Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data.

When responding to infectious disease outbreaks, rapid and accurate estimation of the epidemic trajectory is critical. However, two common data collection problems affect the reliability of the epidemiological data in real time: missing information on the time of first symptoms, and retrospective revision of historical information, including right censoring. Here, we propose an approach to construct epidemic curves in near real time that addresses these two challenges by 1) imputation of dates of symptom onset for reported cases using a dynamically-estimated "backward" reporting delay conditional distribution, and 2) adjustment for right censoring using the NobBS software package to nowcast cases by date of symptom onset. This process allows us to obtain an approximation of the time-varying reproduction number (Rt) in real time. We apply this approach to characterize the early SARS-CoV-2 outbreak in two Spanish regions between March and April 2020. We evaluate how these real-time estimates compare with more complete epidemiological data that became available later. We explore the impact of the different assumptions on the estimates, and compare our estimates with those obtained from commonly used surveillance approaches. Our framework can help improve accuracy, quantify uncertainty, and evaluate frequently unstated assumptions when recovering the epidemic curves from limited data obtained from public health systems in other locations.

A nowcasting framework for correcting for reporting delays in malaria surveillance.

Time lags in reporting to national surveillance systems represent a major barrier for the control of infectious diseases, preventing timely decision making and resource allocation. This issue is particularly acute for infectious diseases like malaria, which often impact rural and remote communities the hardest. In Guyana, a country located in South America, poor connectivity among remote malaria-endemic regions hampers surveillance efforts, making reporting delays a key challenge for elimination. Here, we analyze 13 years of malaria surveillance data, identifying key correlates of time lags between clinical cases occurring and being added to the central data system. We develop nowcasting methods that use historical patterns of reporting delays to estimate occurred-but-not-reported monthly malaria cases. To assess their performance, we implemented them retrospectively, using only information that would have been available at the time of estimation, and found that they substantially enhanced the estimates of malaria cases. Specifically, we found that the best performing models achieved up to two-fold improvements in accuracy (or error reduction) over known cases in selected regions. Our approach provides a simple, generalizable tool to improve malaria surveillance in endemic countries and is currently being implemented to help guide existing resource allocation and elimination efforts.

Correction: Practical considerations for measuring the effective reproductive number, Rt.

[This corrects the article DOI: 10.1371/journal.pcbi.1008409.].

Extracorporeal Membrane Oxygenation for COVID-19-associated Severe Acute Respiratory Distress Syndrome in Chile: A Nationwide Incidence and Cohort Study.

Rationale: The role of and needs for extracorporeal membrane oxygenation (ECMO) at a population level during the coronavirus disease (COVID-19) pandemic have not been completely established. Objectives: To identify the cumulative incidence of ECMO use in the first pandemic wave and to describe the Nationwide Chilean cohort of ECMO-supported patients with COVID-19. Methods: We conducted a population-based study from March 3 to August 31, 2020, using linked data from national agencies. The cumulative incidence of ECMO use and mortality risk of ECMO-supported patients were calculated and age standardized. In addition, a retrospective cohort analysis was performed. Outcomes were 90-day mortality after ECMO initiation, ECMO-associated complications, and hospital length of stay. Cox regression models were used to explore risk factors for mortality in a time-to-event analysis. Measurements and Main Results: Ninety-four patients with COVID-19 were supported with ECMO (0.42 per population of 100,000, 14.89 per 100,000 positive cases, and 1.2% of intubated patients with COVID-19); 85 were included in the cohort analysis, and the median age was 48 (interquartile range [IQR], 41-55) years, 83.5% were men, and 42.4% had obesity. The median number of pre-ECMO intubation days was 4 (IQR, 2-7), the median PaO2/FiO2 ratio was 86.8 (IQR, 64-99) mm Hg, 91.8% of patients were prone positioned, and 14 patients had refractory respiratory acidosis. Main complications were infections (70.6%), bleeding (38.8%), and thromboembolism (22.4%); 52 patients were discharged home, and 33 died. The hospital length of stay was a median of 50 (IQR, 24-69) days. Lower respiratory system compliance and higher driving pressure before ECMO initiation were associated with increased mortality. A duration of pre-ECMO intubation ≥10 days was not associated with mortality. Conclusions: Documenting nationwide ECMO needs may help in planning ECMO provision for future COVID-19 pandemic waves. The 90-day mortality of the Chilean cohort of ECMO-supported patients with COVID-19 (38.8%) is comparable to that of previous reports.

Practical considerations for measuring the effective reproductive number, Rt.

Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus Disease 2019 (COVID-19) pandemic, policy makers and public health officials are using Rt to assess the effectiveness of interventions and to inform policy. However, estimation of Rt from available data presents several challenges, with critical implications for the interpretation of the course of the pandemic. The purpose of this document is to summarize these challenges, illustrate them with examples from synthetic data, and, where possible, make recommendations. For near real-time estimation of Rt, we recommend the approach of Cori and colleagues, which uses data from before time t and empirical estimates of the distribution of time between infections. Methods that require data from after time t, such as Wallinga and Teunis, are conceptually and methodologically less suited for near real-time estimation, but may be appropriate for retrospective analyses of how individuals infected at different time points contributed to the spread. We advise caution when using methods derived from the approach of Bettencourt and Ribeiro, as the resulting Rt estimates may be biased if the underlying structural assumptions are not met. Two key challenges common to all approaches are accurate specification of the generation interval and reconstruction of the time series of new infections from observations occurring long after the moment of transmission. Naive approaches for dealing with observation delays, such as subtracting delays sampled from a distribution, can introduce bias. We provide suggestions for how to mitigate this and other technical challenges and highlight open problems in Rt estimation.

Estimating lengths-of-stay of hospitalised COVID-19 patients using a non-parametric model: a case study in Galicia (Spain).

Estimating the lengths-of-stay (LoS) of hospitalised COVID-19 patients is key for predicting the hospital beds' demand and planning mitigation strategies, as overwhelming the healthcare systems has critical consequences for disease mortality. However, accurately mapping the time-to-event of hospital outcomes, such as the LoS in the intensive care unit (ICU), requires understanding patient trajectories while adjusting for covariates and observation bias, such as incomplete data. Standard methods, such as the Kaplan-Meier estimator, require prior assumptions that are untenable given current knowledge. Using real-time surveillance data from the first weeks of the COVID-19 epidemic in Galicia (Spain), we aimed to model the time-to-event and event probabilities of patients' hospitalised, without parametric priors and adjusting for individual covariates. We applied a non-parametric mixture cure model and compared its performance in estimating hospital ward (HW)/ICU LoS to the performances of commonly used methods to estimate survival. We showed that the proposed model outperformed standard approaches, providing more accurate ICU and HW LoS estimates. Finally, we applied our model estimates to simulate COVID-19 hospital demand using a Monte Carlo algorithm. We provided evidence that adjusting for sex, generally overlooked in prediction models, together with age is key for accurately forecasting HW and ICU occupancy, as well as discharge or death outcomes.

Identifying Locations with Possible Undetected Imported Severe Acute Respiratory Syndrome Coronavirus 2 Cases by Using Importation Predictions.

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection exported from mainland China could lead to self-sustained outbreaks in other countries. By February 2020, several countries were reporting imported SARS-CoV-2 cases. To contain the virus, early detection of imported SARS-CoV-2 cases is critical. We used air travel volume estimates from Wuhan, China, to international destinations and a generalized linear regression model to identify locations that could have undetected imported cases. Our model can be adjusted to account for exportation of cases from other locations as the virus spreads and more information on importations and transmission becomes available. Early detection and appropriate control measures can reduce the risk for transmission in all locations.

Evaluation of three commercially-available chikungunya virus immunoglobulin G immunoassays.

The emergence of chikungunya virus in the Americas means the affected population is at risk of developing severe, chronic, rheumatologic disease, even months after acute infection. Accurate diagnostic methods for past infections are essential for differential diagnosis and consequence management. This study evaluated three commercially-available chikungunya Immunoglobulin G immunoassays by comparing them to an in-house Enzyme-Linked ImmunoSorbent Assay conducted by the Centers for Disease Control and Prevention (Atlanta, Georgia, United States). Results showed sensitivity and specificity values ranging from 92.8% - 100% and 81.8% - 90.9%, respectively, with a significant number of false-positives ranging from 12.5% - 22%. These findings demonstrate the importance of evaluating commercial kits, especially regarding emerging infectious diseases whose medium and long-term impact on the population is unclear.

First reported enterovirus D68 infection in pediatric patients from the Caribbean region: evidence of spread from the U.S. outbreak.

The 2014 enterovirus D68 (EV-D68) outbreak in the United States raised concerns about the introduction of the virus in the Caribbean region. The objective of this study was to provide rapid evidence of the introduction of EV-D68 strains in the Caribbean region during the 2014 outbreak in the United States, using a relatively simple phylogenetic approach. From October 2014 to May 2015, four EV-D68 cases from two countries (Bermuda and Dominica) were detected at the regional referral laboratory at the Caribbean Public Health Agency (Port of Spain, Trinidad and Tobago) based on molecular testing of respiratory specimens. All cases were children presenting to hospitals with moderate respiratory distress. No cases of acute flaccid paralysis were detected. Phylogenetic analysis of the Caribbean strains showed more than 99% similarity with the 2014 U.S.-outbreak strain, providing evidence of the introduction and circulation of the virus in the region.

Zika fever.

Zika fever is an arboviral systemic disease that has recently become a public health challenge of global concern after its spread through the Americas. This review highlights the current understanding on Zika virus epidemiology, its routes of transmission, clinical manifestations, diagnostic tests, and the current management, prevention and control strategies. It also delves the association between Zika infection and complications, such as microencephaly or Guillem-Barré syndrome.

Severe outcomes of malaria in children under time-varying exposure.

In malaria epidemiology, interpolation frameworks based on available observations are critical for policy decisions and interpreting disease burden. Updating our understanding of the empirical evidence across different populations, settings, and timeframes is crucial to improving inference for supporting public health. Here, via individual-based modeling, we evaluate a large, multicountry, contemporary Plasmodium falciparum severe malaria dataset to better understand the relationship between prevalence and incidence of malaria pediatric hospitalizations - a proxy of malaria severe outcomes- in East-Africa. We find that life-long exposure dynamics, and subsequent protection patterns in children, substantially determine the likelihood of malaria hospitalizations relative to ongoing prevalence at the population level. Unsteady transmission patterns over a lifetime in children -increasing or decreasing- lead to an exponential relationship of hospitalization rates versus prevalence rather than the asymptotic pattern observed under steady transmission. Addressing this increase in the complexity of malaria epidemiology is crucial to update burden assessments via inference models that guide current and future policy decisions.

Association of sociocultural stressors with bipolar disorder onset in Puerto Rican youth growing up as members of a minoritized ethnic group: results from the Boricua Youth Longitudinal Study.

Background: The development of bipolar disorder is currently explained by a complex interaction of genetic and environmental factors. Less is known regarding the influence of sociocultural factors. This study aims to evaluate the incidence and impact of sociocultural factors on bipolar disorder onset in two comparable samples of youth growing up in different social settings. Methods: We leveraged data from two urban population-based cohorts representative of Puerto Rican children growing up in either San Juan (Puerto Rico) or the South Bronx (NYC) and followed up for 17 years. Bipolar disorder diagnoses were based on retrospective self-reports on the World Health Organization Composite International Diagnostic Interview. We used a causal inference approach to estimate associations of sociocultural factors with bipolar disorder onset after adjusting for potential confounders. Findings: We found that South Bronx children, who grew up as a minoritized group, had twice the risk of bipolar disorder onset as young adults, with an incidence rate of 2.22 new cases per 1000 person-years compared to 1.08 new cases in San Juan (incidence rate difference, 1.13; 95% CI, 0.09-1.20). After adjusting for potential confounders, South Bronx children had the same lifetime hazard of bipolar disorder onset compared to San Juan children. However, our analysis demonstrated that caregivers' exposure to societal cultural stress partially explained the increased risk of bipolar disorder onset in the South Bronx, in addition to the potential contribution of genetics. Interpretation: Our results provide evidence that societal cultural stress can increase the risk of lifetime bipolar disorder onset in youth growing up as a minoritized group. Addressing stress in minoritized groups might reduce the risk of bipolar disorder onset. Funding: The Boricua Youth Study has been supported by the National Institutes of HealthMH56401, MH098374, DA033172, and AA020191. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the article.

Daily tenofovir disoproxil fumarate/emtricitabine and hydroxychloroquine for pre-exposure prophylaxis of COVID-19: a double-blind placebo-controlled randomized trial in healthcare workers.

OBJECTIVES: To assess the effect of hydroxychloroquine (HCQ) and Tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) as pre-exposure prophylaxis on COVID-19 risk. METHODS: EPICOS is a double-blind, placebo-controlled randomized trial conducted in Spain, Bolivia, and Venezuela. Healthcare workers with negative SARS-CoV-2 IgM/IgG test were randomly assigned to the following: daily TDF/FTC plus HCQ for 12 weeks, TDF/FTC plus HCQ placebo, HCQ plus TDF/FTC placebo, and TDF/FTC placebo plus HCQ placebo. Randomization was performed in groups of four. Primary outcome was laboratory-confirmed, symptomatic COVID-19. We also studied any (symptomatic or asymptomatic) COVID-19. We compared group-specific 14-week risks via differences and ratios with 95% CIs. RESULTS: Of 1002 individuals screened, 926 (92.4%) were eligible and there were 14 cases of symptomatic COVID-19: 220 were assigned to the TDF/FTC plus HCQ group (3 cases), 231 to the TDF/FTC placebo plus HCQ group (3 cases), 233 to the TDF/FTC plus HCQ placebo group (3 cases), and 223 to the double placebo group (5 cases). Compared with the double placebo group, 14-week risk ratios (95% CI) of symptomatic COVID-19 were 0.39 (0.00-1.98) for TDF + HCQ, 0.34 (0.00-2.06) for TDF, and 0.49 (0.00-2.29) for HCQ. Corresponding risk ratios of any COVID-19 were 0.51 (0.21-1.00) for TDF + HCQ, 0.81 (0.44-1.49) for TDF, and 0.73 (0.41-1.38) for HCQ. Adverse events were generally mild. DISCUSSION: The target sample size was not met. Our findings are compatible with both benefit and harm of pre-exposure prophylaxis with TDF/FTC and HCQ, alone or in combination, compared with placebo.

Pyronaridine-artesunate granules versus artemether-lumefantrine crushed tablets in children with Plasmodium falciparum malaria: a randomized controlled trial.

BACKGROUND: Children are most vulnerable to malaria. A pyronaridine-artesunate pediatric granule formulation is being developed for the treatment of uncomplicated Plasmodium falciparum malaria. METHODS: This phase III, multi-center, comparative, open-label, parallel-group, controlled clinical trial included patients aged ≤12 years, bodyweight ≥5 to <25 kg, with a reported history of fever at inclusion or in the previous 24 h and microscopically-confirmed uncomplicated P. falciparum malaria. Patients were randomized (2:1) to pyronaridine-artesunate granules (60/20 mg) once daily or artemether-lumefantrine crushed tablets (20/120 mg) twice daily, both dosed by bodyweight, orally (liquid suspension) for three days. RESULTS: Of 535 patients randomized, 355 received pyronaridine-artesunate and 180 received artemether-lumefantrine. Day-28 adequate clinical and parasitological response (ACPR), corrected for re-infection using polymerase chain reaction (PCR) genotyping (per-protocol population) was 97.1% (329/339; 95% CI 94.6, 98.6) for pyronaridine-artesunate; 98.8% (165/167; 95% CI 95.7, 99.9) for artemether-lumefantrine. The primary endpoint was achieved: pyronaridine-artesunate PCR-corrected day-28 ACPR was statistically significantly >90% (P < .0001). Pyronaridine-artesunate was non-inferior to artemether-lumefantrine: treatment difference -1.8% (95% CI -4.3 to 1.6). The incidence of drug-related adverse events was 37.2% (132/355) with pyronaridine-artesunate, 44.4% (80/180) with artemether-lumefantrine. Clinical biochemistry results showed similar mean changes versus baseline in the two treatment groups. From day 3 until study completion, one patient in each treatment group had peak alanine aminotransferase (ALT) >3 times the upper limit of normal (ULN) and peak total bilirubin >2xULN (i.e. within the Hy's law definition). CONCLUSIONS: The pyronaridine-artesunate pediatric granule formulation was efficacious and was non-inferior to artemether-lumefantrine. The adverse event profile was similar for the two comparators. Pyronaridine-artesunate should be considered for inclusion in paediatric malaria treatment programmes. TRIAL REGISTRATION: ClinicalTrials.gov: identifier NCT00541385.

Termination of Sustained Ventricular Fibrillation During Radiofrequency Catheter Ablation.

After a ST-segment elevation inferior myocardial infarction, a patient developed multiple drug-refractory ventricular fibrillation (VF), triggered by a stereotypic premature ventricular complex. During an episode of sustained VF, catheter ablation of the moderator band terminated VF, with transition into monomorphic ventricular tachycardia. To the best of our knowledge, this is the first-in-human report of termination of VF during delivery of radiofrequency energy, which suggests that the focal area on moderator band of Purkinje system had an active role in the perpetuation of VF. (Level of Difficulty: Advanced.).

Feasibility and safety of a transvenous lead extraction program implementation in South America: Challenges, early outcomes, and global collaboration-A single-center experience.

Background: Transvenous lead extraction is the standard of care for cardiac implantable electronic device (CIED) malfunction/infection-related removal. However, data on its performance and results in underdeveloped countries are limited. Objective: The purpose of this study was to report the feasibility and efficacy of a lead extraction program in a tertiary hospital in Chile, South America. Methods: Patients requiring CIED removal at the Electrophysiology Division of the Hospital las Higuera's were retrospectively analyzed. Outcomes including procedure-related mortality, procedural success and failure, and cardiac and vascular complications were reported. Results: A total of 15 patients were analyzed (median age 68 [interquartile range 52-75] years; 80% male). Patients with lead extraction difficulty index >10 represented 33% of patients. Infection was the indication for removal in all patients, with pocket infection (80%). Mechanical rotational tools were used in 66% of cases, and a total of 29 leads were removed. Procedural success was accomplished in 93% of cases. There was 1 (7%) intraprocedural complication and no procedure-related mortality. Conclusions: The development of a lead management program is feasible, safe, and effective in underdeveloped countries.

Human Trypanosoma cruzi chronic infection leads to individual level steady-state parasitemia: Implications for drug-trial optimization in Chagas disease.

Currently available drugs against Trypanosoma cruzi infection, which causes 12000 deaths annually, have limitations in their efficacy, safety and tolerability. The evaluation of therapeutic responses to available and new compounds is based on parasite detection in the bloodstream but remains challenging because a substantial proportion of infected individuals have undetectable parasitemia even when using diagnostic tools with the highest accuracy. We characterize parasite dynamics which might impact drug efficacy assessments in chronic Chagas by analyzing pre- and post-treatment quantitative-PCR data obtained from blood samples collected regularly over a year. We show that parasitemia remains at a steady-state independently of the diagnostic sensitivity. This steady-state can be probabilistically quantified and robustly predicted at an individual level. Furthermore, individuals can be assigned to categories with distinct parasitological status, allowing a more detailed evaluation of the efficacy outcomes and adjustment for potential biases. Our analysis improves understanding of parasite dynamics and provides a novel background for optimizing future drug efficacy trials in Chagas disease. Trial Registration: original trial registered with ClinicalTrials.gov, number NCT01489228.

Empiric ablation of polymorphic ventricular tachycardia/fibrillation in the absence of a mappable trigger: Prospective feasibility and efficacy of pacemap matching to defibrillator electrograms.

BACKGROUND: Catheter ablation strategies for ventricular fibrillation (VF) and polymorphic ventricular tachycardia (PMVT) are not established when spontaneous triggers are rare or absent. OBJECTIVE: The purpose of this study was to report the feasibility and efficacy of a novel empiric ablation strategy of pacemapping to stored implantable cardioverter-defibrillator (ICD) template electrograms (SITE) of the clinical premature ventricular contraction (PVC) trigger. METHODS: Fifteen patients with drug-refractory VF/PMVT receiving defibrillator shocks without identifiable and mappable PVC triggers were prospectively analyzed. The protocol incorporated systematic pacemapping from known arrhythmogenic sites (moderator band/right ventricular [RV] papillary muscles, left conduction system/Purkinje network, outflow tracts) with real-time comparison between the paced ICD electrogram (EGM) morphology and SITE. RESULTS: Regions within the left Purkinje network yielded the best pacemap match for the SITE of the clinical PVC trigger in 55% of ablation targets (left posterior fascicle 6, left septal fascicle 1, left anterior fascicle 5), followed by the RV moderator band region in 14% (n = 3), RV papillary muscles in 13% (n = 3), periaortic region in 14% (n = 3), and left ventricular anterolateral papillary muscle in 4% (n = 1). Freedom from ICD therapies off antiarrhythmic drug (AAD) was 64% at 6 months and 48% at 12 months. Shock burden was reduced from 4 (2-6) to 0 (0-1) (P = .001), and use of AADs was reduced from 2 (1-2) to 0 (0-1) (P = .001). CONCLUSION: In the absence of a mappable trigger, an empiric strategy of interrogating the Purkinje network, papillary muscles, and outflow tract regions by pacemap matching with SITE of the clinical PVC is feasible to guide ablation. A significant reduction in VF/PMVT therapy burden and AAD utilization was observed after a single procedure.

High coverage COVID-19 mRNA vaccination rapidly controls SARS-CoV-2 transmission in long-term care facilities.

Background: Residents of Long-Term Care Facilities (LTCFs) represent a major share of COVID-19 deaths worldwide. Measuring the vaccine effectiveness among the most vulnerable in these settings is essential to monitor and improve mitigation strategies. Methods: We evaluate the early effect of the administration of BNT162b2-mRNA vaccine to individuals older than 64 years residing in LTCFs in Catalonia, Spain. We monitor all the SARS-CoV-2 documented infections and deaths among LTCFs residents once more than 70% of them were fully vaccinated (February-March 2021). We develop a modeling framework based on the relationship between community and LTCFs transmission during the pre-vaccination period (July-December 2020). We compute the total reduction in SARS-CoV-2 documented infections and deaths among residents of LTCFs over time, as well as the reduction in the detected transmission for all the LTCFs. We compare the true observations with the counterfactual predictions. Results: We estimate that once more than 70% of the LTCFs population are fully vaccinated, 74% (58-81%, 90% CI) of COVID-19 deaths and 75% (36-86%, 90% CI) of all expected documented infections among LTCFs residents are prevented. Further, detectable transmission among LTCFs residents is reduced up to 90% (76-93%, 90% CI) relative to that expected given transmission in the community. Conclusions: Our findings provide evidence that high-coverage vaccination is the most effective intervention to prevent SARS-CoV-2 transmission and death among LTCFs residents. Widespread vaccination could be a feasible avenue to control the COVID-19 pandemic conditional on key factors such as vaccine escape, roll out and coverage.