Analysis Of Surveillance Data Research Articles

801. IDSA Featured Oral Abstract: 25 Years of Varicella Vaccination Program in the United States: Health Impact during 1995–2019

Abstract Background In 1995, the United States was the first country to introduce universal childhood varicella vaccination. High vaccine coverage was attained among young children, ≥ 90% since 2007. In 2007, the policy was changed from 1-dose to a 2-dose program. We describe the impact of 25 years of the U.S. varicella vaccination program on varicella disease nationally. Methods We reviewed published data and analyzed overall and age-specific trends for rates from the pre-vaccine period (1990–1994) through 2019 for varicella incidence using National Notifiable Diseases Surveillance System data, hospitalizations using National Inpatient Sample data, and deaths using National Center for Health Statistics data. We present trends in persons aged < 50 years, which captures most varicella burden and avoids misclassified herpes zoster in older people. Outbreak (≥ 5 varicella cases epidemiologically linked) characteristics were assessed for 1995–2019 and were informed by published data and analysis of surveillance data reported to CDC. Results Within the 10 years of the 1-dose program, varicella incidence, hospitalization, and mortality rates declined dramatically (71%–90%) vs. pre-vaccine. However, limited transmission continued in school settings which informed the change to a 2-dose policy. By 2019, declines reached > 97% for incidence and 94% and 97% for hospitalizations and deaths, respectively. The greatest decline occurred among persons aged < 20 years, born during the varicella vaccination program, with 99%, 97%, and > 99% reduction in incidence, hospitalizations, and deaths, respectively. The 2-dose program further reduced the number, size, and duration of outbreaks vs. the 1-dose program; over the entire program, the proportion of outbreaks with < 10 cases increased from 28% to 73%. Conclusion The varicella vaccination program significantly reduced varicella morbidity and mortality in the U.S. Twenty-five years into the program, pediatric varicella hospitalization has become a rare event and varicella deaths in persons aged < 20 years are practically eliminated in the U.S. Annually, > 3.8 million cases, 10,500 hospitalizations, and 100 deaths from varicella are now prevented in the United States due to the varicella vaccination program. Disclosures All Authors: No reported disclosures.

Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden.

The real-time analysis of infectious disease surveillance data is essential in obtaining situational awareness about the current dynamics of a major public health event such as the COVID-19 pandemic. This analysis of e.g., time-series of reported cases or fatalities is complicated by reporting delays that lead to under-reporting of the complete number of events for the most recent time points. This can lead to misconceptions by the interpreter, for instance the media or the public, as was the case with the time-series of reported fatalities during the COVID-19 pandemic in Sweden. Nowcasting methods provide real-time estimates of the complete number of events using the incomplete time-series of currently reported events and information about the reporting delays from the past. In this paper we propose a novel Bayesian nowcasting approach applied to COVID-19-related fatalities in Sweden. We incorporate additional information in the form of time-series of number of reported cases and ICU admissions as leading signals. We demonstrate with a retrospective evaluation that the inclusion of ICU admissions as a leading signal improved the nowcasting performance of case fatalities for COVID-19 in Sweden compared to existing methods.

Trends and disparities in 44 national notifiable infectious diseases in China: An analysis of national surveillance data from 2010 to 2019.

Research assessing the changing epidemiology of infectious diseases in China after the implementation of new healthcare reform in 2009 was scarce. We aimed to get the latest trends and disparities of nationalnotifiable infectious diseases by age, sex, province, and season in China from 2010 to 2019. The number of incident cases and deaths, incidence rate, and mortality of 44 national notifiable infectious diseases by sex, age groups, and provincial regions from 2010 to 2019 were extracted from the China Information System for Disease Control and Prevention and official reports and divided into six kinds of infectious diseases by transmission routes and three classes (A-C) in this descriptive study. Estimated annual percentage changes (EAPCs) were calculated to quantify the temporal trends of incidence and mortality rate. We calculated the concentration index to measure economic-related inequality. Segmented interrupted time-series analysis was used to estimate the impact of the COVID-19 pandemic on the epidemic of notifiable infectious diseases. The trend of incidence rate on six kinds of infectious diseases by transmission routes was stable, while only mortality of sexual, blood-borne, and mother-to-child-borne infectious diseases increased from 0.6466 per 100 000 population in 2010 to 1.5499 per 100 000 population in 2019 by 8.76% per year (95% confidence interval [CI]: 6.88-10.68). There was a decreasing trend of incidence rate on Class-A infectious diseases (EAPC = -16.30%; 95%CI: -27.93 to -2.79) and Class-B infectious diseases (EAPC = -1.05%; 95%CI: -1.56 to -0.54), while an increasing trend on Class-C infectious diseases (EAPC = 6.22%; 95%CI: 2.13-10.48). For mortality, there was a decreasing trend on Class-C infectious diseases (EAPC = -14.76%; 95%CI: -23.46 to -5.07), and an increasing trend on Class-B infectious diseases (EAPC = 4.56%; 95%CI: 2.44-6.72). In 2019, the infectious diseases with the highest incidence rate and mortality were respiratory diseases (340.95 per 100 000 population), and sexual, blood-borne, and mother-to-child-borne infectious diseases (1.5459 per 100 000 population), respectively. The greatest increasing trend of incidence rate was observed in seasonal influenza, from 4.83 per 100 000 population in 2010 to 253.36 per 100 000 population in 2019 by 45.16% per year (95%CI: 29.81-62.33), especially among females and children aged 0-4 years old. The top disease with the highest mortality was still AIDs, which had the highest average yearly mortality in 24 provinces from 2010 to 2019, and its incidence rate (EAPC = 14.99%; 95%CI: 8.75-21.59) and mortality (EAPC = 9.65; 95%CI: 7.71-11.63) both increased from 2010 to 2019, especially among people aged 44-59 years old and 60 or older. Male incidence rate and mortality were higher than females each year from 2010 to 2018 on 29 and 10 infectious diseases, respectively. Additionally, sex differences in the incidence and mortality of AIDS were becoming larger. The curve lay above the equality line, with the negative value of the concentration index, which indicated that economic-related health disparities exist in the distribution of incidence rate and mortality of respiratory diseases (incidence rate: the concentration index = -0.063, p < 0.0001; mortality: the concentration index = -0.131, p < 0.001), sexual, blood-borne, and mother-to-child-borne infectious diseases (incidence rate: the concentration index = -0.039, p = 0.0192; mortality: the concentration index = -0.207, p < 0.0001), and the inequality disadvantageous to the poor (pro-rich). Respiratory diseases (Dec-Jan), intestinal diseases (May-Jul), zoonotic infectious diseases (Mar-Jul), and vector-borne infectious diseases (Sep-Oct) had distinct seasonal epidemic patterns. In addition, segmented interrupted time-series analyses showed that, after adjusting for potential seasonality, autocorrelation, GDP per capita, number of primary medical institutions, and other factors, there was no significant impact of COVID-19 epidemic on the monthly incidence rate of six kinds of infectious diseases by transmission routes from 2018 to 2020 (all p > 0.05). The incidence rates of six kinds of infectious diseases were stable in the past decade, and incidence rates of Class-A and Class-B infectious diseases were decreasingbecause of comprehensive prevention and control measures and a strengthened health system after the implementation of the new healthcare reform in China since2009. However, age, gender, regional, and economic disparities were still observed. Concerted efforts are needed to reduce the impact of seasonal influenza (especially among children aged 0-4 years old) and the mortality of AIDs (especially among people aged 44-59 years old and 60 or older). More attention should be paid to the disparities in the burden of infectious diseases.

Recent HIV infection among newly diagnosed cases and associated factors in the Amhara regional state, Northern Ethiopia: HIV case surveillance data analysis (2019-2021).

Distinguishing a recent from long-standing HIV infection is a critical step to reduce new infections in 2030. Therefore, this analysis determines the proportion of recent HIV infections among newly diagnosed cases and associated factors in the Amhara regional state between 2019 and 2021. We got the HIV case-based surveillance dataset (July 2019 up to August 12/2021) from the Amhara Public Health Institute. Recent infection is an infection gained within the last 12 months as identified by Asante recency test kits. Logistic regression was carried out to identify factors associated with recent infection. Adjusted odd with 95% CI and a p-value of < 0.05 was considered to declare significant associations. Out of 5,689 eligible cases, 3,129 (55%) recency tests had been performed. The proportion of recent HIV infection is 443 (14.2%, 95% CI: 13, 15.4%). High proportion of recent infections is reported from Bahir Dar city (23.3%), Central Gondar (17.7%), West Gojjam (16.5%), North Shewa (16.5%) and South Gondar zones (15.7%). Besides, the proportion of recent infection is high among clients aged ≥ 51 years (32.4%), illicit drug users (30.6 %), homelessness (28.5%), current commercial sex workers (27.9%), prisoners (21.1%), and among clients with invasive medical procedures (22.2%). Recent infection is significantly associated with females (AOR: 1.9, 95% CI: 1.2-3.1), secondary and above education (AOR: 2.1, 95% CI: 1.3-3.4), commercial sex workers (AOR: 1.8, 95% CI: 1.2-2.7), having contact with index case (AOR: 0.5, 95% CI: 0.3-0.8) and illicit drug utilization (AOR: 3.6, 95% CI: 1.1-12.4). In the Amhara region, the proportion of recent HIV infection is high with marked variation across sociodemographic characteristics. We identified the risk or preventive factors associated with a recent infection. Therefore, all HIV responders should target their prevention efforts toward hot spot areas and sub-populations to stop further transmission.

Associations between COVID-19 and hospitalisation with respiratory and non-respiratory conditions: a record linkage study.

To assess associations between SARS-CoV-2 infection and the incidence of hospitalisation with selected respiratory and non-respiratory conditions in a largely SARS-CoV-2 vaccine-naïve population . Self-control case series; analysis of population-wide surveillance and administrative data for all laboratory-confirmed COVID-19 cases notified to the Victorian Department of Health (onset, 23 January 2020 - 31 May 2021; ie, prior to widespread vaccination rollout) and linked hospital admissions data (admission dates to 30 September 2021). Hospitalisation of people with acute COVID-19; incidence rate ratios (IRRs) comparing incidence of hospitalisations with defined conditions (including cardiac, cerebrovascular, venous thrombo-embolic, coagulative, and renal disorders) from three days before to within 89 days of onset of COVID-19 with incidence during baseline period (60-365 days prior to COVID-19 onset). A total of 20 594 COVID-19 cases were notified; 2992 people (14.5%) were hospitalised with COVID-19. The incidence of hospitalisation within 89 days of onset of COVID-19 was higher than during the baseline period for several conditions, including myocarditis and pericarditis (IRR, 14.8; 95% CI, 3.2-68.3), thrombocytopenia (IRR, 7.4; 95% CI, 4.4-12.5), pulmonary embolism (IRR, 6.4; 95% CI, 3.6-11.4), acute myocardial infarction (IRR, 3.9; 95% CI, 2.6-5.8), and cerebral infarction (IRR, 2.3; 95% CI, 1.4-3.9). SARS-CoV-2 infection is associated with higher incidence of hospitalisation with several respiratory and non-respiratory conditions. Our findings reinforce the value of COVID-19 mitigation measures such as vaccination, and awareness of these associations should assist the clinical management of people with histories of SARS-CoV-2 infection.

Spatial epidemiology of bacterial meningitis in the Upper West Region of Ghana: Analysis of disease surveillance data 2018-2020.

The use of a Geographic Information System in identifying meningitis hotspots in the Upper West Region (UWR) remains underutilized, making spatial targeting of meningitis hotspots difficult. We therefore utilized surveillance data enabled with GIS technology to target meningitis outbreaks in the UWR. Secondary data analysis was conducted in the study. The dynamics of bacterial meningitis in space and time were studied using epidemiological data from 2018 to 2020. Spot map and choropleths were used to depict the distribution of cases in the region. Moran's I statistics were used to assess spatial autocorrelation. Getis-Ord Gi*(d) and Anselin Local Moran's statistics were used to identify hotspots and spatial outliers within the study area. A Geographic Weighted Regression model was also used to examine how socio bio-climatic conditions influence the spread of meningitis. There were 1176 cases of bacterial meningitis, 118 deaths, and 1058 survivors between 2018 and 2020. Nandom municipality had the highest Attack Rate (AR) at 492/100,000 persons, followed by Nadowli-Kaleo district at 314/100,000 persons. Jirapa had the highest case fatality rate (CFR) at 17%. The spatio-temporal analysis showed spatial diffusion of meningitis prevalence from the western half of the UWR to the east with a significant number of hotpots and cluster outliers. Bacterial meningitis does not occur at random. Populations (10.9%) under sub-districts identified as hotspots are exceptionally at higher risk of outbreaks. Targeted interventions should be directed towards clustered hotspots, focusing on zones with low prevalence fenced off by high prevalence zones.

Resistance patterns among drug-resistant tuberculosis patients and trends-over-time analysis of national surveillance data in Gabon, Central Africa

ObjectiveRoutinely generated surveillance data are important for monitoring the effectiveness of MDR-TB control strategies. Incidence of rifampicin-resistant tuberculosis (RR-TB) is a key indicator for monitoring MDR-TB.MethodsIn a longitudinal nationwide retrospective study, 8 years (2014–2021) of sputum samples from presumptively drug-resistant tuberculosis patients from all regions of Gabon were referred to the national tuberculosis reference laboratory. Samples were analysed using GeneXpert MTB/RIF and Genotype MTBDRsl version 2/Line Probe Assay.ResultsOf 3057 sputum samples from presumptive tuberculosis patients, both from local hospital and from referral patients, 334 were RR-TB. The median patient age was 33 years (interquartile range 26–43); one third was newly diagnosed drug-resistant tuberculosis patients; one-third was HIV-positive. The proportion of men with RR-TB was significantly higher than that of women (55% vs 45%; p < 0.0001). Patients aged 25–35 years were most affected (32%; 108/334). The cumulative incidence of RR-TB was 17 (95% CI 15–19)/100,000 population over 8 years. The highest incidences were observed in 2020 and 2021. A total of 281 samples were analysed for second-line drug resistance. The proportions of study participants with MDR-TB, pre-XDR-TB and XDR-TB were 90.7% (255/281), 9% (25/281) and 0.3% (1/281), respectively. The most-common mutations in fluoroquinolones resistance isolates was gyrA double mutation gyrA MUT3B and MUT3C (23%; 4/17). Most (64%; 6/8) second-line injectable drugs resistance isolates were characterised by missing both rrs WT2 and MUT2 banding.ConclusionThe increasing incidence of MDR-TB infection in Gabon is alarming. It is highest in the 25–35 years age category. The incidence of MDR-TB infection in treatment-naïve patients calls for case finding and contact tracing strategy improvement.

BLOODPAC: Collaborating to chart a path towards blood-based screening for early cancer detection.

BLOODPAC: Collaborating to chart a path towards blood-based screening for early cancer detection.

Managing cutaneous melanoma of the eyelid: Evidence from surveillance, epidemiology, and end results (SEER) program

Ramachandran and Phan's investigation of Mohs Micrographic Surgery (MMS) versus Wide Local Excision (WLE) for T1 stage eyelid melanoma1 has important implications for plastic surgery. The study, based on analysis of Surveillance, Epidemiology, and End Results (SEER) Program data, found comparable overall survival and cancer-specific survival for MMS and WLE at over 5-years median follow-up. The non-inferiority of MMS is a promising result. Despite significant surgical innovation in periorbital reconstruction,2–4 the eyelid remains a high-risk site for functional and aesthetic impairments after surgery.

Malaria outbreak facilitated by increased mosquito breeding sites near houses and cessation of indoor residual spraying, Kole district, Uganda, January-June 2019

BackgroundIn June 2019, surveillance data from the Uganda’s District Health Information System revealed an outbreak of malaria in Kole District. Analysis revealed that cases had exceeded the outbreak threshold from January 2019. The Ministry of Health deployed our team to investigate the areas and people affected, identify risk factors for disease transmission, and recommend control and prevention measures.MethodsWe conducted an outbreak investigation involving a matched case-control study. We defined a confirmed case as a positive malaria test in a resident of Aboke, Akalo, Alito, and Bala sub-counties of Kole District January–June 2019. We identified cases by reviewing outpatient health records. Exposures were assessed in a 1:1 matched case-control study (n = 282) in Aboke sub-county. We selected cases systematically from 10 villages using probability proportionate to size and identified age- and village-matched controls. We conducted entomological and environmental assessments to identify mosquito breeding sites. We plotted epidemic curves and overlaid rainfall, and indoor residual spraying (IRS). Case-control exposures were combined into: breeding site near house, proximity to swamp and breeding site, and proximity to swamp; these were compared to no exposure in a logistic regression analysis.ResultsOf 18,737 confirmed case-patients (AR = 68/1,000), Aboke sub-county residents (AR = 180/1,000), children < 5 years (AR = 94/1,000), and females (AR = 90/1,000) were most affected. Longitudinal analysis of surveillance data showed decline in cases after an IRS campaign in 2017 but an increase after IRS cessation in 2018–2019. Overlay of rainfall and case data showed two malaria upsurges during 2019, occurring 35–42 days after rainfall increases. Among 141 case-patients and 141 controls, the combination of having mosquito breeding sites near the house and proximity to swamps increased the odds of malaria 6-fold (OR = 6.6, 95% CI = 2.24–19.7) compared to no exposures. Among 84 abandoned containers found near case-patients’ and controls’ houses, 14 (17%) had mosquito larvae. Adult Anopheles mosquitoes, larvae, pupae, and pupal exuviae were identified near affected houses.ConclusionStagnant water formed by increased rainfall likely provided increased breeding sites that drove this outbreak. Cessation of IRS preceded the malaria upsurges. We recommend re-introduction of IRS and removal of mosquito breeding sites in Kole District.

Surveillance, contact tracing and characteristics of SARS-CoV-2 transmission in educational settings in Northern Italy, September 2020 to April 2021.

BackgroundThe role of school contacts in the spread of the virus and the effectiveness of school closures in controlling the epidemic is still debated. We aimed to quantify the risk of transmission of SARS-CoV-2 in the school setting by type of school, characteristics of the index case and calendar period in the Province of Reggio Emilia (RE), Italy. The secondary aim was to estimate the speed of implementation of contact tracing.MethodsA population-based analysis of surveillance data on all COVID-19 cases occurring in RE, Italy, from 1 September 2020, to 4 April 2021, for which a school contact and/or exposure was suspected. An indicator of the delay in contact tracing was calculated as the time elapsed since the index case was determined to be positive and the date on which the swab test for classmates was scheduled (or most were scheduled).ResultsOverall, 30,184 and 13,608 contacts among classmates and teachers/staff, respectively, were identified and were recommended for testing, and 43,214 (98.7%) underwent the test. Secondary transmission occurred in about 40% of the investigated classes, and the overall secondary case attack rate was 4%. This rate was slightly higher when the index case was a teacher but with almost no differences by type of school, and was stable during the study period. Speed of implementation of contact tracing increased during the study period, with the time from index case identification to testing of contacts being reduced from seven to three days. The ability to identify the possible source of infection in the index case also increased.ConclusionsDespite the spread of the Alpha variant during the study period in RE, the secondary case attack rate remained stable from school reopening in September 2020 until the beginning of April 2021.

Quantifying spatial heterogeneity of malaria in the endemic Papua region of Indonesia: Analysis of epidemiological surveillance data

As control efforts progress towards elimination, malaria is likely to become more spatially concentrated in few local areas. The purpose of this study was to quantify and characterise spatial heterogeneity in malaria transmission-intensity across highly endemic Indonesian Papua. We analysed individual-level malaria surveillance data for nearly half a million cases (2019–2020) reported in the Papua and West Papua provinces and adapted the Gini index approach to quantify spatial heterogeneity at the district and health-unit levels. In this context, high Gini index implies disproportionately distributed malaria cases across the region. We showed malaria incidence trends and the spatial and temporal distribution of sociodemographic characteristics and aetiological parasites among cases. While Papua province accounted for the majority of malaria cases reported in the region and had seen a rise in transmission since 2015, West Papua province had maintained a comparatively low incidence. We observed that Gini index estimates were high, particularly when the lower spatial scale of health units was evaluated. The Gini index appears to be inversely associated to annual parasite-incidence, as well as the proportions of vivax malaria, male sex, and adults. This study suggests that areas with varying levels of transmission-intensities exhibited distinct characteristics. Malaria was distributed in a markedly disproportionate manner throughout the region, emphasising the need for spatially targeted interventions. Periodic quantification and characterisation of risk heterogeneity at various spatial levels using routine malaria surveillance data may aid in tracking progress towards elimination and guiding evidence-informed prioritisation of resource allocation. The study was funded by the Australian Government Department of Foreign Affairs and Trade Indo-Pacific Centre for Health Security through the Strengthening Preparedness in the Asia-Pacific Region through Knowledge (SPARK) project.

Clinical and economic burdens of recurrence following nephrectomy for intermediate high- or high-risk renal cell carcinoma: A retrospective analysis of Surveillance, Epidemiology, and End Results-Medicare data.

BACKGROUND: Renal cell carcinoma (RCC) is associated with a high risk of recurrence. Although RCC has been shown to impose a substantial burden on patients, little is known about the incremental clinical and economic burden attributable to disease recurrence. With recent advances in the RCC-therapeutic landscape, including adjuvant therapies, it is important to quantify the clinical and economic burden associated with RCC recurrence to better evaluate the potential impact of treatment in this patient population. OBJECTIVE: To quantify the incremental clinical and economic burden associated with disease recurrence among patients with intermediate high-risk and high-risk RCC postnephrectomy. METHODS: Data from the Surveillance, Epidemiology, and End Results-Medicare database (2007-2016) were used to identify patients with newly diagnosed, intermediate high-risk or high-risk RCC following nephrectomy. Patients with a diagnosis of metastatic disease or repeat nephrectomy or initiating a systemic treatment for advanced RCC were grouped as the recurrence cohort; patients without evidence of recurrence were grouped as the cohort without recurrence. Health care resource utilization (HRU), health care costs (2019 US dollars), and overall survival (OS) were compared between cohorts with and without recurrence, adjusting for demographic and clinical characteristics. RESULTS: A total of 269 patients with recurrence and 374 patients without recurrence were analyzed. Mean age was 75.2 and 75.7 years (P = 0.383), respectively, and 64.7% and 57.8% (P = 0.076) of patients were male, respectively. Median follow-up duration was 17 and 28 months, respectively. Patients with recurrence had a significantly shorter OS relative to patients without recurrence (adjusted hazard ratio = 6.00; 95% CI = 4.24-8.48; P < 0.001). Additionally, compared with patients without recurrence, patients with recurrence had significantly more inpatient admissions (0.16 vs 0.04 admissions per person-month [PM]; adjusted incidence rate ratio [aIRR] = 3.88; 95% CI = 3.12-4.81), outpatient visits (3.06 vs 1.77 visits per PM; aIRR = 1.68; 95% CI = 1.56-1.81), emergency department visits (0.10 vs 0.05 visits per PM; aIRR = 2.11; 95% CI = 1.66-2.68), and days hospitalized (1.40 vs 0.35 days per PM; aIRR = 6.73; 95% CI = 4.95-9.15) per patient per month (all P < 0.001). Adjusted mean monthly health care costs per patient were significantly higher among patients with recurrence vs patients without recurrence (differences of all-cause total costs, total medical costs, and pharmacy cost per month: $6,320, $4,924, and $1,387; all P < 0.001). CONCLUSIONS: RCC recurrence is associated with a significant increase in mortality, HRU, and health care costs, highlighting the substantial unmet need in patients with intermediate high-risk and high-risk RCC postnephrectomy when adjuvant therapies are not widely available. DISCLOSURES: Dr Sundaram is an employee of Merck Sharp & Dohme LLC., a subsidiary of Merck & Co., Inc., and holds stock in AbbVie, Abbott, Johnson & Johnson, Bristol Myers Squibb, and Merck & Co., Inc. Dr Bhattacharya is an employee of Merck Sharp & Dohme LLC., a subsidiary of Merck & Co., Inc., and holds stock in Merck & Co., Inc. Dr Adejoro and Dr Rogerio were employees of Merck Sharp & Dohme LLC., a subsidiary of Merck & Co., Inc. at the time of study conduct. Dr Adejoro holds stock in Johnson & Johnson. Dr Song, Dr Zhang, Mr Carley, and Dr Signorovitch are employees of Analysis Group, Inc., a consulting firm that received funding from Merck & Co., Inc. for the conduct of this research. Ms Zhu was an employee of Analysis Group, Inc. at the time of study conduct. Dr Haas is a Professor of Medicine at the Perelman School of Medicine, University of Pennsylvania and also serves on the advisory board for Aveo, Calithera and Exelixis, Co. Financial support for this study was provided by Merck & Co., Inc. The study sponsor was involved in the design and conduct of the study; collection, management, analysis, interpretation of data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Can more information be extracted from bovine TB skin test outcomes to inform animal risk management? A retrospective observational animal-level study

Continual tailoring of control programmes of endemic pathogens during long-term eradication campaigns requires detailed analysis of surveillance data to inform evidence-based policy. Bovine tuberculosis is a disease where long-term control and eradication programs are in train in several countries. The primary diagnostic tool, the intradermal tuberculin test, used to identify infected animals can be interpreted using different criteria and cut-offs, facilitating flexibility in its use as a basis to inform interventions.We investigated the comparative risk of animals failing a single intradermal comparative tuberculin test (SICTT) based on their previous tuberculin test result following a higher risk test-type (reactor retest of an infected herd). The study was a retrospective cohort design, and the primary exposure was the test status following a reactor retest classified as mutually exclusive categories based on bovine and avian tuberculin reactions: standard interpretation inconclusive (Sdi), severe interpretation inconclusive (Svi), single intradermal test (SIT) reactors (SITr), SIT inconclusive (SITi), avian tuberculin reactors (Ar), and test negative animals. Random effects multivariable logistic regression was used to investigate future risk. Cross-validation and downscaling was used to explore model performance. Alternate models with differing outcome test types were also explored.The models were trained on 844,207 observations from June 2018 to June 2021. Sdi, Svi, SITr, SITi and Ar were associated with the following odds ratios 12.242 (95 %CIs: 5.236–28.625; p < 0.001), 4.101 (95 %CIs: 3.423–4.913; p < 0.001), 2.503 (95 %CIs: 1.878–3.338; p < 0.001), 1.741 (95 %CIs: 1.195–2.538; p = 0.004) and 1.065 (95 %CIs: 0.833–1.361; p = 0.616) for failing the next test, respectively. High model performance was achieved with inclusion of random effects for both training and test evaluation datasets (AUC: 0.94; Balanced accuracy: 0.84), but fixed-effects only predictions exhibited moderate performance (AUC: 0.70; Balanced accuracy: 0.69). This reflects that 55 % of the risk of test failure relates to between herd heterogeneity based on intra-class correlation, while controlling for fixed effects. Other factors that were associated with increasing risk included age (older cohorts were at greater risk than the youngest cohort), breakdown history of the herd (greater number of breakdowns prior to the study period), and the time between exposure test and outcome test.These results provide further evidence to inform risk-based management policies for TB, including the removal of Sdi animals in higher risk situations, supplementary testing of cattle based on tuberculin responses and the provision of risk management advice to herd owners. The results characterise the future animal-level risk posed by Svis and suggest this risk may require policy led interventions.

Evaluation of a health systems strengthening intervention to improve Ebola Virus Disease infection prevention and control in the Democratic Republic of the Congo

Background The Democratic Republic of Congo declared their tenth outbreak of Ebola in North Kivu in 2018, which was the second-largest in the world and took place in an active conflict zone. Transmission of Ebola occurs by direct contact with infected bodily fluids and can occur within facilities when infection prevention and control (IPC) precautions are not strictly practised. Methods To develop infection prevention and control (IPC) standards in health facilities, 45 medical students were trained and placed in 101 health facilities to mentor healthcare workers and support IPC practices between February and October 2019. A mixed-methods retrospective evaluation of quality improvement in North Kivu was conducted in October and November 2019 to capture key lessons from such a pilot IPC project. Five focus groups (N=49) and 42 key-informant interviews were conducted in addition to a secondary analysis of surveillance and programmatic data collected during the intervention. Results The intervention contributed 1.83 times (95% confidence interval, CI=1.10-3.06) to increased the likelihood of health facilities achieving an IPC score of 80% or above compared with facilities that did not receive the intervention. Overall, we found the odds of Ebola cases declining three times more likely in Butembo and Katwa (odds ratio, OR=3.00, 95% CI=1.87-5.62) relative to ten health zones in the region that were not reached by the intervention. Conclusions The results are difficult to attribute to any one type of intervention, given the number of other interventions implemented concurrently during the outbreak response. Further evaluations should be conducted to assess the cost-effectiveness of using medical students in conflict resolution and IPC, and to assess the suitability of scaling these approaches to other settings and diseases.

Trends of key surveillance performance indicators of acute flaccid paralysis: a descriptive analysis, Uganda, 2015–2020

BackgroundPolio is disease caused by poliovirus which can in turn cause irreversible paralytic disease, presenting as Acute Flaccid Paralysis (AFP). A sensitive AFP surveillance system, in which all reported AFP cases are evaluated, first to determine if they are true AFP cases or not, is key for tracking polio eradication. True AFP cases are then later categorized as polio AFP or non-polio AFP (NPAFP) cases. Sensitivity is defined by meeting an annual NPAFP rate/100,000 population < 15 years of ≥ 4/100,000, and an annual stool adequacy (SA) rate of ≥ 80%. We describe Uganda’s AFP surveillance performance between 2015–2020, based on the WHO-recommended indicators, including; NPAFP and stool adequacy rate.MethodsWe performed a descriptive analysis of national AFP surveillance data, 2015–2020 obtained from ministry of health. We evaluated proportion of reported AFP cases that were true AFP, and changes in NPAFP and stool adequacy (SA) rate over the study period. We evaluated the trends in achieving the targeted NPAFP and SA rates from 2015–2020. We used QGIS to illustrate patterns in NPAFP and SA rates across districts and subregions.ResultsAmong 3,605 AFP cases reported and investigated countrywide from 2015–2020, 3,475 (96%) were true AFP cases. All the true AFP cases were non-polio related. District reporting was near-complete (97–100% each year). Overall, the mean NPAFP rate declined from 3.1/100,000 in 2015 to 2.1/100,000 in 2020. Less than 40% of districts met the NPAFP target rate in all years. The proportion of districts achieving the NPAFP target rate of ≥ 4/100,000 significantly declined from 35% in 2015 to 20% in 2020. The mean annual SA rate nationally was 88% from 2015–2020. Only 66% of districts achieved the SA target rate of ≥ 80% in the study period. The proportion of districts with SA rate ≥ 80% significantly increased from 68 to 80% between 2015 and 2020.ConclusionMost districts reported AFP cases. However, there was a decline in the NPAFP rate from 2015–2020 and few districts achieved the target rate. The suboptimal AFP surveillance system performance leaves the country at risk of missing ongoing poliovirus transmission. We recommend health worker training on active AFP searches, intensified supportive supervision, increase the number of environmental surveillance sentinel sites to boost AFP surveillance in the country, and periodic review meetings with districts to assess AFP surveillance performance.

Characterising persons diagnosed with HIV as either recent or long-term using a cross-sectional analysis of recent infection surveillance data collected in Malawi from September 2019 to March 2020

ObjectivesIn Malawi, a recent infection testing algorithm (RITA) is used to characterise infections of persons newly diagnosed with HIV as recent or long term. This paper shares results from recent...

Epidemiology, diagnostics and factors associated with mortality during a cholera epidemic in Nigeria, October 2020–October 2021: a retrospective analysis of national surveillance data

ObjectivesNigeria reported an upsurge in cholera cases in October 2020, which then transitioned into a large, disseminated epidemic for most of 2021. This study aimed to describe the epidemiology, diagnostic...

Trends and determinants of pregnancy loss in eastern Ethiopia from 2008 to 2019: analysis of health and demographic surveillance data

BackgroundPregnancy losses remain a neglected issue and it will be taking more than a century before a pregnant woman in Sub Sahara has the same chance of her baby being born alive as a woman in a high-income country. Pregnancy loss data are limited and not universal in Sub Saharan countries. This study was aimed to assess the magnitude and determinants of pregnancy loss in eastern Ethiopia.MethodsThis study was conducted in, open continues and dynamic cohort of population, Kersa Health and Demographic Survillance site (HDSS) in Eastern Ethiopia in 2008–2019. All mothers who had known pregnancy outcomes during the period and reside in Kersa HDSS were considered. The prevalence proportions were calculated as the sum of all pregnancy loss divided by the number births in the specified year. Log-Binomial regression was used to determine factors associated with pregnancy loss. Prevalence Proportion Ratio (PPR) was used to report the magnitude and strength of association. A p-value of less than 0.05 was considered statistically significant.ResultsFrom 39,153 included pregnancies, 810 (20.7; 95%CI:19.32, 22.15 per 1000 births) experienced pregnancy loss. Stillbirth was higher than abortion (11.14 Vs. 9.55 per 1000 births). Lacking own income (aPPR:1.26; 95%CI: 1.01, 1.58), being daily laborer (aPPR:1.44; 95%:1.08, 306) history of previous pregnancy loss (aPPR:2.26, 95%CI:1.69, 3.03), unwanted pregnancy (aPPR:1.26; 95%CI:1.01, 1.80), not receiving antenatal care (aPPR:1.59; 95%CI: 1.19, 2.13) and not receive the TT-vaccine during pregnancy (aPPR:1.33; 95%CI: 1.08, 1.80) were positively associated with pregnancy loss.ConclusionsThe overall rate pregnancy loss was ranged between 19.32, 22.15 per 1000 births with higher still births than miscarriage or abortion. Pregnancy loss was positively associated with social factors reproductive health factors, and maternal health service utilization.

COVID-19 mortality and excess mortality among working-age residents in California, USA, by occupational sector: a longitudinal cohort analysis of mortality surveillance data

BackgroundDuring the first year of the COVID-19 pandemic, workers in essential sectors had higher rates of SARS-CoV-2 infection and COVID-19 mortality than those in non-essential sectors. It is unknown whether disparities in pandemic-related mortality across occupational sectors have continued to occur during the periods of SARS-CoV-2 variants and vaccine availability.MethodsIn this longitudinal cohort study, we obtained data from the California Department of Public Health on all deaths occurring in the state of California, USA, from Jan 1, 2016, to Dec 31, 2021. We restricted our analysis to residents of California who were aged 18–65 years at time of death and died of natural causes. We classified the occupational sector into nine essential sectors; non-essential; or unemployed or without an occupation provided on the death certificate. We calculated the number of COVID-19 deaths in total and per capita that occurred in each occupational sector. Separately, using autoregressive integrated moving average models, we estimated total, per-capita, and relative excess natural-cause mortality by week between March 1, 2020, and Nov 30, 2021, stratifying by occupational sector. We additionally stratified analyses of occupational risk into counties with high versus low vaccine uptake, categorising high-uptake regions as counties where at least 50% of the population were fully vaccinated according to US guidelines by Aug 1, 2021.FindingsFrom March 1, 2020, to Nov 30, 2021, 24 799 COVID-19 deaths were reported in residents of California aged 18–65 years and an estimated 28 751 (95% prediction interval 27 853–29 653) excess deaths. People working in essential sectors were associated with higher COVID-19 deaths and excess deaths than were those working in non-essential sectors, with the highest per-capita COVID-19 mortality in the agriculture (131·8 per 100 000 people), transportation or logistics (107·1 per 100 000), manufacturing (103·3 per 100 000), facilities (101·1 per 100 000), and emergency (87·8 per 100 000) sectors. Disparities were wider during periods of increased infections, including during the Nov 29, 2020, to Feb 27, 2021, surge in infections, which was driven by the delta variant (B.1.617.2) and occurred during vaccine uptake. During the June 27 to Nov 27, 2021 surge, emergency workers had higher COVID-19 mortality (113·7 per 100 000) than workers from any other sector. Workers in essential sectors had the highest COVID-19 mortality in counties with low vaccination uptake, a difference that was more pronounced during the period of the delta infection surge during Nov 29, 2020, to Feb 27, 2021.InterpretationWorkers in essential sectors have continued to bear the brunt of high COVID-19 and excess mortality throughout the pandemic, particularly in the agriculture, emergency, manufacturing, facilities, and transportation or logistics sectors. This high death toll has continued during periods of vaccine availability and the delta surge. In an ongoing pandemic without widespread vaccine coverage and with anticipated threats of new variants, the USA must actively adopt policies to more adequately protect workers in essential sectors.FundingUS National Institute on Aging, Swiss National Science Foundation, and US National Institute on Drug Abuse.