Innovative platforms for data aggregation, linkage and analysis in the context of pandemic and epidemic intelligence.

During the COVID-19 pandemic, open-access platforms that aggregate, link and analyse data were transformative for global public health surveillance. This perspective explores the work of three of these platforms: Our World In Data (OWID), Johns Hopkins University (JHU) COVID-19 Dashboard (later complemented by the Coronavirus Resource Center), and Global.Health, which were presented in the second World Health Organization (WHO) Pandemic and Epidemic Intelligence Innovation Forum. These platforms, operating mostly within academic institutions, added value to public health data that are collected by government agencies by providing additional real-time public health intelligence about the spread of the virus and the evolution of the public health emergency. Information from these platforms was used by health professionals, political decision-makers and members of the public alike. Further engagement between government and non-governmental surveillance efforts can accelerate the improvements needed in public health surveillance overall. Increasing the diversity of public health surveillance initiatives beyond the government sector comes with several benefits: technology innovation in data science, engagement of additional highly skilled professionals, greater transparency and accountability for government agencies, and new opportunities to engage with members of society.

Finite Element Modeling of Planus and Rectus Foot Types for the Study of First Metatarsophalangeal and First Metatarsocuneiform Joint Contact Mechanics.

The foot is a highly complex biomechanical system for which finite element (FE) modeling has been used to evaluate its loading environment. However, there is limited knowledge of first metatarsophalangeal (MTP) and first metatarsocuneiform (MTC) joint contact mechanics. Our goal was to develop a framework for FE modeling of the medial forefoot which could accurately predict experimental measurements of first MTP and first MTC joint loading. Simulations of planus and rectus foot types were conducted for midstance of gait. A custom-built force-controlled cadaveric test-rig was used to derive intracapsular pressure sensor measurements of contact pressure, force, and area during quasi-static loading. The FE model was driven under the same boundary and loading conditions as the cadaver. Mesh sensitivity analyses and best-fit calibrations of moduli for first MTP and first MTC joint cartilage were performed. Consistent with previous experimental research, a lower compressive modulus was best-fit to the first MTP compared to first MTC joint at 10 MPa and 20 MPa, respectively. Mean errors in contact pressures, forces, and areas were 24%, 4%, and 40% at the first MTP joint and 23%, 12%, and 19% at the first MTC joint, respectively. The present developmental framework may provide a basis for future modeling of first MTP and first MTC joint contact mechanics. This study acts as a precursor to validation of realistic physiological loading across gait to investigate joint loading, foot type biomechanics, and surgical interventions of the medial forefoot.

The World Health Organization's public health intelligence activities during the COVID-19 pandemic response, December 2019 to December 2021.

The coronavirus disease (COVID-19) presented a unique opportunity for the World Health Organization (WHO) to utilise public health intelligence (PHI) for pandemic response. WHO systematically captured mainly unstructured information (e.g. media articles, listservs, community-based reporting) for public health intelligence purposes. WHO used the Epidemic Intelligence from Open Sources (EIOS) system as one of the information sources for PHI. The processes and scope for PHI were adapted as the pandemic evolved and tailored to regional response needs. During the early months of the pandemic, media monitoring complemented official case and death reporting through the International Health Regulations mechanism and triggered alerts. As the pandemic evolved, PHI activities prioritised identifying epidemiological trends to supplement the information available through indicator-based surveillance reported to WHO. The PHI scope evolved over time to include vaccine introduction, emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, unusual clinical manifestations and upsurges in cases, hospitalisation and death incidences at subnational levels. Triaging the unprecedented high volume of information challenged surveillance activities but was managed by collaborative information sharing. The evolution of PHI activities using multiple sources in WHO's response to the COVID-19 pandemic illustrates the future directions in which PHI methodologies could be developed and used.

Increased transmissibility and global spread of SARS-CoV-2 variants of concern as at June 2021.

We present a global analysis of the spread of recently emerged SARS-CoV-2 variants and estimate changes in effective reproduction numbers at country-specific level using sequence data from GISAID. Nearly all investigated countries demonstrated rapid replacement of previously circulating lineages by the World Health Organization-designated variants of concern, with estimated transmissibility increases of 29% (95% CI: 24-33), 25% (95% CI: 20-30), 38% (95% CI: 29-48) and 97% (95% CI: 76-117), respectively, for B.1.1.7, B.1.351, P.1 and B.1.617.2.

Automated Classification of Changes of Direction in Soccer Using Inertial Measurement Units.

Changes of direction (COD) are an important aspect of soccer match play. Understanding the physiological and biomechanical demands on players in games allows sports scientists to effectively train and rehabilitate soccer players. COD are conventionally recorded using manually annotated time-motion video analysis which is highly time consuming, so more time-efficient approaches are required. The aim was to develop an automated classification model based on multi-sensor player tracking device data to detect COD > 45°. Video analysis data and individual multi-sensor player tracking data (GPS, accelerometer, gyroscopic) for 23 academy-level soccer players were used. A novel 'GPS-COD Angle' variable was developed and used in model training; along with 24 GPS-derived, gyroscope and accelerometer variables. Video annotation was the ground truth indicator of occurrence of COD > 45°. The random forest classifier using the full set of features demonstrated the highest accuracy (AUROC = 0.957, 95% CI = 0.956-0.958, Sensitivity = 0.941, Specificity = 0.772. To balance sensitivity and specificity, model parameters were optimised resulting in a value of 0.889 for both metrics. Similarly high levels of accuracy were observed for random forest models trained using a reduced set of features, accelerometer-derived variables only, and gyroscope-derived variables only. These results point to the potential effectiveness of the novel methodology implemented in automatically identifying COD in soccer players.

Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19.

We report key epidemiologic parameter estimates for coronavirus disease identified in peer-reviewed publications, preprint articles, and online reports. Range estimates for incubation period were 1.8-6.9 days, serial interval 4.0-7.5 days, and doubling time 2.3-7.4 days. The effective reproductive number varied widely, with reductions attributable to interventions. Case burden and infection fatality ratios increased with patient age. Implementation of combined interventions could reduce cases and delay epidemic peak up to 1 month. These parameters for transmission, disease severity, and intervention effectiveness are critical for guiding policy decisions. Estimates will likely change as new information becomes available.

Evidence of behaviour change during an Ebola virus disease outbreak, Sierra Leone.

OBJECTIVE: To evaluate changes in Ebola-related knowledge, attitudes and prevention practices during the Sierra Leone outbreak between 2014 and 2015. METHODS: Four cluster surveys were conducted: two before the outbreak peak (3499 participants) and two after (7104 participants). We assessed the effect of temporal and geographical factors on 16 knowledge, attitude and practice outcomes. FINDINGS: Fourteen of 16 knowledge, attitude and prevention practice outcomes improved across all regions from before to after the outbreak peak. The proportion of respondents willing to: (i) welcome Ebola survivors back into the community increased from 60.0% to 89.4% (adjusted odds ratio, aOR: 6.0; 95% confidence interval, CI: 3.9-9.1); and (ii) wait for a burial team following a relative's death increased from 86.0% to 95.9% (aOR: 4.4; 95% CI: 3.2-6.0). The proportion avoiding unsafe traditional burials increased from 27.3% to 48.2% (aOR: 3.1; 95% CI: 2.4-4.2) and the proportion believing spiritual healers can treat Ebola decreased from 15.9% to 5.0% (aOR: 0.2; 95% CI: 0.1-0.3). The likelihood respondents would wait for burial teams increased more in high-transmission (aOR: 6.2; 95% CI: 4.2-9.1) than low-transmission (aOR: 2.3; 95% CI: 1.4-3.8) regions. Self-reported avoidance of physical contact with corpses increased in high but not low-transmission regions, aOR: 1.9 (95% CI: 1.4-2.5) and aOR: 0.8 (95% CI: 0.6-1.2), respectively. CONCLUSION: Ebola knowledge, attitudes and prevention practices improved during the Sierra Leone outbreak, especially in high-transmission regions. Behaviourally-targeted community engagement should be prioritized early during outbreaks.

Ebola Virus Infection Associated with Transmission from Survivors.

Ebola virus (EBOV) can persist in immunologically protected body sites in survivors of Ebola virus disease, creating the potential to initiate new chains of transmission. From the outbreak in West Africa during 2014-2016, we identified 13 possible events of viral persistence-derived transmission of EBOV (VPDTe) and applied predefined criteria to classify transmission events based on the strength of evidence for VPDTe and source and route of transmission. For 8 events, a recipient case was identified; possible source cases were identified for 5 of these 8. For 5 events, a recipient case or chain of transmission could not be confidently determined. Five events met our criteria for sexual transmission (male-to-female). One VPDTe event led to at least 4 generations of cases; transmission was limited after the other events. VPDTe has increased the importance of Ebola survivor services and sustained surveillance and response capacity in regions with previously widespread transmission.

Incidence and etiology of infectious diarrhea from a facility-based surveillance system in Guatemala, 2008-2012.

BACKGROUND: Diarrhea is a major cause of morbidity and mortality, yet incidence and etiology data are limited. We conducted laboratory-based diarrhea surveillance in Guatemala. METHODS: A diarrhea case was defined as ≥3 loose stools in a 24-h period in a person presenting to the surveillance facilities. Epidemiologic data and stool specimens were collected. Specimens were tested for bacterial, parasitic, and viral pathogens. Yearly incidence was adjusted for healthcare seeking behaviors determined from a household survey conducted in the surveillance catchment area. RESULTS: From November 2008 to December 2012, the surveillance system captured 5331 diarrhea cases; among these 1381 (26%) had specimens tested for all enteric pathogens of interest. The adjusted incidence averaged 659 diarrhea cases per 10,000 persons per year, and was highest among children aged < 5 years, averaging 1584 cases per 10,000 children per year. Among 1381 (26%) specimens tested for all the pathogens of interest, 235 (17%) had a viral etiology, 275 (20%) had a bacterial, 50 (4%) had parasites, and 86 (6%) had co-infections. Among 827 (60%) specimens from children aged < 5 years, a virus was identified in 196 (23%) patients; 165 (20%) had norovirus and 99 (12%) rotavirus, including co-infections. Among 554 patients aged ≥5 years, 103 (19%) had a bacterial etiology, including diarrheagenic Escherichia coli in 94 (17%) cases, Shigella spp. in 31 (6%), Campylobacter spp. in 5 (1%), and Salmonella spp. in 4 (1%) cases. Detection of Giardia and Cryptosporidium was infrequent (73 cases; 5%). CONCLUSIONS: There was a substantial burden of viral and bacterial diarrheal diseases in Guatemala, highlighting the importance of strengthening laboratory capacity for rapid detection and control and for evaluation of public health interventions.

Household Transmission of Ebola Virus: Risks and Preventive Factors, Freetown, Sierra Leone, 2015.

Background: Knowing risk factors for household transmission of Ebola virus is important to guide preventive measures during Ebola outbreaks. Methods: We enrolled all confirmed persons with Ebola who were the first case in a household, December 2014-April 2015, in Freetown, Sierra Leone, and their household contacts. Cases and contacts were interviewed, contacts followed prospectively through the 21-day incubation period, and secondary cases confirmed by laboratory testing. Results: We enrolled 150 index Ebola cases and 838 contacts; 83 (9.9%) contacts developed Ebola during 21-day follow-up. In multivariable analysis, risk factors for transmission included index case death in the household, Ebola symptoms but no reported fever, age <20 years, more days with wet symptoms; and providing care to the index case (P < .01 for each). Protective factors included avoiding the index case after illness onset and a piped household drinking water source (P < .01 for each). Conclusions: To reduce Ebola transmission, communities should rapidly identify and follow-up all household contacts; isolate those with Ebola symptoms, including those without reported fever; and consider closer monitoring of contacts who provided care to cases. Households could consider efforts to minimize risk by designating one care provider for ill persons with all others avoiding the suspected case.

Associations of HIV Testing, Sexual Risk and Access to Prevention Among Female Sex Workers in the Dominican Republic.

The Caribbean region has one of the highest proportions of HIV in the general female population attributable to sex work. In 2008 (n = 1256) and 2012 (n = 1525) in the Dominican Republic, HIV biological and behavioral surveys were conducted among female sex workers (FSW) in four provinces using respondent driven sampling. Participants were ≥15 years who engaged in intercourse in exchange for money in the past 6 months and living/working in the study province. There were no statistically significant changes in HIV and other infections prevalence from 2008 to 2012, despite ongoing risky sexual practices. HIV testing and receiving results was low in all provinces. FSW in 2012 were more likely to receive HIV testing and results if they participated in HIV related information and education and had regular checkups at health centers. Further investigation is needed to understand barriers to HIV testing and access to prevention services.

Assessment of Community Event-Based Surveillance for Ebola Virus Disease, Sierra Leone, 2015.

In 2015, community event-based surveillance (CEBS) was implemented in Sierra Leone to assist with the detection of Ebola virus disease (EVD) cases. We assessed the sensitivity of CEBS for finding EVD cases during a 7-month period, and in a 6-week subanalysis, we assessed the timeliness of reporting cases with no known epidemiologic links at time of detection. Of the 12,126 CEBS reports, 287 (2%) met the suspected case definition, and 16 were confirmed positive. CEBS detected 30% (16/53) of the EVD cases identified during the study period. During the subanalysis, CEBS staff identified 4 of 6 cases with no epidemiologic links. These CEBS-detected cases were identified more rapidly than those detected by the national surveillance system; however, too few cases were detected to determine system timeliness. Although CEBS detected EVD cases, it largely generated false alerts. Future versions of community-based surveillance could improve case detection through increased staff training and community engagement.

Multistate US Outbreak of Rapidly Growing Mycobacterial Infections Associated with Medical Tourism to the Dominican Republic, 2013-2014(1).

During 2013, the Maryland Department of Health and Mental Hygiene in Baltimore, MD, USA, received report of 2 Maryland residents whose surgical sites were infected with rapidly growing mycobacteria after cosmetic procedures at a clinic (clinic A) in the Dominican Republic. A multistate investigation was initiated; a probable case was defined as a surgical site infection unresponsive to therapy in a patient who had undergone cosmetic surgery in the Dominican Republic. We identified 21 case-patients in 6 states who had surgery in 1 of 5 Dominican Republic clinics; 13 (62%) had surgery at clinic A. Isolates from 12 (92%) of those patients were culture-positive for Mycobacterium abscessus complex. Of 9 clinic A case-patients with available data, all required therapeutic surgical intervention, 8 (92%) were hospitalized, and 7 (78%) required ≥3 months of antibacterial drug therapy. Healthcare providers should consider infection with rapidly growing mycobacteria in patients who have surgical site infections unresponsive to standard treatment.

Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study.

BACKGROUND: The ongoing West African Ebola epidemic began in December 2013 in Guinea, probably from a single zoonotic introduction. As a result of ineffective initial control efforts, an Ebola outbreak of unprecedented scale emerged. As of 4 May 2015, it had resulted in more than 19,000 probable and confirmed Ebola cases, mainly in Guinea (3,529), Liberia (5,343), and Sierra Leone (10,746). Here, we present analyses of data collected during the outbreak identifying drivers of transmission and highlighting areas where control could be improved. METHODS AND FINDINGS: Over 19,000 confirmed and probable Ebola cases were reported in West Africa by 4 May 2015. Individuals with confirmed or probable Ebola ("cases") were asked if they had exposure to other potential Ebola cases ("potential source contacts") in a funeral or non-funeral context prior to becoming ill. We performed retrospective analyses of a case line-list, collated from national databases of case investigation forms that have been reported to WHO. These analyses were initially performed to assist WHO's response during the epidemic, and have been updated for publication. We analysed data from 3,529 cases in Guinea, 5,343 in Liberia, and 10,746 in Sierra Leone; exposures were reported by 33% of cases. The proportion of cases reporting a funeral exposure decreased over time. We found a positive correlation (r = 0.35, p < 0.001) between this proportion in a given district for a given month and the within-district transmission intensity, quantified by the estimated reproduction number (R). We also found a negative correlation (r = -0.37, p < 0.001) between R and the district proportion of hospitalised cases admitted within ≤4 days of symptom onset. These two proportions were not correlated, suggesting that reduced funeral attendance and faster hospitalisation independently influenced local transmission intensity. We were able to identify 14% of potential source contacts as cases in the case line-list. Linking cases to the contacts who potentially infected them provided information on the transmission network. This revealed a high degree of heterogeneity in inferred transmissions, with only 20% of cases accounting for at least 73% of new infections, a phenomenon often called super-spreading. Multivariable regression models allowed us to identify predictors of being named as a potential source contact. These were similar for funeral and non-funeral contacts: severe symptoms, death, non-hospitalisation, older age, and travelling prior to symptom onset. Non-funeral exposures were strongly peaked around the death of the contact. There was evidence that hospitalisation reduced but did not eliminate onward exposures. We found that Ebola treatment units were better than other health care facilities at preventing exposure from hospitalised and deceased individuals. The principal limitation of our analysis is limited data quality, with cases not being entered into the database, cases not reporting exposures, or data being entered incorrectly (especially dates, and possible misclassifications). CONCLUSIONS: Achieving elimination of Ebola is challenging, partly because of super-spreading. Safe funeral practices and fast hospitalisation contributed to the containment of this Ebola epidemic. Continued real-time data capture, reporting, and analysis are vital to track transmission patterns, inform resource deployment, and thus hasten and maintain elimination of the virus from the human population.