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• Lineage 2 is the prevalent lineage among drug-resistant tuberculosis (TB) in Victoria. • Commonest drug-resistant-TB is isoniazid-resistant TB. • Genomics reveal that drug-resistant TB in Victoria, Australia is primarily imported. Whole genome sequencing (WGS) can identify clusters, transmission patterns, and drug resistance mutations. This is important in low-burden settings such as Australia, as it can assist in efficient contact tracing and surveillance. We conducted a retrospective cohort study using WGS from 155 genomically defined drug-resistant Mycobacterium tuberculosis (DR-TB) isolates collected between 2018-2021 in Victoria, Australia. Bioinformatic analysis was performed to identify resistance-conferring mutations, lineages, clusters and understand how local sequences compared with international context. Of the 155 sequences, 42% were identified as lineage 2 and 35% as lineage 1; 65.8% (102/155) were isoniazid mono-resistant, 8.4% were multi-drug resistant TB and 5.8% were pre-extensively drug-resistant / extensively drug-resistant TB. The most common mutations were observed in katG and fabG1 genes, especially at Ser315Thr and fabG1 -15 C>T for first-line drugs. Ser450Leu was the most frequent mutation in rpoB gene. Phylogenetic analysis confirmed that Victorian DR-TB were associated with importation events. There was little evidence of local transmission with only five isolate pairs. Isoniazid-resistant TB is the commonest DR-TB in Victoria, and the mutation profile is similar to global circulating DR-TB. Most cases are diagnosed among migrants with limited transmission. This study highlights the value of WGS in identification of clusters and resistance-conferring mutations. This information is crucial in supporting disease mitigation and treatment strategies. [ABSTRACT FROM AUTHOR]

Background: Contact tracing (CT) is critical for ebolavirus outbreak response. Ideally, all new cases after the index case should be previously-known contacts (PKC) before their onset, and spend minimal time ill in the community. We assessed the impact of CT during the 2022 Sudan Virus Disease (SVD) outbreak in Uganda. Methods: We collated anonymized data from the SVD case and contacts database to obtain and analyze data on CT performance indicators, comparing confirmed cases that were PKC and were not PKC (NPKC) before onset. We assessed the effect of being PKC on the number of people infected using Poisson regression. Results: There were 3844 contacts of 142 confirmed cases (mean: 22 contacts/case). Forty-seven (33%) confirmed cases were PKC. PKCs had fewer median days from onset to isolation (4 vs 6; P

Objectives: To evaluate the impact of early implementation of public health and social measures (PHSMs) on contact rates over time and explore contact behavior of asymptomatic versus symptomatic cases. Methods: We used the largest contact tracing data in China thus far to estimate the mean contacts over time by age groups and contact settings. We used bootstrap with replacement to quantify the uncertainty of contact matrixes. The Pearson correlation was performed to demonstrate the number of contacts over time in relation to the evolution of restrictions. In addition, we analyzed the index cases with a high number of contacts and index cases that produced a high number of secondary cases. Results: Rapidly adapted PHSMs can reduce the mean contact rates in public places while increasing the mean contact rates within households. The mean contact rates were 11.81 (95% confidence interval, 11.61-12.01) for asymptomatic (at the time of investigation) cases and 6.70 (95% confidence interval, 6.54-6.87) for symptomatic cases. The percentage of asymptomatic cases (at the time of investigation) meeting >50 close contacts make up more than 65% of the overall cases. The percentage of asymptomatic cases producing >10 secondary cases account for more than 80% of the overall cases. Conclusion: PHSMs may increase the contacts within the household, necessitating the need for pertinent prevention strategies at home. Asymptomatic cases can contribute significantly to Omicron transmission. By making asymptomatic people aware that they are already contagious, hence limiting their social contacts, it is possible to lower the transmission risk.

• A total of 66,583 close contacts were included to estimate contact patterns. • Interventions reduce contact in public but increase contact within households. • Asymptomatic cases account for over 65% of cases with a high number of contacts. • Asymptomatic cases make up over 80% of cases that caused a high number of secondary cases. To evaluate the impact of early implementation of public health and social measures (PHSMs) on contact rates over time and explore contact behavior of asymptomatic versus symptomatic cases. We used the largest contact tracing data in China thus far to estimate the mean contacts over time by age groups and contact settings. We used bootstrap with replacement to quantify the uncertainty of contact matrixes. The Pearson correlation was performed to demonstrate the number of contacts over time in relation to the evolution of restrictions. In addition, we analyzed the index cases with a high number of contacts and index cases that produced a high number of secondary cases. Rapidly adapted PHSMs can reduce the mean contact rates in public places while increasing the mean contact rates within households. The mean contact rates were 11.81 (95% confidence interval, 11.61-12.01) for asymptomatic (at the time of investigation) cases and 6.70 (95% confidence interval, 6.54-6.87) for symptomatic cases. The percentage of asymptomatic cases (at the time of investigation) meeting >50 close contacts make up more than 65% of the overall cases. The percentage of asymptomatic cases producing >10 secondary cases account for more than 80% of the overall cases. PHSMs may increase the contacts within the household, necessitating the need for pertinent prevention strategies at home. Asymptomatic cases can contribute significantly to Omicron transmission. By making asymptomatic people aware that they are already contagious, hence limiting their social contacts, it is possible to lower the transmission risk. [ABSTRACT FROM AUTHOR]

Objectives: An outbreak of the SARS-CoV-2 Delta variant occurred in Guangzhou in 2021. This study aimed to identify the transmission dynamics and epidemiological characteristics of the Delta variant outbreak to formulate an effective prevention strategy. Methods: A total of 13102 close contacts and 69 index cases were collected. The incubation period, serial interval, and time interval from the exposure of close contacts to the symptom onset of cases were estimated. Transmission risks based on the exposure time and various characteristics were also assessed. Results: The mean time from exposure to symptom onset among non-household presymptomatic transmission was 3.83 ± 2.29 days, the incubation period was 5 days, and the serial interval was 3 days. The secondary attack rate was high within 4 days before onset and 4–10 days after symptom onset. Compared with other contact types, household contact had a higher transmission risk. The transmission risk increased with the number and frequency of contact with index cases. Cycle threshold (Ct) values were associated with lower transmission risk (adjusted odds ratio [OR] 0.93 [95% CI 0.88–0.99] for ORF 1ab gene; adjusted OR 0.91 [95% CI 0.86–0.97] for N gene). Conclusion: The contact tracing period may need to be extended to 4 days before symptom onset. The low Ct value of index cases, the high number and frequency of contact with index cases, and household contacts were associated with a higher transmission risk of SARS-CoV-2 Delta.

Background: Denmark is a low-incidence country for tuberculosis (TB) and multidrug-resistant (MDR) TB at 5 and 0.05 cases per 100,000 population, respectively. Until 2018, the transmission of MDR-TB was nonexistent except for a few pairwise related family cases. In this study, we describe the first MDR-TB outbreak in Denmark. Methods: On the basis of genotyping of all Mycobacterium tuberculosis (Mtb) culture-positive cases in Denmark spanning 3 decades, 6 molecular- and epidemiologically linked Danish-born cases were identified as the first cluster of an MDR-TB in Denmark. The primary case was diagnosed posthumously in 2010 followed by 5 epidemiologically linked cases from 2018 to 2019. Results and conclusion: Through a combination of routine Mtb genotyping and clinical epidemiological surveillance data, we identified the first Danish MDR-TB outbreak spanning 10 years and were able to disclose the specific transmission pathways in detail, which helped guide the outbreak investigations. The occurrence of an MDR-TB outbreak in a resource-rich low TB incidence setting such as Denmark highlights the importance of a collaborative control system combining classic contact tracing; timely identification of drug-resistant TB through rapid diagnostics; and a close collaboration between clinicians and classical- and molecular epidemiologists for the benefit of TB control.

• Early isolation and care for Ebola disease patients curbs outbreak spread. • We analyzed factors affecting time from symptom onset to effective isolation. • Few cases were isolated early after symptom onset in the 2022 Uganda SVD outbreak. • Delays in effective isolation were reduced for patients with onset later in the outbreak. • Individual and health facility factors influenced time to effective isolation. Early isolation and care for Ebola disease patients at Ebola Treatment Units (ETU) curb outbreak spread. We evaluated time to ETU entry and associated factors during the 2022 Sudan virus disease (SVD) outbreak in Uganda. We included persons with RT-PCR-confirmed SVD with onset September 20-November 30, 2022. We categorized days from symptom onset to ETU entry ("delays") as short (≤2), moderate (3-5), and long (≥6); the latter two were "delayed isolation." We categorized symptom onset timing as "earlier" or "later," using October 15 as a cut-off. We assessed demographics, symptom onset timing, and awareness of contact status as predictors for delayed isolation. We explored reasons for early vs late isolation using key informant interviews. Among 118 case-patients, 25 (21%) had short, 43 (36%) moderate, and 50 (43%) long delays. Seventy-five (64%) had symptom onset later in the outbreak. Earlier symptom onset increased risk of delayed isolation (crude risk ratio = 1.8, 95% confidence interval (1.2-2.8]). Awareness of contact status and SVD symptoms, and belief that early treatment-seeking was lifesaving facilitated early care-seeking. Patients with long delays reported fear of ETUs and lack of transport as contributors. Delayed isolation was common early in the outbreak. Strong contact tracing and community engagement could expedite presentation to ETUs. [ABSTRACT FROM AUTHOR]

• Propensity for rapid transmission of the L4.1.2.1 sublineage in northern Tunisia. • The L4.1.2.1 sublineage is the primary cause of multidrug-resistant tuberculosis outbreaks in northern Tunisia. • A single L4.1.2.1 ancestor clone fuels the overall multidrug-resistant tuberculosis epidemic. We sought to capture the evolutionary itinerary of the Mycobacterium tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, where it caused a major multidrug-resistant (MDR) tuberculosis outbreak in a context strictly negative for HIV infection. We combined whole genome sequencing and Bayesian approaches using a representative collection of drug-susceptible and drug-resistant L4.1.2.1/Haarlem clinical strains (n = 121) recovered from the outbreak region over 16 years. In the absence of drug resistance, the L4.1.2.1/Haarlem sublineage showed a propensity for rapid transmission as witnessed by the high clustering (44.6%) and recent transmission rates (25%), as well as the reduced mean distance between genome pairs. The entire pool of L4.1.2.1/Haarlem MDR strains was found to be linked to either the aforementioned major outbreak (68 individuals, 2001-2016) or to a minor, newly uncovered outbreak (six cases, 2001-2011). Strikingly, the two outbreaks descended independently from a common ancestor that can be dated back to 1886. Our data point to the intrinsic propensity for rapid transmission of the M. tuberculosis L4.1.2.1/Haarlem sublineage in northern Tunisia, linking the overall MDR tuberculosis epidemic to a single ancestor. These findings bring out the important role of the bacillus' genetic background in the emergence of successful MDR M. tuberculosis clones. [ABSTRACT FROM AUTHOR]

Background: Coronavirus disease 2019 (COVID-19) has spread rapidly across the world. Tunisia reacted early to COVID-19, resulting in a low number of infections during the first wave of the pandemic. This study was performed to model the effects of different interventions on the evolution of cases and to compare these with the Tunisian experience. Methods: A stochastic transmission model was used to quantify the reduction in number of cases of COVID-19 with the interventions of contact tracing, compliance with isolation, and a general lockdown. Results: In the model, increasing contact tracing from 20% to 80% after the first 100 cases reduced the cumulative number of infections (CNI) by 52% in 1 month. Similarly, increased compliance with isolation from 20% to 80% after the first 100 cases reduced the CNI by 45%. These reductions were smaller if the interventions were implemented after 1000 cases. A general lockdown reduced the CNI by 97% after the first 100 cases. Tunisia implemented its general lockdown after 75 cases were confirmed, which reduced the cumulative number of infected cases by 86% among the general population. Conclusions: This study shows that the early application of critical interventions contributes significantly to reducing infections and the evolution of COVID-19 in a country. Tunisia’s early success with the control of COVID-19 is explained by its quick response.

From late March through April 2021, we experienced a cluster of patients with COVID-19, named "Cluster K", with rapid severe illness compared with those who were infected before. Patients with COVID-19 who were enrolled in this study were divided into two groups: 66 patients from November 2020 to March 2021 (group A) and 37 patients whose infection links were traced from Cluster K (group B). The primary outcome was mortality rate, and the secondary outcome was maximal oxygen flow rate as the severity of the disease. Viral genome sequences were compared between the two groups. Mortality rates were 6.1% in group A and 16.2% in group B (odds ratio: 2.97, 95% confidence interval: 0.65–15.38). The patients in group B required high oxygen flow rate (O 2 ≥10 l/min) in the earlier clinical course (P = 0.029). Viral genome sequences revealed five amino acid mutations; of these, four were found on three nonstructural proteins (NSPs): one in nsp3 and nsp15, two in nsp6 (one of them is near the potential sites under positive selective pressure). Another one was on the S protein. This study suggests that mutations in NSPs, especially nsp6, are associated with adverse clinical outcome in patients with COVID-19. [ABSTRACT FROM AUTHOR]

• Public support for control measures differed in Singapore, Hong Kong, and Malaysia • There is strong public support for vaccination requirements for travelers in Asia • Our study highlights the impact of sociopolitical influences on public perception • Public attitudes toward such control measures should be continually monitored Several countries have implemented control measures to limit SARS-CoV-2 spread, including digital contact tracing, digital monitoring of quarantined individuals, and testing of travelers. These raise ethical issues around privacy, personal freedoms, and equity. However, little is known regarding public acceptability of these measures. In December 2020, we conducted a survey among 3635 respondents in Singapore, Hong Kong, and Malaysia to understand public perceptions on the acceptability of COVID-19 control measures. Hong Kong respondents were much less supportive of digital contact tracing and monitoring devices than those in Malaysia and Singapore. Around three-quarters of Hong Kong respondents perceived digital contact tracing as an unreasonable restriction of individual freedom; <20% trusted that there were adequate local provisions preventing these data being used for other purposes. This was the opposite in Singapore, where nearly 3/4 of respondents agreed that there were adequate data protection rules locally. In contrast, only a minority of Hong Kong respondents viewed mandatory testing and vaccination for travelers as unreasonable infringements of privacy or freedom. Less than 2/3 of respondents in all territories were willing to be vaccinated against COVID-19, with a quarter of respondents undecided. However, support for differential travel restrictions for vaccinated and unvaccinated individuals was high in all settings. Our findings highlight the importance of sociopolitical context in public perception of public health measures and emphasize the need to continually monitor public attitudes toward such measures to inform implementation and communication strategies. [ABSTRACT FROM AUTHOR]

ABSTRACT: OBJECTIVE: To determine the effect of contact tracing on the treatment outcomes of index tuberculosis (TB) cases in Uganda. METHODS: We evaluated TB cases registered at an urban public health facility in Uganda in 2015–2020. We extracted data from the unit's TB and contact tracing registers. Treatment outcomes were classified as cure, loss to follow-up, death and treatment failure. Treatment success was the sum of cure and treatment completion. RESULTS: Among 778 TB cases, contact tracing was conducted for 455 (58.5%). Compared with cases without contract tracing (n=323), cases with contract tracing (n=455) had higher treatment success (92.5% vs 79.3%) and cure rates (57.1% vs 39.9%) and lower loss to follow-up (3.5% vs 9.3%), treatment failure (0.4% vs 1.6%) and death (3.5% vs 9.9%) (P

Background: While the role of contact tracing in the containment of the COVID-19 epidemic remains important until vaccines are widely available, literature on objectively measurable indicators for the effectiveness of contact tracing is scarce. We suggest the diagnostic serial interval, the time between the diagnosis of the infector and infectee, as a new indicator for the effectiveness of contact tracing. Methods: Using an agent-based simulation model, we demonstrate how the diagnostic serial interval correlates with the course of the epidemic. We consider four scenarios of how diagnosis and subsequent isolation are triggered: 1. never, 2. by symptoms, 3. by symptoms and loose contact tracing, 4. by symptoms and tight contact tracing. We further refine scenarios 3 and 4 with different lengths of target diagnostic serial intervals. Results: Scenarios 1 and 2 did not yield a notable difference. In scenarios 3 and 4, however, contact tracing led to a decrease of the height of the epidemic as well as the cumulative proportion of infected agents. Generally, the shorter the diagnostic serial interval was, the smaller the peak of the epidemic became, and the more proportion of the population remained susceptible at the end of the epidemic. Conclusion: A short target diagnosis interval is critical for contact tracing to be effective in the epidemic control. The diagnosis interval can be used to assess and guide the contact tracing strategy.

ABSTRACT: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) sublineage B.1.617.2 or Delta, a variant that began circulating in India and is becoming dominant in the USA, has been responsible for significant morbidity and mortality. In May 2021, the Delta variant was upgraded to a variant of concern by international authorities. This article reports a cluster of SARS-CoV-2 Delta cases detected in Boston, Massachusetts, in May 2021 involving a recent traveller from India and subsequent transmission to two of three close contacts. All three close contacts experienced the same primary exposure events but differed in vaccination status. The two close contacts that eventually tested positive were unvaccinated. The other close contact had received one dose of the BNT162b (Pfizer-BioNTech) vaccine prior to exposure, and received their second dose 2 days after exposure. This case series illustrates the effectiveness of partial vaccination in blocking transmission of the Delta variant to vaccinated individuals under circumstances where the probability of transmission for unvaccinated individuals is high.

On November 20, 2019, the Sierra Leone International Health Regulations (IHR) National Focal Point was notified of an exported case of Lassa fever in The Netherlands, by a Dutch doctor who previously practiced in a rural hospital in Sierra Leone. This report describes the extent of the outbreak, possible sources of infection, and the outbreak response measures taken. Response measures implemented to control the outbreak included coordination across multiple countries and cities, outbreak investigation, active case finding, contact tracing and monitoring, laboratory investigation, and isolation and treatment of cases. We report a hospital-associated outbreak that resulted in 3 confirmed cases (health workers) and 2 probable cases (patients). The case fatality rate was 60%, whereas the secondary attack rate was 14%. Two cases involved exportations to The Netherlands. Failure to detect the index case and poor adherence to infection prevention and control (IPC) protocols contributed to disease spread. Pregnancy status and nonspecific signs and symptoms of the index case contributed to failure in early case detection. Rapid activation of national and subnational incident management systems resulted in rapid outbreak control. We recommend regular training for clinicians on surveillance and IPC protocols and strengthening in-country Lassa virus diagnostic capacity. [ABSTRACT FROM AUTHOR]

• Elucidating the first Danish MDR-TB outbreak spanning 10 years. • Combining classic and molecular epidemiology with clinical information. • Molecular genotyping data reveals an unknown MDR-TB outbreak source. • MDR-TB can occur in a resource-rich TB low incidence setting. Denmark is a low-incidence country for tuberculosis (TB) and multidrug-resistant (MDR) TB at 5 and 0.05 cases per 100,000 population, respectively. Until 2018, the transmission of MDR-TB was nonexistent except for a few pairwise related family cases. In this study, we describe the first MDR-TB outbreak in Denmark. On the basis of genotyping of all Mycobacterium tuberculosis (Mtb) culture-positive cases in Denmark spanning 3 decades, 6 molecular- and epidemiologically linked Danish-born cases were identified as the first cluster of an MDR-TB in Denmark. The primary case was diagnosed posthumously in 2010 followed by 5 epidemiologically linked cases from 2018 to 2019. Through a combination of routine Mtb genotyping and clinical epidemiological surveillance data, we identified the first Danish MDR-TB outbreak spanning 10 years and were able to disclose the specific transmission pathways in detail, which helped guide the outbreak investigations. The occurrence of an MDR-TB outbreak in a resource-rich low TB incidence setting such as Denmark highlights the importance of a collaborative control system combining classic contact tracing; timely identification of drug-resistant TB through rapid diagnostics; and a close collaboration between clinicians and classical- and molecular epidemiologists for the benefit of TB control. [ABSTRACT FROM AUTHOR]

• Time for tracing close contacts may need expanding to 4 days before symptom onset • Low Ct values were associated with a higher risk of SARS-CoV-2 transmission • Presymptomatic transmission was common in the epidemic of Delta variant An outbreak of the SARS-CoV-2 Delta variant occurred in Guangzhou in 2021. This study aimed to identify the transmission dynamics and epidemiological characteristics of the Delta variant outbreak to formulate an effective prevention strategy. A total of 13102 close contacts and 69 index cases were collected. The incubation period, serial interval, and time interval from the exposure of close contacts to the symptom onset of cases were estimated. Transmission risks based on the exposure time and various characteristics were also assessed. The mean time from exposure to symptom onset among non-household presymptomatic transmission was 3.83 ± 2.29 days, the incubation period was 5 days, and the serial interval was 3 days. The secondary attack rate was high within 4 days before onset and 4–10 days after symptom onset. Compared with other contact types, household contact had a higher transmission risk. The transmission risk increased with the number and frequency of contact with index cases. Cycle threshold (Ct) values were associated with lower transmission risk (adjusted odds ratio [OR] 0.93 [95% CI 0.88–0.99] for ORF 1ab gene; adjusted OR 0.91 [95% CI 0.86–0.97] for N gene). The contact tracing period may need to be extended to 4 days before symptom onset. The low Ct value of index cases, the high number and frequency of contact with index cases, and household contacts were associated with a higher transmission risk of SARS-CoV-2 Delta. [ABSTRACT FROM AUTHOR]

Background: Contact tracing has been a central control measure for coronavirus disease 2019 (COVID-19) transmission. However, without consideration of the needs of specific populations, public health interventions can exacerbate health inequities. Aim: The purpose of this rapid review was to determine if and how health inequities were included in the design of contact tracing interventions in epidemic settings. Methods: A search of the electronic databases MEDLINE and Web of Science was conducted. The following inclusion criteria were applied for article selection: (1) described the design of contact tracing interventions, (2) published between 2013 and 2020 in English, French, Spanish, Chinese, or Portuguese, (3) and included at least 50% of empiricism, according to the Automated Classifier of Texts on Scientific Studies (ATCER) tool. Various tools were used to extract data. Results: Following screening of the titles and abstracts of 230 articles, 39 met the inclusion criteria. Only seven references were retained after full text review. None of the selected studies considered health inequities in the design of contact tracing interventions. Conclusions: The use of tools/concepts for incorporating health inequities, such as the REFLEX-ISS tool, and ‘proportionate universalism’ when designing contact tracing interventions, would enable practitioners, decision-makers, and researchers to better consider health inequities.

Background: The complete contact tracing of coronavirus disease-19 (COVID-19) cases in South Korea allows a unique opportunity to investigate cluster characteristics. This study aimed to investigate all reported COVID-19 clusters in the Seoul metropolitan area from January 23 to September 24, 2020. Methods: Publicly available COVID-19 data was collected from the Seoul Metropolitan City and Gyeonggi Province. Community clusters with ≥5 cases were characterized by size and duration, categorized using K-means clustering, and the correlation between the types of clusters and the level of social distancing investigated. Results: A total of 134 clusters comprised of 4033 cases were identified. The clusters were categorized into small (type I and II), medium (type III), and large (type IV) clusters. A comparable number of daily reported cases in different time periods were composed of different types of clusters. Increased social distancing was related to a shift from large to small-sized clusters. Conclusions: Classification of clusters may provide opportunities to understand the pattern of COVID-19 outbreaks better and implement more effective suppression strategies. Social distancing administered by the government may effectively suppress large clusters but may not effectively control small and sporadic clusters.

• Mycobacterium tuberculosis (Mtb) DNA is detected in the peripheral blood cells of donors with tuberculosis (TB) or TB infection. • Mtb DNA is detected in the peripheral blood cells of donors with presumptive TB. • Mtb DNA detection is more frequent in peripheral CD34+ cells. • CD34+ cells may represent a niche for Mtb. • Mtb DNA in peripheral blood cells may be a new microbial biomarker. To investigate whether Mycobacterium tuberculosis (Mtb) DNA is detected in peripheral blood mononuclear cells (PBMC) of subjects with tuberculosis (TB) or TB infection (TBI) living in a low-burden country. We prospectively enrolled 57 patients with TB, 41 subjects with TBI, and 39 controls in Rome, Italy. PBMC were isolated, cluster of differentiation (CD)34+ and CD34− cells were immunomagnetic separated, DNA was extracted, and digital polymerase chain reaction for IS 6110 and rpoB sequences was used to detect Mtb DNA in PBMC subsets and unfractionated PBMC. We detected Mtb DNA at a low copy number in CD34+ cells in 4o f 30 (13%) patients with TB, 2 of 24 (8%) subjects with TBI, and 1 of 24 (4%) controls. Mtb DNA was detected in unfractionated PBMC in 3 of 51 (6%) patients with TB, 2 of 38 (5%) subjects with TBI, and 2 of 36 (6%) controls. In CD34− cells, only 1 of 31 (3%) subjects with TBI tested positive for Mtb DNA. Mtb DNA was detected at low frequencies and levels in the PBMC of subjects with TBI and donors with TB living in a low-burden country. In particular, Mtb DNA was detected more frequently in CD34+ cells, supporting the hypothesis that these cells may represent a Mtb niche. This finding informs biological understanding of Mtb pathogenesis and may support the development of a microbial blood biomarker for Mtb infection. [ABSTRACT FROM AUTHOR]

• 64% of residents in a SARS-CoV-2-affected dormitory were infected by July 2020 • < 0.2% of the Singapore general population were infected with SARS-CoV-2 in 2020 • SARS-CoV-2 spread can be suppressed with prompt, wide-ranging interventions • High-risk, crowded settings require special consideration in preparedness planning • Lowering densities in these settings is key to reducing vulnerability to outbreaks Since January 2020, Singapore has implemented comprehensive measures to suppress SARS-CoV-2. Despite this, the country has experienced contrasting epidemics, with limited transmission in the community and explosive outbreaks in migrant worker dormitories. To estimate SARS-CoV-2 infection incidence among migrant workers and the general population in Singapore. Prospective serological cohort studies. Two cohort studies — in a migrant worker dormitory and in the general population in Singapore. 478 residents of a SARS-CoV-2-affected migrant worker dormitory were followed up between May and July 2020, with blood samples collected on recruitment and after 2 and 6 weeks. In addition, 937 community-dwelling adult Singapore residents, for whom pre-pandemic sera were available, were recruited. These individuals also provided a serum sample on recruitment in November/December 2020. Exposure to SARS-CoV-2 in a densely populated migrant worker dormitory and in the general population. The main outcome measures were the incidences of SARS-CoV-2 infection in migrant workers and in the general population, as determined by the detection of neutralizing antibodies against SARS-CoV-2, and adjusting for assay sensitivity and specificity using a Bayesian modeling framework. No evidence of community SARS-CoV-2 exposure was found in Singapore prior to September 2019. It was estimated that < 2 per 1000 adult residents in the community were infected with SARS-CoV-2 in 2020 (cumulative seroprevalence: 0.16%; 95% CrI: 0.008–0.72%). Comparison with comprehensive national case notification data suggested that around 1 in 4 infections in the general population were associated with symptoms. In contrast, in the migrant worker cohort, almost two-thirds had been infected by July 2020 (cumulative seroprevalence: 63.8%; 95% CrI: 57.9–70.3%); no symptoms were reported in almost all of these infections. Our findings demonstrate that SARS-CoV-2 suppression is possible with strict and rapid implementation of border restrictions, case isolation, contact tracing, quarantining, and social-distancing measures. However, the risk of large-scale epidemics in densely populated environments requires specific consideration in preparedness planning. Prioritization of these settings in vaccination strategies should minimize the risk of future resurgences and potential spillover of transmission to the wider community. [ABSTRACT FROM AUTHOR]

Aim: Comprehensive case investigation and contact tracing are crucial to prevent community spread of COVID-19. We demonstrated a utility of using traditional contact tracing measures supplemented with symptom tracking and contact management system to assist public health workers with high efficiency. Methods: A centralized contact tracing system was developed to support data linkage, cross-jurisdictional coordination, and follow-up of contacts’ health status. We illustrated the process of how digital tools support contact tracing and management of COVID-19 cases and measured the timeliness from case detection to contact monitoring to evaluate system performance. Results: Among the 8051 close contacts of the 487 confirmed cases (16.5 close contacts/case, 95% CI [13.9–19.1]), the median elapsed time from last exposure to quarantine was three days (IQR 1–5). By implementing the approach of self-reporting using automatic text-messages and web-app, the percentage of health status updates from self-reporting increased from 22.5% to 61.5%. The high proportion of secondary cases detected via contact tracing (88%) might reduce the R0 to under one and minimize the impact of local transmission in the community. Conclusion: Comprehensive contact tracing and management with complementary technology would still be a pillar of strategies for containing outbreaks during de-escalation or early in the next wave of COVID-19 pandemic.

Background: The clinical onset serial interval is often used as a proxy for the transmission interval of an infectious disease. For SARS-CoV-2/COVID-19, data on clinical onset serial intervals is limited, since symptom onset dates are not routinely recorded and do not exist in asymptomatic carriers. Methods: We define the diagnostic serial interval as the time between the diagnosis dates of the infector and infectee. Based on the DS4C project data on SARS-CoV-2/COVID-19 in South Korea, we estimate the means of the diagnostic serial interval, the clinical onset serial interval, and the difference between the two. We use the balanced cluster bootstrap method to construct 95% bootstrap confidence intervals. Results: The mean of the diagnostic serial interval was estimated to be 3.63 days (95% CI: 3.24, 4.01). The diagnostic serial interval was significantly shorter than the clinical onset serial interval (estimated mean difference −1.12 days, 95% CI: −1.98, −0.26). Conclusions: The relatively short diagnostic serial intervals of SARS-CoV-2/COVID-19 in South Korea are likely due to the country’s extensive efforts towards contact tracing. We propose the mean diagnostic serial interval as a new indicator for the effectiveness of a country’s contact tracing as part of the epidemic surveillance.

Background: The epidemiological importance of asymptomatic individuals who would never develop illness, compared to those who eventually develop symptoms, has yet to be fully clarified. Methods: The very first cluster data in Tokyo and Kanagawa (n = 36) were analyzed. Movement of all close contact was restricted for 14 days and they underwent laboratory testing with polymerase chain reaction. The reproduction numbers of symptomatic and asymptomatic cases were estimated. Results: The reproduction number for symptomatic cases was estimated to be 1.2 (95% confidence interval (CI): 0.5–2.9). The relative infectiousness of asymptomatically infected cases was estimated to be 0.27 (95% CI: 0.03–0.81) of symptomatic cases. Conclusion: The relative transmissibility of asymptomatic cases is limited. Observing clusters starting with symptomatic transmission might be sufficient for the control.

Coronavirus disease 2019 (COVID-19) has spread rapidly across the world. Tunisia reacted early to COVID-19, resulting in a low number of infections during the first wave of the pandemic. This study was performed to model the effects of different interventions on the evolution of cases and to compare these with the Tunisian experience. A stochastic transmission model was used to quantify the reduction in number of cases of COVID-19 with the interventions of contact tracing, compliance with isolation, and a general lockdown. In the model, increasing contact tracing from 20% to 80% after the first 100 cases reduced the cumulative number of infections (CNI) by 52% in 1 month. Similarly, increased compliance with isolation from 20% to 80% after the first 100 cases reduced the CNI by 45%. These reductions were smaller if the interventions were implemented after 1000 cases. A general lockdown reduced the CNI by 97% after the first 100 cases. Tunisia implemented its general lockdown after 75 cases were confirmed, which reduced the cumulative number of infected cases by 86% among the general population. This study shows that the early application of critical interventions contributes significantly to reducing infections and the evolution of COVID-19 in a country. Tunisia's early success with the control of COVID-19 is explained by its quick response. [ABSTRACT FROM AUTHOR]

• Public health interventions for COVID-19 need to be rapid, strict, and adaptive. • Active case-finding and extensive testing reduces community exposure to COVID-19. • Targeted lockdowns and community surveillance is effective to contain clusters. • Border control does not prevent but can delay the introduction of COVID-19. • Interventions should be implemented in combination to maximize effectiveness. Background: Vietnam implemented various public health interventions such as contact tracing and testing, mandatory quarantine, and lockdowns in response to coronavirus disease 2019 (COVID-19). However, the effects of these measures on the epidemic remain unclear. Methods: This article describes the public health interventions in relation to COVID-19 incidence. Maximum likelihood estimations were used to assess containment delays (time between symptom onset and start of isolation) and multivariable regression was employed to identify associated factors between interventions and COVID-19 incidence. The effective reproductive numbers (Rt) were calculated based on transmission pairs. Results: Interventions were introduced periodically in response to the epidemic. Overall, 817 (55.4%) among 1474 COVID-19 cases were imported. Based on a serial interval of 8.72 ± 5.65 days, it was estimated that Rt decreased to below 1 (lowest at 0.02, 95% CI 0–0.12) during periods of strict border control and contact tracing, and increased ahead of new clusters. The main method to detect cases shifted over time from passive notification to active case-finding at immigration or in lockdown areas, with containment delays showing significant differences between modes of case detection. Conclusions: A combination of early, strict, and consistently implemented interventions is crucial to control COVID-19. Low-middle income countries with limited capacity can contain COVID-19 successfully using non-pharmaceutical interventions. [ABSTRACT FROM AUTHOR]

• Coronavirus in a war and conflict zone. • The existence of the first COVID-19 cases in the northern part of Yemen. • Call for prompt action, due to high secondary attack rate among health workers. • Contact tracing is essential in tracking and breaking chains of transmission of COVID-19. Confirm existence of COVID-19 outbreak, conduct contact tracing, and recommend control measures. Two COVID-19 cases in Sana'a Capital met the WHO case definition. Data were collected from cases and contacts who were followed for 14 days. Nasopharyngeal swabs were taken for confirmation by Polymerase Chain Reaction (PCR). Two confirmed Yemeni male patients aged 20 and 40 years who had no travel history were admitted to hospital on 24 April 2020. Regarding the first patient, symptoms started on April 18th, 2020 then the patient improved and was discharged on May 5th, while the second patient's symptoms started on April 22nd but the patient died on April 29th, 2020. Both patients had 54 contacts, 17 (32%) were health workers (HWs). Four contacts (7%) were confirmed, two of them were HWs that needed hospitalization. The secondary attack rate (sAR) was 12% among HWs compared to 5% among other contacts. First COVID-19 outbreak was confirmed among Yemeni citizens with a high sAR among HWs. Strict infection control among HWs should be ensured. Physical distancing and mask-wearing with appropriate disinfecting measures should be promoted especially among contacts. There is a need to strengthen national capacities to assess, detect, and respond to public health emergencies. [ABSTRACT FROM AUTHOR]

Background: Hong Kong, a Special Administrative Region of China, recorded its first confirmed coronavirus disease 2019 (COVID-19) case on 23 January 2020. We reviewed the case epidemiology and the various public health measures implemented from January to May 2020. Methods: The epidemiological and clinical characteristics of the cases recorded in different phases of the epidemic were described and compared, and the effectiveness of the public health measures implemented were reviewed using the changes in the daily number of confirmed cases and the interval from symptom onset to hospital admission. Results: Between January and May 2020, 1084 confirmed COVID-19 cases were reported, about 70% of which had a history of travel during the incubation period. The case fatality ratio was 0.4%. The local epidemic progressed through four phases: (1) preparedness and imported infection from mainland China, (2) local transmission, (3) imported infection from overseas countries associated with local transmission, and (4) controlled imported infection with limited local transmission, with an eventual reduction of the daily case number and minimization of the onset-to-admission interval. Various public health measures, including enhanced surveillance, border control, and social distancing, were introduced in phases in response to the prevailing local and global situations. Discussion: The overall containment strategy in Hong Kong led to a stabilization of the number of cases and the absence of a community-wide outbreak during the 4.5 m after the first case was reported. This strategy of containment might serve as an example for future planning of preparedness and response against novel infectious agents.

Background: Vietnam implemented various public health interventions such as contact tracing and testing, mandatory quarantine, and lockdowns in response to coronavirus disease 2019 (COVID-19). However, the effects of these measures on the epidemic remain unclear.Methods: This article describes the public health interventions in relation to COVID-19 incidence. Maximum likelihood estimations were used to assess containment delays (time between symptom onset and start of isolation) and multivariable regression was employed to identify associated factors between interventions and COVID-19 incidence. The effective reproductive numbers (Rt) were calculated based on transmission pairs.Results: Interventions were introduced periodically in response to the epidemic. Overall, 817 (55.4%) among 1474 COVID-19 cases were imported. Based on a serial interval of 8.72 ± 5.65 days, it was estimated that Rt decreased to below 1 (lowest at 0.02, 95% CI 0–0.12) during periods of strict border control and contact tracing, and increased ahead of new clusters. The main method to detect cases shifted over time from passive notification to active case-finding at immigration or in lockdown areas, with containment delays showing significant differences between modes of case detection.Conclusions: A combination of early, strict, and consistently implemented interventions is crucial to control COVID-19. Low-middle income countries with limited capacity can contain COVID-19 successfully using non-pharmaceutical interventions.

Objectives: Confirm existence of COVID-19 outbreak, conduct contact tracing, and recommend control measures. Methods: Two COVID-19 cases in Sana’a Capital met the WHO case definition. Data were collected from cases and contacts who were followed for 14 days. Nasopharyngeal swabs were taken for confirmation by Polymerase Chain Reaction (PCR). Results: Two confirmed Yemeni male patients aged 20 and 40 years who had no travel history were admitted to hospital on 24 April 2020. Regarding the first patient, symptoms started on April 18th, 2020 then the patient improved and was discharged on May 5th, while the second patient’s symptoms started on April 22nd but the patient died on April 29th, 2020. Both patients had 54 contacts, 17 (32%) were health workers (HWs). Four contacts (7%) were confirmed, two of them were HWs that needed hospitalization. The secondary attack rate (sAR) was 12% among HWs compared to 5% among other contacts. Conclusions: First COVID-19 outbreak was confirmed among Yemeni citizens with a high sAR among HWs. Strict infection control among HWs should be ensured. Physical distancing and mask-wearing with appropriate disinfecting measures should be promoted especially among contacts. There is a need to strengthen national capacities to assess, detect, and respond to public health emergencies.

• In early 2020, the first large COVID-19 outbreak outside China occurred in Daegu • The SARS-CoV-2 strain involved in Daegu outbreak has an R0 of 3.6 (range: 2.3 to 5.6) • The Daegu outbreak was successfully controlled without restricting movement. • A combination of social distancing and testing-contact tracing is highly effective. • Both interventions must be enacted for successful control of an COVID-19 outbreak In Spring 2020, South Korea applied non-lockdown social distancing (avoiding mass gathering and non-essential social engagement, without restricting the movement of people who were not patients or contacts), testing-and-isolation (testing), and tracing-and-quarantine the contacts (contact tracing) to successfully control the first large-scale COVID-19 outbreak outside China. However, the relative contributions of these two interventions remain uncertain. We constructed an SEIR model of SARS-CoV-2 transmission (disproportionately through superspreading events) and fit the model to outbreak data in Daegu, South Korea, from February to April 2020. We assessed the effect of non-lockdown social distancing (population-wide control measures) and/or testing-contact tracing (individual-specific control measures), alone or combined, in terms of the basic reproductive number (R0) and the trajectory of the epidemic. The point estimate for baseline R0 is 3.6 (sensitivity analyses range: 2.3 to 5.6). Combined interventions of non-lockdown social distancing and testing-contact tracing can suppress R0 to less than one and rapidly contain the epidemic, even under the worst scenario with a high baseline R0 of 5.6. In contrast, either intervention alone will fail to suppress R0. Non-lockdown social distancing alone just postpones the peak of the epidemic, while testing-contact tracing alone only flattens the curve but does not contain the outbreak. To successfully control a large-scale COVID-19 outbreak, both non-lockdown social distancing and testing-contact tracing must be implemented. The two interventions are synergistic. [ABSTRACT FROM AUTHOR]

• This SARS-CoV-2 outbreak was contained by extensive contact tracing and proactive isolation. • Rigorous measures enabled the end of the outbreak to be declared quickly. • Less stringent control would have meant lower confidence that the outbreak was over. • Public vigilance was still required for several weeks after the final case. • Later identification of the outbreak could have led to more infections. A hospital-related cluster of 22 cases of coronavirus disease 2019 (COVID-19) occurred in Taiwan in January–February 2021. Rigorous control measures were introduced and could only be relaxed once the outbreak was declared over. Each day after the apparent outbreak end, we estimated the risk of future cases occurring in order to inform decision-making. Probabilistic transmission networks were reconstructed, and transmission parameters (the reproduction number R and overdispersion parameter k) were estimated. The reporting delay during the outbreak was estimated (Scenario 1). In addition, a counterfactual scenario with less effective interventions characterized by a longer reporting delay was considered (Scenario 2). Each day, the risk of future cases was estimated under both scenarios. The values of R and k were estimated to be 1.30 ((95% credible interval (CI) 0.57–3.80) and 0.38 (95% CI 0.12–1.20), respectively. The mean reporting delays considered were 2.5 days (Scenario 1) and 7.8 days (Scenario 2). Following the final case, ttthe inferred probability of future cases occurring declined more quickly in Scenario 1 than Scenario 2. Rigorous control measures allowed the outbreak to be declared over quickly following outbreak containment. This highlights the need for effective interventions, not only to reduce cases during outbreaks but also to allow outbreaks to be declared over with confidence. [ABSTRACT FROM AUTHOR]

• Tuberculosis (TB) contact tracing identifies undiagnosed TB in index TB case contacts • We determined the effect of contact tracing on outcomes of index TB cases • Contact tracing was associated with higher treatment success and cure • It was also associated with lower death, loss to follow-up and treatment failure To determine the effect of contact tracing on the treatment outcomes of index tuberculosis (TB) cases in Uganda. We evaluated TB cases registered at an urban public health facility in Uganda in 2015–2020. We extracted data from the unit's TB and contact tracing registers. Treatment outcomes were classified as cure, loss to follow-up, death and treatment failure. Treatment success was the sum of cure and treatment completion. Among 778 TB cases, contact tracing was conducted for 455 (58.5%). Compared with cases without contract tracing (n=323), cases with contract tracing (n=455) had higher treatment success (92.5% vs 79.3%) and cure rates (57.1% vs 39.9%) and lower loss to follow-up (3.5% vs 9.3%), treatment failure (0.4% vs 1.6%) and death (3.5% vs 9.9%) (P <0.001). Contact tracing was associated with higher odds of treatment success (adjusted odds ratio (aOR) 3.00, 95% CI 1.92–4.70, P <0.001) and cure (aOR 3.11, 95% CI 1.97–4.90, P <0.001), and lower odds of loss to follow-up (aOR 0.33, (0.13–0.83), P =0.018) and death (aOR 0.38, (0.20–0.72), P =0.003). TB contact tracing should be conducted consistently not only for the benefit of identifying new TB cases but also to promote treatment success of index cases. [ABSTRACT FROM AUTHOR]

• The diagnostic serial interval (DSI) is an indicator for contact tracing effectiveness. • The effect of contact tracing varies drastically in the DSI range of 2–6 days. • The timeliness of contact tracing is crucial in containing the epidemic. While the role of contact tracing in the containment of the COVID-19 epidemic remains important until vaccines are widely available, literature on objectively measurable indicators for the effectiveness of contact tracing is scarce. We suggest the diagnostic serial interval, the time between the diagnosis of the infector and infectee, as a new indicator for the effectiveness of contact tracing. Using an agent-based simulation model, we demonstrate how the diagnostic serial interval correlates with the course of the epidemic. We consider four scenarios of how diagnosis and subsequent isolation are triggered: 1. never, 2. by symptoms, 3. by symptoms and loose contact tracing, 4. by symptoms and tight contact tracing. We further refine scenarios 3 and 4 with different lengths of target diagnostic serial intervals. Scenarios 1 and 2 did not yield a notable difference. In scenarios 3 and 4, however, contact tracing led to a decrease of the height of the epidemic as well as the cumulative proportion of infected agents. Generally, the shorter the diagnostic serial interval was, the smaller the peak of the epidemic became, and the more proportion of the population remained susceptible at the end of the epidemic. A short target diagnosis interval is critical for contact tracing to be effective in the epidemic control. The diagnosis interval can be used to assess and guide the contact tracing strategy. [ABSTRACT FROM AUTHOR]

• This review assessed the performance of the SD Biosensor antigen test compared to RT-PCR. • It reported a sensibility of 69.86% and specificity of 99.61%. • The SD Biosensor antigen test enabled rapid identification of asymptomatic individuals. Screening, testing and contact tracing plays a pivotal role in control of the COVID-19 pandemic. To enable this it is necessary to increase the testing capacity. This study compared a SARS-CoV-2 rapid antigen test (RAT) and RT-PCR in 842 asymptomatic individuals from Tarapacá, Chile. A sensitivity of 69.86%, specificity of 99.61%, PPV of 94.44% and NPP of 97.22% with Ct values (Ct > 27) that were significantly higher among individuals with false-negative RAT were reported. These results support the fact that RAT might have a significant impact on the identification of asymptomatic carriers in areas that lack suitable laboratories to perform SARS-CoV-2 real-time RT-PCR diagnostics, or the results take more than 24–48 h, as well as zones with high traffic of individuals such as border/customs, airports, interregional bus, train stations or in any mass testing campaign requiring rapid results. [ABSTRACT FROM AUTHOR]

• The negative converting ratio was 16.4% and 41.0% on days 7 and 14, respectively. • 34.1% and 60.3% of subjects had least one negative RT-PCR result on days 7 and 14. • Joint testing represents an effective means of minimizing the misdiagnosis. The real-time polymerase chain reaction (RT-PCR) test is recommended for the diagnosis of COVID-19 and provides a powerful tool to identify new infections and facilitate contact tracing. In fact, as the prevalence of COVID-19 decreases, this RT-PCR testing remains as the main preventive measure to avoid rebound. However, inconsistent results can lead to misdiagnoses in the clinic. These inconsistencies are due to the variability in (1) the collection times of biological samples post infection, and (2) sampling procedures. We applied the Kaplan–Meier method and multivariate logistic regression on RT-PCR results from 258 confirmed patients with COVID-19 to evaluate the factors associated with negative conversion. We also estimated the proportion (%) of negative conversion among patients who had tested twice or more, and compared the proportions arising from oropharyngeal swabs, sputum, and combined double testing, respectively. The proportion of negative conversion was 6.7% on day 4, 16.4% on day 7, 41.0% at 2 weeks, and 61.0% at 3 weeks post-admission. We also found that 34.1% and 60.3% of subjects had at least one negative RT-PCR result on days 7 and 14 after the onset of symptoms, respectively. The proportion of negative conversions following sputum testing was higher than that from oropharyngeal swabs in the early stages but this declined after the onset of symptoms. In the absence of effective treatments or vaccines, efficient testing strategies are critical if we are to control the COVID-19 epidemic. According to this study, early, consecutive and combined double testing, will be the key to identify infected patients, particularly for asymptomatic and mild symptomatic cases. These strategies will minimize misdiagnosis and the ineffective isolation of infected patients. [ABSTRACT FROM AUTHOR]

• Health inequities can worsen in epidemic settings and should be better considered. • Appropriate planning of contact tracing as a disease control measure is crucial. • Proportionate universalism should be applied in public health interventions. • Tools such as REFLEX-ISS may improve the consideration of health inequities. Contact tracing has been a central control measure for coronavirus disease 2019 (COVID-19) transmission. However, without consideration of the needs of specific populations, public health interventions can exacerbate health inequities. The purpose of this rapid review was to determine if and how health inequities were included in the design of contact tracing interventions in epidemic settings. A search of the electronic databases MEDLINE and Web of Science was conducted. The following inclusion criteria were applied for article selection: (1) described the design of contact tracing interventions, (2) published between 2013 and 2020 in English, French, Spanish, Chinese, or Portuguese, (3) and included at least 50% of empiricism, according to the Automated Classifier of Texts on Scientific Studies (ATCER) tool. Various tools were used to extract data. Following screening of the titles and abstracts of 230 articles, 39 met the inclusion criteria. Only seven references were retained after full text review. None of the selected studies considered health inequities in the design of contact tracing interventions. The use of tools/concepts for incorporating health inequities, such as the REFLEX-ISS tool, and 'proportionate universalism' when designing contact tracing interventions, would enable practitioners, decision-makers, and researchers to better consider health inequities. [ABSTRACT FROM AUTHOR]

• All the reported COVID-19 clusters were identified and categorized in South Korea. • COVID-19 clusters are categorized into large, medium, and small clusters. • Cluster distributions are correlated with the government's social distancing measures. The complete contact tracing of coronavirus disease-19 (COVID-19) cases in South Korea allows a unique opportunity to investigate cluster characteristics. This study aimed to investigate all reported COVID-19 clusters in the Seoul metropolitan area from January 23 to September 24, 2020. Publicly available COVID-19 data was collected from the Seoul Metropolitan City and Gyeonggi Province. Community clusters with ≥5 cases were characterized by size and duration, categorized using K-means clustering, and the correlation between the types of clusters and the level of social distancing investigated. A total of 134 clusters comprised of 4033 cases were identified. The clusters were categorized into small (type I and II), medium (type III), and large (type IV) clusters. A comparable number of daily reported cases in different time periods were composed of different types of clusters. Increased social distancing was related to a shift from large to small-sized clusters. Classification of clusters may provide opportunities to understand the pattern of COVID-19 outbreaks better and implement more effective suppression strategies. Social distancing administered by the government may effectively suppress large clusters but may not effectively control small and sporadic clusters. [ABSTRACT FROM AUTHOR]

• We identified 169 circulating lineages across 16 South American countries. • SARS-CoV-2 lineage B is the most prevalent lineage in South America. • Emergent lineages of SARS-CoV2 are a plausible threat to the region. To evaluate the genomic diversity and geographic distribution of SARS-CoV-2 lineages in South America. SARS-CoV-2 lineages from a public dataset of 5583 South American genome assemblies were analyzed. Polymorphisms in the main open reading frames were identified and compared to those in the main lineages of epidemiological concern: B.1.1.7 (UK) and B.1.351 (South Africa). Across 16 South American countries, 169 lineages were identified; major lineage B had the greatest diversity and broadest geographic distribution. Seventeen predominant lineages were analyzed revealing 2 dominant lineages of concern: P.1 (Brazilian variant) and B.1.1.7 with 94 and 28 genomes, respectively, both with 33 polymorphisms (other lineages displayed ≤24 polymorphisms). A high number of polymorphisms were detected with a limited number of common variable positions, in common with the profile of the main lineages of epidemiological concern. The ever-increasing genetic diversity of SARS-CoV-2 continues to lead to novel lineage emergence. Various variants and lineages are now present across South America, dominated by major lineage B. The circulation of P.1 and B.1.1.7 and the high number of polymorphisms highlight the importance of genomic surveillance to determine introduction events, identify transmission chains, trace emergence, and implement prevention, vaccination and control strategies. [ABSTRACT FROM AUTHOR]

• P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. • A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). • The study revealed a good agreement between genetic and epidemiological data. • Oman's robust surveillance system was very efficient to guide the outbreak investigation processes in the country, • The study illustrates the future importance of molecular epidemiology to lead the national response to outbreaks and pandemics. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been proven to be lethal to human health, which affects almost every corner of the world. The objectives of this study were to add context to the global data and international genomic consortiums, and to give insight into the efficiency of the contact tracing system in Oman. We combined epidemiological data and whole-genome sequence data from 94 samples of SARS-CoV-2 in Oman to understand the origins, genetic variation, and transmissibility. The whole-genome size of sequence data was obtained through a customized SARS-COV-2 research panel. Amplifier methods ranged from 26 Kbp to 30 Kbp and were submitted to GISAID. The study found that P323L (94.7%) is the most common mutation, followed by D614G (92.6%) Spike protein mutation. A unique mutation, I280V, was first reported in Oman and was associated with a rare lineage, B.1.113 (10.6%). In addition, the study revealed a good agreement between genetic and epidemiological data. Oman's robust surveillance system was very efficient in guiding the outbreak investigation processes in the country, the study illustrates the future importance of molecular epidemiology in leading the national response to outbreaks and pandemics. [ABSTRACT FROM AUTHOR]

• COVID-19 measures were applied on similar dates in provinces throughout China. • Disease severity was much greater in Hubei compared with other provinces. • Provincial data on epidemics and interventions is available for further research. In this data collation study, we aimed to provide a comprehensive database describing the epidemic trends and responses during the first wave of coronavirus disease 2019 (COVID-19) throughout the main provinces in China. From mid-January to March 2020, we extracted publicly available data regarding the spread and control of COVID-19 from 31 provincial health authorities and major media outlets in mainland China. Based on these data, we conducted descriptive analyses of the epidemic in the six most-affected provinces. School closures, travel restrictions, community-level lockdown, and contact tracing were introduced concurrently around late January but subsequent epidemic trends differed among provinces. Compared with Hubei, the other five most-affected provinces reported a lower crude case fatality ratio and proportion of critical and severe hospitalised cases. From March 2020, as the local transmission of COVID-19 declined, switching the focus of measures to the testing and quarantine of inbound travellers may have helped to sustain the control of the epidemic. Aggregated indicators of case notifications and severity distributions are essential for monitoring an epidemic. A publicly available database containing these indicators and information regarding control measures is a useful resource for further research and policy planning in response to the COVID-19 epidemic. [ABSTRACT FROM AUTHOR]

• SARS-CoV-2 antigen testing for asymptomatic hospital visitors was low-yielding. • COVID-19 cases were identified in < 0.01% of hospital visitors over 2 months. • No evidence of nosocomial transmission from hospital visitors was identified. Retrospective contact tracing, enabled by the use of automated visitor-management systems and digital contact tracing, together with rapid antigen detection (RAD) for SARS-CoV-2 among visitors staying ≥ 30 minutes, identified COVID-19 cases in < 0.01% (6/72 605) of hospital visitors to a large hospital campus over an 8-week study period. The potential for nosocomial transmission of SARS-CoV-2 from hospital visitors was thus very low, and could be further mitigated by universal mask-wearing among staff and visitors. [ABSTRACT FROM AUTHOR]

• mRNA SARS-CoV-2 vaccines prevent the spread of the Delta variant. • A partially vaccinated individual was protected against the Delta variant after exposure. • Epidemiology combined with contact tracing improves outbreak response. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) sublineage B.1.617.2 or Delta, a variant that began circulating in India and is becoming dominant in the USA, has been responsible for significant morbidity and mortality. In May 2021, the Delta variant was upgraded to a variant of concern by international authorities. This article reports a cluster of SARS-CoV-2 Delta cases detected in Boston, Massachusetts, in May 2021 involving a recent traveller from India and subsequent transmission to two of three close contacts. All three close contacts experienced the same primary exposure events but differed in vaccination status. The two close contacts that eventually tested positive were unvaccinated. The other close contact had received one dose of the BNT162b (Pfizer-BioNTech) vaccine prior to exposure, and received their second dose 2 days after exposure. This case series illustrates the effectiveness of partial vaccination in blocking transmission of the Delta variant to vaccinated individuals under circumstances where the probability of transmission for unvaccinated individuals is high. [ABSTRACT FROM AUTHOR]

• Robust contact tracing with an integrated system effectively intervenes early transmission of COVID-19 in Taiwan. • Developing an integrated management system to support traditional contact tracing is critical in response to control the spread of COVID-19. • Management tools augment the capacity and decrease workloads of contact tracers, which improve contact tracing effectiveness. Comprehensive case investigation and contact tracing are crucial to prevent community spread of COVID-19. We demonstrated a utility of using traditional contact tracing measures supplemented with symptom tracking and contact management system to assist public health workers with high efficiency. A centralized contact tracing system was developed to support data linkage, cross-jurisdictional coordination, and follow-up of contacts' health status. We illustrated the process of how digital tools support contact tracing and management of COVID-19 cases and measured the timeliness from case detection to contact monitoring to evaluate system performance. Among the 8051 close contacts of the 487 confirmed cases (16.5 close contacts/case, 95% CI [13.9–19.1]), the median elapsed time from last exposure to quarantine was three days (IQR 1–5). By implementing the approach of self-reporting using automatic text-messages and web-app, the percentage of health status updates from self-reporting increased from 22.5% to 61.5%. The high proportion of secondary cases detected via contact tracing (88%) might reduce the R0 to under one and minimize the impact of local transmission in the community. Comprehensive contact tracing and management with complementary technology would still be a pillar of strategies for containing outbreaks during de-escalation or early in the next wave of COVID-19 pandemic. [ABSTRACT FROM AUTHOR]

• New diagnostic serial interval (DSI): time between diagnoses of infector & infectee. • DSI is defined regardless of symptoms and easy to obtain. • In South Korea, mean DSI was found to be short: 3.63 days (95% CI: 3.24, 4.01). • Mean DSI is potentially a new indicator for effectiveness of epidemic surveillance. The clinical onset serial interval is often used as a proxy for the transmission interval of an infectious disease. For SARS-CoV-2/COVID-19, data on clinical onset serial intervals is limited, since symptom onset dates are not routinely recorded and do not exist in asymptomatic carriers. We define the diagnostic serial interval as the time between the diagnosis dates of the infector and infectee. Based on the DS4C project data on SARS-CoV-2/COVID-19 in South Korea, we estimate the means of the diagnostic serial interval, the clinical onset serial interval, and the difference between the two. We use the balanced cluster bootstrap method to construct 95% bootstrap confidence intervals. The mean of the diagnostic serial interval was estimated to be 3.63 days (95% CI: 3.24, 4.01). The diagnostic serial interval was significantly shorter than the clinical onset serial interval (estimated mean difference −1.12 days, 95% CI: −1.98, −0.26). The relatively short diagnostic serial intervals of SARS-CoV-2/COVID-19 in South Korea are likely due to the country's extensive efforts towards contact tracing. We propose the mean diagnostic serial interval as a new indicator for the effectiveness of a country's contact tracing as part of the epidemic surveillance. [ABSTRACT FROM AUTHOR]

• Hong Kong reported more than 1000 COVID-19 cases between January and May 2020. • The COVID-19 epidemic in Hong Kong was characterized by several waves of imported cases followed by limited local transmissions. • A series of public health intervention were implemented in Hong Kong in response to the local and overseas disease situations. • The multi-pronged strategy of border control, social distancing, enhanced surveillance, and contact tracing resulted in the successful prevention of a community-wide outbreak and containment of the epidemic in Hong Kong. Hong Kong, a Special Administrative Region of China, recorded its first confirmed coronavirus disease 2019 (COVID-19) case on 23 January 2020. We reviewed the case epidemiology and the various public health measures implemented from January to May 2020. The epidemiological and clinical characteristics of the cases recorded in different phases of the epidemic were described and compared, and the effectiveness of the public health measures implemented were reviewed using the changes in the daily number of confirmed cases and the interval from symptom onset to hospital admission. Between January and May 2020, 1084 confirmed COVID-19 cases were reported, about 70% of which had a history of travel during the incubation period. The case fatality ratio was 0.4%. The local epidemic progressed through four phases: (1) preparedness and imported infection from mainland China, (2) local transmission, (3) imported infection from overseas countries associated with local transmission, and (4) controlled imported infection with limited local transmission, with an eventual reduction of the daily case number and minimization of the onset-to-admission interval. Various public health measures, including enhanced surveillance, border control, and social distancing, were introduced in phases in response to the prevailing local and global situations. The overall containment strategy in Hong Kong led to a stabilization of the number of cases and the absence of a community-wide outbreak during the 4.5 m after the first case was reported. This strategy of containment might serve as an example for future planning of preparedness and response against novel infectious agents. [ABSTRACT FROM AUTHOR]

• The loci (GTA)9, (AT)17, (AT)15, (TA)18, (TTC)21 and (TA)10 are more highly polymorphic than other loci. • The VNTR profile generated a low-density clustering pattern in the counties of Sichuan and Yunnan. • Clusters were observed from the isolates from Hunan and Guizhou provinces at the county levels. • The most predominantly reported SNP was 3K followed by SNP 1D. • We detected the novel SNP 3J that has not yet been reported in China. • Maximum genotype stability was observed in current and long-standing strains. Understanding the nature of Mycobacterium leprae transmission is vital to implement better control strategies for leprosy elimination. The present study expands the knowledge of county-level strain diversity, distribution, and transmission patterns of leprosy in endemic provinces of China. We genetically characterized 290 clinical isolates of M. leprae from four endemic provinces using variable number tandem repeats (VNTR) and single nucleotide polymorphisms (SNPs). Attained genetic profiles and cluster consequences were contrasted with geographical and migration features of leprosy at county levels. Considering the allelic variability of 17 VNTR loci by the discriminatory index, (GTA)9, (AT)17, (AT)15, (TA)18, (TTC)21, and (TA)10 are reported to be more highly polymorphic than other loci. The VNTR profile generated the low-density clustering pattern in the counties of Sichuan and Yunnan, whereas clusters have been observed from the isolates from Huayuan (N = 6), Yongding (N = 3), Zixing (N = 3), Chenxi (N = 2) and Zhongfang (N = 2) counties of Hunan, and Zhijin (N = 3), Anlong (N = 2), Zhenning (N = 2), and Xixiu (N = 2) counties of Guizhou. In some clusters, people's social relations have been observed between villages. From the 290 clinical isolates, the most predominantly reported SNP was 3K (278, 95.8%), followed by SNP 1D (10, 3.4%), which are typically observed to be predominant in China. We also detected the novel SNP 3J (2, 0.8%), which has not yet been reported in China. The clustering pattern of M. leprae indicates the transmission of leprosy still persists at county levels, suggesting that there is a need to implement better approaches for tracing the close contacts of leprosy patients. [ABSTRACT FROM AUTHOR]

• Updated clinical guidance on MDR-TB is needed. • Several new MDR-TB diagnostics have been recently approved by WHO to complement existing tools. • To design a regimen, 4–5 active drugs are needed with a treatment duration up to 24 months. • Post-treatment sequelae might require pulmonary rehabilitation. • LTBI management and infection control are core elements of the MDR-TB public health approach. The continuous flow of new research articles on MDR-TB diagnosis, treatment, prevention and rehabilitation requires frequent update of existing guidelines. This review is aimed at providing clinicians and public health staff with an updated and easy-to-consult document arising from consensus of Global Tuberculosis Network (GTN) experts. The core published documents and guidelines have been reviewed, including the recently published MDR-TB WHO rapid advice and ATS/CDC/ERS/IDSA guidelines. After a rapid review of epidemiology and risk factors, the clinical priorities on MDR-TB diagnosis (including whole genome sequencing and drug-susceptibility testing interpretations) and treatment (treatment design and management, TB in children) are discussed. Furthermore, the review comprehensively describes the latest information on contact tracing and LTBI management in MDR-TB contacts, while providing guidance on post-treatment functional evaluation and rehabilitation of TB sequelae, infection control and other public health priorities. [ABSTRACT FROM AUTHOR]

• High frequency of TST positivity in TB contacts from Brazil was observed. • SNPs in type-I IFN pathway, DNA and RNA sensing genes were screened in TB contacts. • SNPs in PYHIN1-IFI16-AIM2 and in IRF7 were linked to altered susceptibility to TB. Host genetic polymorphisms may be important in determining susceptibility to Mycobacterium tuberculosis (Mtb) infection, but their role is not fully understood. Detection of microbial DNA and activation of type I interferon (IFN) pathways regulate macrophage responses to Mtb infection. We examined whether seven candidate gene SNPs were associated with tuberculin skin test (TST) positivity in close contacts of microbiologically confirmed pulmonary TB patients in Brazil. Independent associations with TST positivity were tested using multivariable logistic regression (using genotypes and clinical variables) and genetic models. Among 482 contacts of 145 TB index cases, 296 contacts were TST positive. Multivariable regression analysis adjusted for population admixture, age, family relatedness, sex and clinical variables related to increased TB risk demonstrated that SNPs in PYHIN1-IFI16-AIM2 rs1101998 (adjusted OR [aOR]: 3.72; 95%CI = 1.15–12.0; p = 0.028) and in PYHIN1-IFI16-AIM2 rs1633256 (aOR = 24.84; 95%CI = 2.26–272.95; p = 0.009) were associated with TST positivity in a recessive model. Furthermore, an IRF7 polymorphism (rs11246213) was associated with reduced odds of TST positivity in a dominant model (aOR: 0.50, 95%CI: 0.26-0.93; p = 0.029). Polymorphisms in PYHIN1- IFI16 -AIM2 rs1633256, rs1101998 and in IRF7 rs11246213 were associated with altered susceptibility to Mtb infection in this Brazilian cohort. [ABSTRACT FROM AUTHOR]

• Cluster-based approach in Japan brought all contacts under close observation with laboratory testing. • The very first cluster in Tokyo and Kanagawa (n = 36) that included 12 asymptomatic individuals was analyzed. • Relative infectiousness of asymptomatically infected cases was estimated to be 0.27 (95% CI: 0.03–0.81) of symptomatic cases. The epidemiological importance of asymptomatic individuals who would never develop illness, compared to those who eventually develop symptoms, has yet to be fully clarified. The very first cluster data in Tokyo and Kanagawa (n = 36) were analyzed. Movement of all close contact was restricted for 14 days and they underwent laboratory testing with polymerase chain reaction. The reproduction numbers of symptomatic and asymptomatic cases were estimated. The reproduction number for symptomatic cases was estimated to be 1.2 (95% confidence interval (CI): 0.5–2.9). The relative infectiousness of asymptomatically infected cases was estimated to be 0.27 (95% CI: 0.03–0.81) of symptomatic cases. The relative transmissibility of asymptomatic cases is limited. Observing clusters starting with symptomatic transmission might be sufficient for the control. [ABSTRACT FROM AUTHOR]