Faster Detection of Poliomyelitis Outbreaks to Support Polio Eradication

The origins and risk factors for serotype-2 vaccine-derived poliovirus (VDPV2) emergences in Africa during 2016-2019

Serotype 2 oral poliovirus vaccine (OPV2) can revert to regain wild-type neurovirulence and spread to cause emergences of vaccine-derived poliovirus (VDPV2). After its global withdrawal from routine immunisation in 2016, outbreak response use has created a cycle of VDPV2 emergences that threaten eradication. We implemented a hierarchical model based on VP1 region genetic divergence, time, and location to attribute emergences to campaigns and identify risk factors. We found that a 10 percentage point increase in population immunity in children under 5 years at the campaign time and location corresponds to a 18.0% decrease (95% CrI:6.3%-28%) in per-campaign relative risk, and that campaign size is associated with emergence risk (relative risk scaling with population size to a power of 0.80, (95% CrI:0.50-1.10). Our results imply how Sabin OPV2 can be used alongside the genetically stable but supply-limited novel OPV2 (listed for emergency use in November 2020) to minimise emergence risk.

Modelling the spread of serotype-2 vaccine derived-poliovirus outbreak in Pakistan and Afghanistan to inform outbreak control strategies in the context of the COVID-19 pandemic

Background

Since July 2019, Pakistan and Afghanistan have been facing an outbreak of serotype-2 circulating vaccine derived poliovirus (cVDPV2) in addition to continued transmission of serotype-1 wild poliovirus (WPV1) and SARS-CoV-2 in 2020. Understanding the risks of cVDPV2 transmission due to pause of global vaccination efforts and the impact of potential vaccination response strategies in the current context of COVID-19 mitigation measures is critical.

Methods

We developed a stochastic, geographically structured mathematical model of cVDPV2 transmission which captures both mucosal and humoral immunity separately and allows for reversion of serotype-2 oral polio vaccine (OPV2) virus to cVDPV2 following vaccine administration. The model includes geographic heterogeneities in vaccination coverage, population immunity and population movement. The model was fitted to historic cVDPV2 cases in Pakistan and Afghanistan between January 2010-April 2016 and July 2019-March 2020 using iterated particle filtering. The model was used to simulate spread of cVDPV2 infection from July 2019 to explore impact of various proposed vaccination responses on stopping transmission and risk of spread of reverted Sabin-2 under varying assumptions of impacts from COVID-19 lockdown measures on movement patterns as well as declines in vaccination coverage.

Results

Simulated monthly incidence of cVDPV2 from the best-fit model demonstrated general spatio-temporal alignment with observed cVDPV2 cases. The model predicted substantial spread of cVDPV2 infection, with widespread transmission through 2020 in the absence of any vaccination activities. Vaccination responses were predicted to substantially reduce transmission and case burden, with a greater impact from earlier responses and those with larger geographic scope. While the greatest risk of seeding reverted Sabin-2 was predicted in areas targeted with OPV2, subsequent spread was greatest in areas with no or delayed response. The proposed vaccination strategy demonstrated ability to stop the cVDPV2 outbreak (with low risk of reverted Sabin-2 spread) by February 2021.

Conclusion

Outbreak response vaccination campaigns against cVDPV2 will be challenging throughout the COVID-19 pandemic but must be implemented urgently when feasible to stop transmission of cVDPV2.

Enterovirus Surveillance (EVSurv) in Germany

The major aim of the enterovirus surveillance (EVSurv) in Germany is to prove the absence of poliovirus circulation in the framework of the Global Polio Eradication Program (GPEI). Therefore, a free-of-charge enterovirus diagnostic is offered to all hospitals for patients with symptoms compatible with a polio infection. Within the quality proven laboratory network for enterovirus diagnostic (LaNED), stool and cerebrospinal fluid (CSF) samples from patients with suspected aseptic meningitis/encephalitis or acute flaccid paralysis (AFP) are screened for enterovirus (EV), typing is performed in all EV positive sample to exclude poliovirus infections. Since 2006, ≈200 hospitals from all 16 German federal states have participated annually. On average, 2500 samples (70% stool, 28% CSF) were tested every year. Overall, the majority of the patients studied are children <15 years. During the 15-year period, 53 different EV serotypes were detected. While EV-A71 was most frequently detected in infants, E30 dominated in older children and adults. Polioviruses were not detected. The German enterovirus surveillance allows monitoring of the circulation of clinically relevant serotypes resulting in continuous data about non-polio enterovirus epidemiology.

Real-time prediction model of cVDPV2 outbreaks to aid outbreak response vaccination strategies

BACKGROUND

Circulating vaccine-derived poliovirus outbreaks are spreading more widely than anticipated, which has generated a crisis for the global polio eradication initiative. Effectively responding with vaccination activities requires a rapid risk assessment. This assessment is made difficult by the low case-to-infection ratio of type 2 poliovirus, variable transmissibility, changing population immunity, surveillance delays, and limited vaccine supply from the global stockpile. The geographical extent of responses have been highly variable between countries.

METHODS

We develop a statistical spatio-temporal model of short-term, district-level poliovirus spread that incorporates known risk factors, including historical wild poliovirus transmission risk, routine immunization coverage, population immunity, and exposure to the outbreak virus.

RESULTS

We find that proximity to recent cVDPV2 cases is the strongest risk factor for spread of an outbreak, and find significant associations between population immunity, historical risk, routine immunization, and environmental surveillance (p < 0.05). We examine the fit of the model to type 2 vaccine derived poliovirus spread since 2016 and find that our model predicts the location of cVDPV2 cases well (AUC = 0.96). We demonstrate use of the model to estimate appropriate scope of outbreak response activities to current outbreaks.

CONCLUSION

As type 2 immunity continues to decline following the cessation of tOPV in 2016, outbreak responses to new cVDPV2 detections will need to be faster and larger in scope. We provide a framework that can be used to support decisions on the appropriate size of a vaccination response when new detections are identified. While the model does not account for all relevant local factors that must be considered in the overall vaccination response, it enables a quantitative basis for outbreak response size.

Using Timeliness Metrics to Track Progress and Identify Gaps in Disease Surveillance

Timely outbreak detection and response can translate into illnesses averted and lives saved. As such, timeliness is an important criterion for evaluating performance of infectious disease surveillance systems. Through the use of clearly defined outbreak milestones, timeliness metrics can capture the speed of outbreak detection, verification, response, and other key actions across the timeline of an outbreak and evaluate progress over time. In this article, we describe a series of country-level pilot studies designed to assess the feasibility and utility of tracking timeliness metrics and highlight key findings. We then discuss subsequent efforts to develop a timeliness metrics measurement framework through expert consultation and provide recommendations for implementation. National surveillance programs, international agencies, and donor organizations can use timeliness metrics to identify gaps in surveillance performance and track progress toward improved global health security.

Evaluating the reliability and validity of secondary reporting to measure gender-based violence in conflict and disaster

Background

Accurately identifying the magnitude of gender-based violence (GBV) in humanitarian settings is hindered by logistical and methodological complexities. The ‘Neighborhood Method’, an adapted household survey that uses primary and secondary reporting to assess the prevalence of GBV in humanitarian settings, reduces the length of time and cost associated with traditional surveys. Primary female adult respondents disclose incidents of physical violence, intimate and non-intimate partner rape for themselves, other females in their homes (standard reporting) and other women and children in their social networks (secondary reporting). This study examines the reliability and validity of this inclusion of secondary reporting to determine the comparability of the Neighborhood Method to a traditional survey approach.

Methods

Drawing on data from 1180 women reporting on 3744 females in respondent households and 15,086 in neighboring households across four humanitarian settings (Ethiopia/ Somalia, Liberia, Sri Lanka, and Uganda), reliability of secondary reporting was measured through intra-class correlation coefficients (ICCs) and Cohen’s kappas. Validity was assessed using two-sample z-tests for differences between standard versus secondary reporting.

Results

Prevalence estimates comparing a respondent’s household with a neighboring household show closer agreement (ICC: 0.999–0.986) than self-reports vs. secondary reporting on a female counterpoint in a neighboring home (ICC: 0.939–0.98). Kappa statistics analyzing the reliability of two separate neighbors reporting on a third neighbor showed moderate agreement beyond chance alone (κ = 0.45 for physical violence and 0.48 for rape). Prevalence rates corresponded between standard and secondary reports (i.e. showed no statistical difference) in 18 out of 24 compared populations.

Conclusions

For prevalence of GBV, secondary reporting about neighbors can serve as a useful adjunct to standard survey methodology. Findings offer important initial insights into the consistency and accuracy of secondary reporting as a tool for field epidemiologists in humanitarian settings.

Review of poliovirus modeling performed from 2000 to 2019 to support global polio eradication

INTRODUCTION

Over the last 20 years (2000-2019) the partners of the Global Polio Eradication Initiative (GPEI) invested in the development and application of mathematical models of poliovirus transmission as well as economics, policy, and risk analyses of polio endgame risk management options, including policies related to poliovirus vaccine use during the polio endgame.

AREAS COVERED

This review provides a historical record of the polio studies published by the three modeling groups that primarily performed the bulk of this work. This review also systematically evaluates the polio transmission and health economic modeling papers published in English in peer-reviewed journals from 2000 to 2019, highlights differences in approaches and methods, shows the geographic coverage of the transmission modeling performed, identified common themes, and discusses instances of similar or conflicting insights or recommendations.

EXPERT OPINION

Polio modeling performed during the last 20 years substantially impacted polio vaccine choices, immunization policies, and the polio eradication pathway. As the polio endgame continues, national preferences for polio vaccine formulations and immunization strategies will likely continue to change. Future modeling will likely provide important insights about their cost-effectiveness and their relative benefits with respect to controlling polio and potentially achieving and maintaining eradication.

Cluster Detection Mechanisms for Syndromic Surveillance Systems: Systematic Review and Framework Development

Background

The time lag in detecting disease outbreaks remains a threat to global health security. The advancement of technology has made health-related data and other indicator activities easily accessible for syndromic surveillance of various datasets. At the heart of disease surveillance lies the clustering algorithm, which groups data with similar characteristics (spatial, temporal, or both) to uncover significant disease outbreak. Despite these developments, there is a lack of updated reviews of trends and modelling options in cluster detection algorithms.

Objective

Our purpose was to systematically review practically implemented disease surveillance clustering algorithms relating to temporal, spatial, and spatiotemporal clustering mechanisms for their usage and performance efficacies, and to develop an efficient cluster detection mechanism framework.

Methods

We conducted a systematic review exploring Google Scholar, ScienceDirect, PubMed, IEEE Xplore, ACM Digital Library, and Scopus. Between January and March 2018, we conducted the literature search for articles published to date in English in peer-reviewed journals. The main eligibility criteria were studies that (1) examined a practically implemented syndromic surveillance system with cluster detection mechanisms, including over-the-counter medication, school and work absenteeism, and disease surveillance relating to the presymptomatic stage; and (2) focused on surveillance of infectious diseases. We identified relevant articles using the title, keywords, and abstracts as a preliminary filter with the inclusion criteria, and then conducted a full-text review of the relevant articles. We then developed a framework for cluster detection mechanisms for various syndromic surveillance systems based on the review.

Results

The search identified a total of 5936 articles. Removal of duplicates resulted in 5839 articles. After an initial review of the titles, we excluded 4165 articles, with 1674 remaining. Reading of abstracts and keywords eliminated 1549 further records. An in-depth assessment of the remaining 125 articles resulted in a total of 27 articles for inclusion in the review. The result indicated that various clustering and aberration detection algorithms have been empirically implemented or assessed with real data and tested. Based on the findings of the review, we subsequently developed a framework to include data processing, clustering and aberration detection, visualization, and alerts and alarms.

Conclusions

The review identified various algorithms that have been practically implemented and tested. These results might foster the development of effective and efficient cluster detection mechanisms in empirical syndromic surveillance systems relating to a broad spectrum of space, time, or space-time.

Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda

Background

Precision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential.

Methods

Using a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens.

Results

Among 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses.

Conclusions

Using a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.

A systematic review of aberration detection algorithms used in public health surveillance

The algorithms used for detecting anomalies have evolved substantially over the last decade to take advantage of advances in informatics and to accommodate changes in surveillance data. We identified 145 studies since 2007 that evaluated statistical methods used to detect aberrations in public health surveillance data. For each study, we classified the analytic methods and reviewed the evaluation metrics. We also summarized the practical usage of the detection algorithms in public health surveillance systems worldwide. Traditional methods (e.g., control charts, linear regressions) were the focus of most evaluation studies and continue to be used commonly in practice. There was, however, an increase in the number of studies using forecasting methods and studies applying machine learning methods, hidden Markov models, and Bayesian framework to multivariate datasets. Evaluation studies demonstrated improved accuracy with more sophisticated methods, but these methods do not appear to be used widely in public health practice.

Profile of polio-compatible cases in Nigeria, 2006-2016

Background

The tremendous progress made by Nigeria towards polio eradication has recently suffered a setback with the isolation of circulating vaccine-derived poliovirus (cVDPV) type 2 from environmental samples and confirmation of four wild poliovirus (WPV) cases from acute flaccid paralysis (AFP) cases, with dates of onset of paralysis in July and August 2016. All these viruses were confirmed from the security-challenged northeastern state of Borno. Polio-compatible cases exist in Nigeria, and they indicate surveillance failure. Surveillance, therefore, has to be strengthened for the country to achieve certification. The objective of this paper is to highlight the epidemiological profile and magnitude of polio-compatible cases in Nigeria during the reporting period, as well as immunization and surveillance response activities conducted to close immunity and surveillance gaps.

Methods

We conducted a retrospective review of AFP surveillance performance and polio-compatible cases in Nigeria between 2006 and 2016 from the AFP database at the World Health Organization Country Office. We also reviewed and compared key epidemiological features of polio-compatible cases with those of wild poliovirus cases during the reporting period.

Results

The non-polio AFP rate improved from 6.5 in 2006 to 19.5 in 2016. The corresponding figures for stool adequacy rates were 88 and 98%. The total number of polio-compatible cases reported during the reporting period was 888, with the highest number (194) of cases reported in 2006 and the least (24) in 2016. Clusters of polio-compatible cases were reported every year during the reporting period except in 2015. The highest number (65) of polio-compatible cases in clusters was reported in 2006. The key epidemiological features of polio-compatible and wild poliovirus cases were similar.

Conclusion

AFP surveillance performance has improved significantly during the reporting period. Surveillance gaps still existed as shown by the presence of orphan viruses and polio-compatible cases, and these gaps need to be identified and closed to achieve certification.

Type 2 Poliovirus Detection after Global Withdrawal of Trivalent Oral Vaccine

BACKGROUND

Mass campaigns with oral poliovirus vaccine (OPV) have brought the world close to the eradication of wild poliovirus. However, to complete eradication, OPV must itself be withdrawn to prevent outbreaks of vaccine-derived poliovirus (VDPV). Synchronized global withdrawal of OPV began with serotype 2 OPV (OPV2) in April 2016, which presented the first test of the feasibility of eradicating all polioviruses.

METHODS

We analyzed global surveillance data on the detection of serotype 2 Sabin vaccine (Sabin-2) poliovirus and serotype 2 vaccine-derived poliovirus (VDPV2, defined as vaccine strains that are at least 0.6% divergent from Sabin-2 poliovirus in the viral protein 1 genomic region) in stool samples from 495,035 children with acute flaccid paralysis in 118 countries and in 8528 sewage samples from four countries at high risk for transmission; the samples were collected from January 1, 2013, through July 11, 2018. We used Bayesian spatiotemporal smoothing and logistic regression to identify and map risk factors for persistent detection of Sabin-2 poliovirus and VDPV2.

RESULTS

The prevalence of Sabin-2 poliovirus in stool samples declined from 3.9% (95% confidence interval [CI], 3.5 to 4.3) at the time of OPV2 withdrawal to 0.2% (95% CI, 0.1 to 2.7) at 2 months after withdrawal, and the detection rate in sewage samples declined from 71.0% (95% CI, 61.0 to 80.0) to 13.0% (95% CI, 8.0 to 20.0) during the same period. However, 12 months after OPV2 withdrawal, Sabin-2 poliovirus continued to be detected in stool samples (<0.1%; 95% CI, <0.1 to 0.1) and sewage samples (8.0%; 95% CI, 5.0 to 13.0) because of the use of OPV2 in response to VDPV2 outbreaks. Nine outbreaks were reported after OPV2 withdrawal and were associated with low coverage of routine immunization (odds ratio, 1.64 [95% CI, 1.14 to 2.54] per 10% absolute decrease) and low levels of population immunity (odds ratio, 2.60 [95% CI, 1.35 to 5.59] per 10% absolute decrease) within affected countries.

CONCLUSIONS

High population immunity has facilitated the decline in the prevalence of Sabin-2 poliovirus after OPV2 withdrawal and restricted the circulation of VDPV2 to areas known to be at high risk for transmission. The prevention of VDPV2 outbreaks in these known areas before the accumulation of substantial cohorts of children susceptible to type 2 poliovirus remains a high priority. (Funded by the Bill and Melinda Gates Foundation and the World Health Organization.).

Finding Outbreaks Faster

Rapid detection, reporting, and response to an infectious disease outbreak are critical to prevent localized health events from emerging as pandemic threats. Metrics to evaluate the timeliness of these critical activities, however, are lacking. Easily understood and comparable measures for tracking progress and encouraging investment in rapid detection, reporting, and response are sorely needed. We propose that the timeliness of outbreak detection, reporting, laboratory confirmation, response, and public communication should be considered as measures for improving global health security at the national level, allowing countries to track progress over time and inform investments in disease surveillance.