptomatic cases and symptomatic cases who did not seek medical attention were major drivers of the outbreak. Furthermore, each resident had about 30 close contacts and each infected resident spread to 4.4 (IQR 3.5-5.3) others at the start of the outbreak. The final attack rate of the current outbreak was 76.2% (IQR 70.6-98.0%) and could be reduced by further 10% under a modified dormitory housing condition. These findings are important when designing living environments in a post COVID-19 future to reduce disease spread and facilitate rapid implementation of outbreak control measures.
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COVID-19/prevenção & controle , COVID-19/transmissão , Surtos de Doenças/prevenção & controle , Densidade Demográfica , SARS-CoV-2/fisiologia , COVID-19/epidemiologia , Surtos de Doenças/estatística & dados numéricos , Humanos , FilogeniaRESUMO
BACKGROUND: We present a novel approach for exiting coronavirus disease 2019 (COVID-19) lockdowns using a 'risk scorecard' to prioritize activities to resume whilst allowing safe reopening. METHODS: We modelled cases generated in the community/week, incorporating parameters for social distancing, contact tracing and imported cases. We set thresholds for cases and analysed the effect of varying parameters. An online tool to facilitate country-specific use including the modification of parameters (https://sshsphdemos.shinyapps.io/covid_riskbudget/) enables visualization of effects of parameter changes and trade-offs. Local outbreak investigation data from Singapore illustrate this. RESULTS: Setting a threshold of 0.9 mean number of secondary cases arising from a case to keep R < 1, we showed that opening all activities excluding high-risk ones (e.g. nightclubs) allows cases to remain within threshold; while opening high-risk activities would exceed the threshold and result in escalating cases. An 80% reduction in imported cases per week (141 to 29) reduced steady-state cases by 30% (295 to 205). One-off surges in cases (due to superspreading) had no effect on the steady state if the R remains <1. Increasing the effectiveness of contact tracing (probability of a community case being isolated when infectious) by 33% (0.6 to 0.8) reduced cases by 22% (295 to 231). Cases grew exponentially if the product of the mean number of secondary cases arising from a case and (1-probability of case being isolated) was >1. CONCLUSIONS: Countries can utilize a 'risk scorecard' to balance relaxations for travel and domestic activity depending on factors that reduce disease impact, including hospital/ICU capacity, contact tracing, quarantine and vaccination. The tool enabled visualization of the combinations of imported cases and activity levels on the case numbers and the trade-offs required. For vaccination, a reduction factor should be applied both for likelihood of an infected case being present and a close contact getting infected.
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COVID-19 , Controle de Doenças Transmissíveis , Busca de Comunicante , Humanos , Quarentena , SARS-CoV-2RESUMO
BACKGROUND: Host determinants of severe coronavirus disease 2019 include advanced age, comorbidities and male sex. Virologic factors may also be important in determining clinical outcome and transmission rates, but limited patient-level data is available. METHODS: We conducted an observational cohort study at seven public hospitals in Singapore. Clinical and laboratory data were collected and compared between individuals infected with different SARS-CoV-2 clades. Firth's logistic regression was used to examine the association between SARS-CoV-2 clade and development of hypoxia, and quasi-Poisson regression to compare transmission rates. Plasma samples were tested for immune mediator levels and the kinetics of viral replication in cell culture were compared. FINDINGS: 319 patients with PCR-confirmed SARS-CoV-2 infection had clinical and virologic data available for analysis. 29 (9%) were infected with clade S, 90 (28%) with clade L/V, 96 (30%) with clade G (containing D614G variant), and 104 (33%) with other clades 'O' were assigned to lineage B.6. After adjusting for age and other covariates, infections with clade S (adjusted odds ratio (aOR) 0·030 (95% confidence intervals (CI): 0·0002-0·29)) or clade O (B·6) (aOR 0·26 (95% CI 0·064-0·93)) were associated with lower odds of developing hypoxia requiring supplemental oxygen compared with clade L/V. Patients infected with clade L/V had more pronounced systemic inflammation with higher concentrations of pro-inflammatory cytokines, chemokines and growth factors. No significant difference in the severity of clade G infections was observed (aOR 0·95 (95% CI: 0·35-2·52). Though viral loads were significantly higher, there was no evidence of increased transmissibility of clade G, and replicative fitness in cell culture was similar for all clades. INTERPRETATION: Infection with clades L/V was associated with increased severity and more systemic release of pro-inflammatory cytokines. Infection with clade G was not associated with changes in severity, and despite higher viral loads there was no evidence of increased transmissibility.
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COVID-19/etiologia , COVID-19/transmissão , SARS-CoV-2/genética , SARS-CoV-2/patogenicidade , Adulto , Fatores Etários , Idoso , COVID-19/epidemiologia , COVID-19/imunologia , Comorbidade , Feminino , Humanos , Hipóxia/terapia , Hipóxia/virologia , Masculino , Pessoa de Meia-Idade , Singapura/epidemiologia , Carga ViralRESUMO
BACKGROUND: We hypothesize that comprehensive surveillance of COVID-19 in Singapore has facilitated early case detection and prompt contact tracing and, with community-based measures, contained spread. We assessed the effectiveness of containment measures by estimating transmissibility (effective reproduction number, (Equation is included in full-text article.)) over the course of the outbreak. METHODS: We used a Bayesian data augmentation framework to allocate infectors to infectees with no known infectors and determine serial interval distribution parameters via Markov chain Monte Carlo sampling. We fitted a smoothing spline to the number of secondary cases generated by each infector by respective onset dates to estimate (Equation is included in full-text article.)and evaluated increase in mean number of secondary cases per individual for each day's delay in starting isolation or quarantine. RESULTS: As of April 1, 2020, 1000 COVID-19 cases were reported in Singapore. We estimated a mean serial interval of 4.6 days [95% credible interval (CI) = 4.2, 5.1] with a SD of 3.5 days (95% CI = 3.1, 4.0). The posterior mean (Equation is included in full-text article.)was below one for most of the time, peaking at 1.1 (95% CI = 1.0, 1.3) on week 9 of 2020 due to a spreading event in one of the clusters. Eight hundred twenty-seven (82.7%) of cases infected less than one person on average. Over an interval of 7 days, the incremental mean number of cases generated per individual for each day's delay in starting isolation or quarantine was 0.03 cases (95% CI = 0.02, 0.05). CONCLUSIONS: We estimate that robust surveillance, active case detection, prompt contact tracing, and quarantine of close contacts kept (Equation is included in full-text article.)below one.
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COVID-19/prevenção & controle , Controle de Doenças Transmissíveis/métodos , Política de Saúde , Número Básico de Reprodução , Teorema de Bayes , COVID-19/epidemiologia , COVID-19/transmissão , Doenças Transmissíveis Importadas/epidemiologia , Doenças Transmissíveis Importadas/prevenção & controle , Doenças Transmissíveis Importadas/transmissão , Busca de Comunicante , Diagnóstico Precoce , Monitoramento Epidemiológico , Humanos , Cadeias de Markov , Programas de Rastreamento , Método de Monte Carlo , Singapura/epidemiologia , ViagemRESUMO
BACKGROUND: The proportion of asymptomatic carriers and transmission risk factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among household and non-household contacts remains unclear. In Singapore, extensive contact tracing by the Ministry of Health for every diagnosed COVID-19 case, and legally enforced quarantine and intensive health surveillance of close contacts provided a rare opportunity to determine asymptomatic attack rates and SARS-CoV-2 transmission risk factors among community close contacts of patients with COVID-19. METHODS: This retrospective cohort study involved all close contacts of confirmed COVID-19 cases in Singapore, identified between Jan 23 and April 3, 2020. Household contacts were defined as individuals who shared a residence with the index COVID-19 case. Non-household close contacts were defined as those who had contact for at least 30 min within 2 m of the index case. All patients with COVID-19 in Singapore received inpatient treatment, with access restricted to health-care staff. All close contacts were quarantined for 14 days with thrice-daily symptom monitoring via telephone. Symptomatic contacts underwent PCR testing for SARS-CoV-2. Secondary clinical attack rates were derived from the prevalence of PCR-confirmed SARS-CoV-2 among close contacts. Consenting contacts underwent serology testing and detailed exposure risk assessment. Bayesian modelling was used to estimate the prevalence of missed diagnoses and asymptomatic SARS-CoV-2-positive cases. Univariable and multivariable logistic regression models were used to determine SARS-CoV-2 transmission risk factors. FINDINGS: Between Jan 23 and April 3, 2020, 7770 close contacts (1863 household contacts, 2319 work contacts, and 3588 social contacts) linked to 1114 PCR-confirmed index cases were identified. Symptom-based PCR testing detected 188 COVID-19 cases, and 7582 close contacts completed quarantine without a positive SARS-CoV-2 PCR test. Among 7518 (96·8%) of the 7770 close contacts with complete data, the secondary clinical attack rate was 5·9% (95% CI 4·9-7·1) for 1779 household contacts, 1·3% (0·9-1·9) for 2231 work contacts, and 1·3% (1·0-1·7) for 3508 social contacts. Bayesian analysis of serology and symptom data obtained from 1150 close contacts (524 household contacts, 207 work contacts, and 419 social contacts) estimated that a symptom-based PCR-testing strategy missed 62% (95% credible interval 55-69) of COVID-19 diagnoses, and 36% (27-45) of individuals with SARS-CoV-2 infection were asymptomatic. Sharing a bedroom (multivariable odds ratio [OR] 5·38 [95% CI 1·82-15·84]; p=0·0023) and being spoken to by an index case for 30 min or longer (7·86 [3·86-16·02]; p<0·0001) were associated with SARS-CoV-2 transmission among household contacts. Among non-household contacts, exposure to more than one case (multivariable OR 3·92 [95% CI 2·07-7·40], p<0·0001), being spoken to by an index case for 30 min or longer (2·67 [1·21-5·88]; p=0·015), and sharing a vehicle with an index case (3·07 [1·55-6·08]; p=0·0013) were associated with SARS-CoV-2 transmission. Among both household and non-household contacts, indirect contact, meal sharing, and lavatory co-usage were not independently associated with SARS-CoV-2 transmission. INTERPRETATION: Targeted community measures should include physical distancing and minimising verbal interactions. Testing of all household contacts, including asymptomatic individuals, is warranted. FUNDING: Ministry of Health of Singapore, National Research Foundation of Singapore, and National Natural Science Foundation of China.
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COVID-19/epidemiologia , SARS-CoV-2/isolamento & purificação , Adolescente , Adulto , Teorema de Bayes , COVID-19/imunologia , COVID-19/transmissão , Criança , China/epidemiologia , Busca de Comunicante , Características da Família , Feminino , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Quarentena , Estudos Retrospectivos , Medição de Risco , Fatores de Risco , SARS-CoV-2/imunologia , Estudos Soroepidemiológicos , Singapura/epidemiologia , Adulto JovemRESUMO
Prior to the implementation of social distancing measures, we monitored the close family contacts of the first 400 cases of COVID-19 in Singapore for SARS-CoV-2 infection to determine the risk of infection with age. Adjusting for gender and household size, the risk of COVID-19 infection in household contacts was found to increase with age.
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COVID-19/epidemiologia , COVID-19/transmissão , Fatores Etários , COVID-19/diagnóstico , Busca de Comunicante , Características da Família , Feminino , Humanos , Masculino , Risco , SARS-CoV-2/isolamento & purificação , Singapura/epidemiologiaRESUMO
Some directly transmitted human pathogens, such as influenza and measles, generate sustained exponential growth in incidence and have a high peak incidence consistent with the rapid depletion of susceptible individuals. Many do not. While a prolonged exponential phase typically arises in traditional disease-dynamic models, current quantitative descriptions of nonstandard epidemic profiles are either abstract, phenomenological, or rely on highly skewed offspring distributions in network models. Here, we create large socio-spatial networks to represent contact behavior using human population-density data, a previously developed fitting algorithm, and gravity-like mobility kernels. We define a basic reproductive number [Formula: see text] for this system, analogous to that used for compartmental models. Controlling for [Formula: see text], we then explore networks with a household-workplace structure in which between-household contacts can be formed with varying degrees of spatial correlation, determined by a single parameter from the gravity-like kernel. By varying this single parameter and simulating epidemic spread, we are able to identify how more frequent local movement can lead to strong spatial correlation and, thus, induce subexponential outbreak dynamics with lower, later epidemic peaks. Also, the ratio of peak height to final size was much smaller when movement was highly spatially correlated. We investigate the topological properties of our networks via a generalized clustering coefficient that extends beyond immediate neighborhoods, identifying very strong correlations between fourth-order clustering and nonstandard epidemic dynamics. Our results motivate the observation of both incidence and socio-spatial human behavior during epidemics that exhibit nonstandard incidence patterns.
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Epidemias/estatística & dados numéricos , Modelos Biológicos , Rede Social , Algoritmos , Análise por Conglomerados , Simulação por Computador , Características da Família , Humanos , Incidência , Informática Médica , Densidade DemográficaRESUMO
A measles outbreak involving 19 adults in a home for the intellectually disabled occurred in Singapore in 2019. Further investigation, including a serological survey, was conducted. Mass vaccination and infection control measures were implemented, terminating further secondary transmission. Seropositivity among residents aged 40 to 49 years (90.7%; 95% confidence interval = 78.4%, 96.3%) was lower than among the Singapore adult population (P < .001). This sheltered population, like others previously reported in the literature, had lower measles immunity than the general community, possibly because of limited social interaction. Targeted catch-up vaccination for similarly vulnerable populations should be considered.
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Surtos de Doenças/prevenção & controle , Deficiência Intelectual/terapia , Vacinação em Massa/estatística & dados numéricos , Vacina contra Sarampo/administração & dosagem , Sarampo/epidemiologia , Sarampo/prevenção & controle , Adulto , Feminino , Humanos , Masculino , Sarampo/imunologia , Pessoa de Meia-Idade , Instituições Residenciais , Singapura/epidemiologiaRESUMO
We compared indicators of influenza activity in 2020 before and after public health measures were taken to reduce coronavirus disease (COVID-19) with the corresponding indicators from 3 preceding years. Influenza activity declined substantially, suggesting that the measures taken for COVID-19 were effective in reducing spread of other viral respiratory diseases.
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COVID-19/epidemiologia , COVID-19/prevenção & controle , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/prevenção & controle , Influenza Humana/epidemiologia , Influenza Humana/prevenção & controle , Pandemias/prevenção & controle , Pneumonia Viral/epidemiologia , Pneumonia Viral/prevenção & controle , Betacoronavirus/patogenicidade , Betacoronavirus/fisiologia , COVID-19/transmissão , Controle de Doenças Transmissíveis/métodos , Controle de Doenças Transmissíveis/organização & administração , Infecções por Coronavirus/transmissão , Humanos , Incidência , Influenza Humana/transmissão , Modelos Estatísticos , Orthomyxoviridae/patogenicidade , Orthomyxoviridae/fisiologia , Distanciamento Físico , Pneumonia Viral/transmissão , Saúde Pública , Fatores de Risco , SARS-CoV-2 , Singapura/epidemiologiaRESUMO
Coronavirus disease 2019 (COVID-19) was first reported in Wuhan, China, in December 2019, and has since spread globally, resulting in >95,000 confirmed COVID-19 cases worldwide by March 5, 2020 (1). Singapore adopted a multipronged surveillance strategy that included applying the case definition at medical consults, tracing contacts of patients with laboratory-confirmed COVID-19, enhancing surveillance among different patient groups (all patients with pneumonia, hospitalized patients in intensive care units [ICUs] with possible infectious diseases, primary care patients with influenza-like illness, and deaths from possible infectious etiologies), and allowing clinician discretion (i.e., option to order a test based on clinical suspicion, even if the case definition was not met) to identify COVID-19 patients. Containment measures, including patient isolation and quarantine, active monitoring of contacts, border controls, and community education and precautions, were performed to minimize disease spread. As of March 5, 2020, a total of 117 COVID-19 cases had been identified in Singapore. This report analyzes the first 100 COVID-19 patients in Singapore to determine the effectiveness of the surveillance and containment measures. COVID-19 patients were classified by the primary means by which they were detected. Application of the case definition and contact tracing identified 73 patients, 16 were detected by enhanced surveillance, and 11 were identified by laboratory testing based on providers' clinical discretion. Effectiveness of these measures was assessed by calculating the 7-day moving average of the interval from symptom onset to isolation in hospital or quarantine, which indicated significant decreasing trends for both local and imported COVID-19 cases. Rapid identification and isolation of cases, quarantine of close contacts, and active monitoring of other contacts have been effective in suppressing expansion of the outbreak and have implications for other countries experiencing outbreaks.
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Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/prevenção & controle , Surtos de Doenças/prevenção & controle , Pneumonia Viral/epidemiologia , Pneumonia Viral/prevenção & controle , Vigilância da População/métodos , Adulto , COVID-19 , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Singapura/epidemiologiaRESUMO
BACKGROUND: Three clusters of coronavirus disease 2019 (COVID-19) linked to a tour group from China, a company conference, and a church were identified in Singapore in February, 2020. METHODS: We gathered epidemiological and clinical data from individuals with confirmed COVID-19, via interviews and inpatient medical records, and we did field investigations to assess interactions and possible modes of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Open source reports were obtained for overseas cases. We reported the median (IQR) incubation period of SARS-CoV-2. FINDINGS: As of Feb 15, 2020, 36 cases of COVID-19 were linked epidemiologically to the first three clusters of circumscribed local transmission in Singapore. 425 close contacts were quarantined. Direct or prolonged close contact was reported among affected individuals, although indirect transmission (eg, via fomites and shared food) could not be excluded. The median incubation period of SARS-CoV-2 was 4 days (IQR 3-6). The serial interval between transmission pairs ranged between 3 days and 8 days. INTERPRETATION: SARS-CoV-2 is transmissible in community settings, and local clusters of COVID-19 are expected in countries with high travel volume from China before the lockdown of Wuhan and institution of travel restrictions. Enhanced surveillance and contact tracing is essential to minimise the risk of widespread transmission in the community. FUNDING: None.
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Busca de Comunicante , Infecções por Coronavirus/epidemiologia , Surtos de Doenças , Pneumonia Viral/epidemiologia , Vigilância da População , Adulto , Betacoronavirus , COVID-19 , Defesa Civil , Congressos como Assunto , Infecções por Coronavirus/transmissão , Feminino , Humanos , Controle de Infecções , Masculino , Pessoa de Meia-Idade , Pandemias , Pneumonia Viral/transmissão , Características de Residência , SARS-CoV-2 , Singapura , ViagemRESUMO
BACKGROUND: With at least 94 countries undergoing or exiting lockdowns for contact suppression to control the COVID-19 outbreak, sustainable and public health-driven exit strategies are required. Here we explore the impact of lockdown and exit strategies in Singapore for immediate planning. METHODS: We use an agent-based model to examine the impacts of epidemic control over 480 days. A limited control baseline of case isolation and household member quarantining is used. We measure the impact of lockdown duration and start date on final infection attack sizes. We then apply a 3-month gradual exit strategy, immediately re-opening schools and easing workplace distancing measures, and compare this to long-term social distancing measures. FINDINGS: At baseline, we estimated 815 400 total infections (21.6% of the population). Early lockdown at 5 weeks with no exit strategy averted 18 500 (2.27% of baseline averted), 21 300 (2.61%) and 22 400 (2.75%) infections for 6, 8 and 9-week lockdown durations. Using the exit strategy averted a corresponding 114 700, 121 700 and 126 000 total cases, representing 12.07-13.06% of the total epidemic size under baseline. This diminishes to 9 900-11 300 for a late 8-week start time. Long-term social distancing at 6 and 8-week durations are viable but less effective. INTERPRETATION: Gradual release exit strategies are critical to maintain epidemic suppression under a new normal. We present final infection attack sizes assuming the ongoing importation of cases, which require preparation for a potential second epidemic wave due to ongoing epidemics elsewhere. FUNDING: Singapore Ministry of Health, Singapore Population Health Improvement Centre.