Strengthening pathogen genomic surveillance for health emergencies: insights from the World Health Organization's regional initiatives.

The onset of the COVID-19 pandemic triggered a rapid scale-up in the use of genomic surveillance as a pandemic preparedness and response tool. As a result, the number of countries with in-country SARS-CoV-2 genomic sequencing capability increased by 40% from February 2021 to July 2022. The Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022-2032 was launched by the World Health Organization (WHO) in March 2022 to bring greater coherence to ongoing work to strengthen genomic surveillance. This paper describes how WHO's tailored regional approaches contribute to expanding and further institutionalizing the use of genomic surveillance to guide pandemic preparedness and response measures as part of a harmonized global undertaking. Challenges to achieving this vision include difficulties obtaining sequencing equipment and supplies, shortages of skilled staff, and obstacles to maximizing the utility of genomic data to inform risk assessment and public health action. WHO is helping to overcome these challenges in collaboration with partners. Through its global headquarters, six regional offices, and 153 country offices, WHO is providing support for country-driven efforts to strengthen genomic surveillance in its 194 Member States, with activities reflecting regional specificities. WHO's regional offices serve as platforms for those countries in their respective regions to share resources and knowledge, engage stakeholders in ways that reflect national and regional priorities, and develop regionally aligned approaches to implementing and sustaining genomic surveillance within public health systems.

Public health research priorities for WHO on COVID-19 in the South-East Asia Region: results of a prioritization survey.

BACKGROUND: Effectively addressing the coronavirus disease 2019 (COVID-19) pandemic caused by the new pathogen requires continuous generation of evidence to inform decision-making. Despite an unprecedented amount of research occurring globally, the need to identify gaps in knowledge and prioritize a research agenda that is linked to public health action is indisputable. The WHO South-East Asia Region (SEAR) is likely to have region-specific research needs. METHODS: We aimed to identify a priority research agenda for guiding the regional and national response to the COVID-19 pandemic in SEAR countries. An online, anonymous research prioritization exercise using recent WHO guidance was conducted among the technical staff of WHO's country and regional offices engaged with the national COVID-19 response during October 2020. They were each asked to contribute up to five priority research ideas across seven thematic areas. These research ideas were reviewed, consolidated and scored by a core group on six parameters: regional specificity, relevance to the COVID-19 response, feasibility within regional research capacity, time to availability for decision-making, likely impact on practice, and promoting equity and gender responsiveness. The total scores for individual suggestions were organized in descending order, and ideas in the upper tertile were considered to be of high priority. RESULTS: A total of 203 priority research ideas were received from 48 respondents, who were primarily research and emergency response focal points in country and regional offices. These were consolidated into 78 research ideas and scored. The final priority research agenda of 27 items covered all thematic areas-health system (n=10), public health interventions (n=6), disease epidemiology (n=5), socioeconomic and equity (n=3), basic sciences (n=1), clinical sciences (n=1) and pandemic preparedness (n=1). CONCLUSIONS: This exercise, a part of WHO's mandate to "shape the research agenda", can help build a research roadmap ensuring efficient use of limited resources. This prioritized research agenda can act as a catalyst for Member States to accelerate research that could impact the COVID-19 response in SEAR.

Early epidemiological investigations: World Health Organization UNITY protocols provide a standardized and timely international investigation framework during the COVID-19 pandemic.

BACKGROUND: The declaration of Coronavirus disease 2019 (COVID-19) as a Public Health Emergency of International Concern (PHEIC) on 30 January 2020 required rapid implementation of early investigations to inform appropriate national and global public health actions. METHODS: The suite of existing pandemic preparedness generic epidemiological early investigation protocols was rapidly adapted for COVID-19, branded the 'UNITY studies' and promoted globally for the implementation of standardized and quality studies. Ten protocols were developed investigating household (HH) transmission, the first few cases (FFX), population seroprevalence (SEROPREV), health facilities transmission (n = 2), vaccine effectiveness (n = 2), pregnancy outcomes and transmission, school transmission, and surface contamination. Implementation was supported by WHO and its partners globally, with emphasis to support building surveillance and research capacities in low- and middle-income countries (LMIC). RESULTS: WHO generic protocols were rapidly developed and published on the WHO website, 5/10 protocols within the first 3 months of the response. As of 30 June 2021, 172 investigations were implemented by 97 countries, of which 62 (64%) were LMIC. The majority of countries implemented population seroprevalence (71 countries) and first few cases/household transmission (37 countries) studies. CONCLUSION: The widespread adoption of UNITY protocols across all WHO regions indicates that they addressed subnational and national needs to support local public health decision-making to prevent and control the pandemic.

Global impact of rotavirus vaccine introduction on rotavirus hospitalisations among children under 5 years of age, 2008-16: findings from the Global Rotavirus Surveillance Network.

BACKGROUND: Rotavirus vaccine use in national immunisation programmes has led to declines in hospital admissions for rotavirus gastroenteritis among children; however, the global impact of rotavirus vaccine introduction has not been described using primary data. We describe the impact of rotavirus vaccine introduction on admissions for acute rotavirus gastroenteritis in primarily low-income and middle-income countries, using 9 years of data from the WHO-coordinated Global Rotavirus Surveillance Network (GRSN). METHODS: Between Jan 1, 2008, and Dec 31, 2016, children younger than 5 years of age who were admitted to hospital with acute gastroenteritis were prospectively enrolled in GRSN sites. We included sites that enrolled children and collected stool specimens monthly and tested at least 100 specimens annually in the impact analysis, with a separate analysis taking into account site continuity. We compared proportions of acute gastroenteritis cases positive for rotavirus in the pre-vaccine and post-vaccine periods and calculated mean proportion changes for WHO regions, with 95% CIs; these findings were then compared with interrupted time series analyses. We did further sensitivity analyses to account for rotavirus vaccination coverage levels and sites that collected specimens for at least 11 months per year and tested at least 80 specimens per year. We also analysed the age distribution of rotavirus-positive cases before and after vaccine introduction. FINDINGS: 403 140 children younger than 5 years of age admitted to hospital with acute gastroenteritis from 349 sites in 82 countries were enrolled over the study period, of whom 132 736 (32·9%) were positive for rotavirus. We included 305 789 children from 198 sites in 69 countries in the impact analysis. In countries that had not introduced rotavirus vaccine in their national immunisation programmes, rotavirus was detected in 38·0% (95% CI 4·8-73·4) of admissions for acute gastroenteritis annually whereas in those that have introduced the vaccine, rotavirus was detected in 23·0% (0·7-57·7) of admissions for acute gastroenteritis, showing a 39·6% (35·4-43·8) relative decline following introduction. Interrupted time series analyses confirmed these findings. Reductions by WHO regions ranged from 26·4% (15·0-37·8) in the Eastern Mediterranean Region to 55·2% (43·0-67·4) in the European Region and were sustained in nine countries (contributing up to 31 sites) for 6-10 years. The age distribution of children with rotavirus gastroenteritis shifted towards older children after rotavirus vaccine introduction. INTERPRETATION: A significant and sustained reduction in the proportion of hospital admissions for acute gastroenteritis due to rotavirus was seen among children younger than 5 years in GRSN sites following rotavirus vaccine introduction. These findings highlight the need to incorporate rotavirus vaccines into immunisation programmes in countries that have not yet introduced them and underline the importance of high-quality surveillance. FUNDING: The GRSN receives funding from Gavi, the Vaccine Alliance and the US Centers for Disease Control and Prevention. No specific funding was provided for this Article.

Burnout subtypes and associated factors among police officers in Sri Lanka: A cross-sectional study.

Even though policing is associated with very high levels of occupational stress and burnout, no studies have been conducted to explore burnout subtypes among police officers globally. Hence, this cross-sectional study was conducted among 750 police officers working in a police division in Sri Lanka to determine the distribution and associations of burnout subtypes using the Burnout Clinical Subtype Questionnaire. The police officers had high scores for frenetic and worn-out subtypes in comparison to the underchallenged subtype. Multivariable analysis elicited a multitude of statistically significant associations with burnout subtypes (p < 0.05). Staff adequacy and fewer working hours were negatively associated with frenetic subtype. Younger police officers had a positive association, while, being married, satisfactory infrastructure facilities, frequent superior guidance, satisfactory higher official support, satisfactory allowances and the opportunity to serve public showed negative associations with underchallenged subtype. Being married, staff adequacy, frequent superior guidance, higher official support, satisfactory allowances, satisfactory social status and overall job satisfaction elicited significant negative associations with worn-out subtype. The findings are suggestive of high burnout subtype profile among the police officers in the study population and the associated factors of the three burnout subtypes are congruent with the characteristics of the burnout subtype profile.

Etiology of Severe Acute Watery Diarrhea in Children in the Global Rotavirus Surveillance Network Using Quantitative Polymerase Chain Reaction.

Background: The etiology of acute watery diarrhea remains poorly characterized, particularly after rotavirus vaccine introduction. Methods: We performed quantitative polymerase chain reaction for multiple enteropathogens on 878 acute watery diarrheal stools sampled from 14643 episodes captured by surveillance of children <5 years of age during 2013-2014 from 16 countries. We used previously developed models of the association between pathogen quantity and diarrhea to calculate pathogen-specific weighted attributable fractions (AFs). Results: Rotavirus remained the leading etiology (overall weighted AF, 40.3% [95% confidence interval {CI}, 37.6%-44.3%]), though the AF was substantially lower in the Americas (AF, 12.2 [95% CI, 8.9-15.6]), based on samples from a country with universal rotavirus vaccination. Norovirus GII (AF, 6.2 [95% CI, 2.8-9.2]), Cryptosporidium (AF, 5.8 [95% CI, 4.0-7.6]), Shigella (AF, 4.7 [95% CI, 2.8-6.9]), heat-stable enterotoxin-producing Escherichia coli (ST-ETEC) (AF, 4.2 [95% CI, 2.0-6.1]), and adenovirus 40/41 (AF, 4.2 [95% CI, 2.9-5.5]) were also important. In the Africa Region, the rotavirus AF declined from 54.8% (95% CI, 48.3%-61.5%) in rotavirus vaccine age-ineligible children to 20.0% (95% CI, 12.4%-30.4%) in age-eligible children. Conclusions: Rotavirus remained the leading etiology of acute watery diarrhea despite a clear impact of rotavirus vaccine introduction. Norovirus GII, Cryptosporidium, Shigella, ST-ETEC, and adenovirus 40/41 were also important. Prospective surveillance can help identify priorities for further reducing the burden of diarrhea.

Immunogenicity of live attenuated Japanese encephalitis SA 14-14-2 vaccine among Sri Lankan children with previous receipt of inactivated JE vaccine.

BACKGROUND: The performance of live attenuated Japanese Encephalitis SA 14-14-2 vaccine (CD-JEV) among children previously given inactivated mouse brain-derived JE vaccine (IMBV) is unknown. We evaluated the safety and immunogenicity of CD-JEV administered to 2- and 5-year-old children in Sri Lanka. METHODS: In this open-label, single arm trial in the Colombo District of Sri Lanka, generally healthy children 2 and 5years of age who had previously received two and three doses of IMBV, respectively, were administered one dose of CD-JEV subcutaneously. Participants were monitored for adverse events for one year post-vaccination. Serum neutralizing antibody responses were evaluated pre and 28 and 365days post-vaccination using JE plaque reduction neutralization test and characterized as the proportion of participants seroconverting. Seroconversion was defined as either reaching a titer considered seroprotective (⩾1:10) among participants with a baseline titer <1:10 or achieving at least a 4-fold rise in titer among participants with a baseline titer ⩾1:10. RESULTS: Of 305 children given CD-JEV, 294 were included in the primary analysis of immunogenicity. Prior to vaccination, 144/147 (98.0%) 2-year-olds and 146/147 (99.3%) 5-year-olds had seroprotective levels. 28days post-vaccination, 79/147 [53.7% (95% CI, 45.3-62.0)] 2-year olds and of 60/147 [40.8% (95% CI, 32.8-49.2)] 5-year olds achieved seroconversion. Among 2-year-olds, geometric mean titers (GMTs) rose from 697 to 3175 28days post-vaccination. Among 5-year-olds, GMTs rose from 926 to 2776. Most adverse reactions were mild, and no serious adverse events were related to study vaccination. CONCLUSION: Administration of CD-JEV to these children with pre-existing neutralizing JE antibody titers was safe and resulted in substantial boosting of antibody levels. These results may inform other countries in Asia considering switching from IMBV to now WHO-prequalified CD-JEV vaccine to combat this disease of public health importance.

A global review of national influenza immunization policies: Analysis of the 2014 WHO/UNICEF Joint Reporting Form on immunization.

INTRODUCTION: The WHO recommends annual influenza vaccination to prevent influenza illness in high-risk groups. Little is known about national influenza immunization policies globally. MATERIAL AND METHODS: The 2014 WHO/UNICEF Joint Reporting Form (JRF) on Immunization was adapted to capture data on influenza immunization policies. We combined this dataset with additional JRF information on new vaccine introductions and strength of immunization programmes, as well as publicly available data on country economic status. Data from countries that did not complete the JRF were sought through additional sources. We described data on country influenza immunization policies and used bivariate analyses to identify factors associated with having such policies. RESULTS: Of 194 WHO Member States, 115 (59%) reported having a national influenza immunization policy in 2014. Among countries with a national policy, programmes target specific WHO-defined risk groups, including pregnant women (42%), young children (28%), adults with chronic illnesses (46%), the elderly (45%), and health care workers (47%). The Americas, Europe, and Western Pacific were the WHO regions that had the highest percentages of countries reporting that they had national influenza immunization policies. Compared to countries without policies, countries with policies were significantly more likely to have the following characteristics: to be high or upper middle income (p<0.0001); to have introduced birth dose hepatitis B virus vaccine (p<0.0001), pneumococcal conjugate vaccine (p=0.032), or human papilloma virus vaccine (p=0.002); to have achieved global goals for diphtheria-tetanus-pertussis vaccine coverage (p<0.0001); and to have a functioning National Immunization Technical Advisory Group (p<0.0001). CONCLUSIONS: The 2014 revision of the JRF permitted a global assessment of national influenza immunization policies. The 59% of countries reporting that they had policies are wealthier, use more new or under-utilized vaccines, and have stronger immunization systems. Addressing disparities in public health resources and strengthening immunization systems may facilitate influenza vaccine introduction and use.

Safety and immunogenicity of live-attenuated Japanese encephalitis SA 14-14-2 vaccine co-administered with measles vaccine in 9-month-old infants in Sri Lanka.

INTRODUCTION: To facilitate introduction of live attenuated SA 14-14-2 Japanese encephalitis vaccine (LJEV) into the National Immunization Programme of Sri Lanka, we evaluated the safety and immunogenicity of co-administration of LJEV and measles vaccine at 9 months of age. Serum immune responses were evaluated post-vaccination on days 28, 180, and 365 using JE neutralization test and anti-measles IgG ELISA. RESULTS: 278 infants received one dose of LJEV and measles vaccine. Of these, 257 were eligible for the per-protocol analysis. On Day 0, 14 infants (5.5%) were seropositive for JE, but none were seropositive for measles. At Day 28, seropositivity rates were 90.7% (95% CI, 86.4-93.9%) for JE and 84.8% (95% CI, 79.8-89.0%) for measles. The geometric mean titer for JE neutralizing antibodies was 111 (95% CI, 90-135), and the geometric mean concentration (GMC) for anti-measles IgG was 375 mI U/mL (95% CI, 351-400 mI U/mL). Over the next year, JE neutralizing antibody responses declined only slightly, with seropositivity at 87.4% (95% CI, 82.6-91.2%) at Day 365. In contrast, measles antibody levels continued to increase over time. Seropositivity for anti-measles IgG reached 97.2% (95% CI, 94.4-98.9%) at Day 365, and the GMC rose to 1202 mI U/mL (95% CI, 1077-1341 mI U/mL). Co-administration of LJEV and measles vaccine was also safe. Most adverse reactions were mild, and no serious adverse events were related to study vaccinations. CONCLUSION: The safety and immunogenicity of LJEV co-administered with measles vaccine in Sri Lankan infants is similar to that seen in other populations, and our results support use of LJEV at 9 months of age. Live SA 14-14-2 vaccine is now prequalified by the WHO for use in infants in Asia, and other countries may wish to introduce LJEV to combat this devastating disease.

Annual risk of tuberculosis infection in Sri Lanka: a low prevalent country with a high BCG vaccination coverage in the South-East Asia Region.

INTRODUCTION: Despite its simplicity, efficiency and reliability, Sri Lanka has not used the Annual Risk of Tuberculosis Infection (ARTI) to assess the prevalence and efficiency of tuberculosis (TB) control. Hence, a national tuberculin survey was conducted to estimate the ARTI. MATERIALS AND METHODS: A school-based, cross-sectional tuberculin survey of 4352 children aged 10 years irrespective of their BCG vaccination or scar status was conducted. The sample was selected from urban, rural and estate strata using two-stage cluster sampling technique. In the first stage, sectors representing three strata were selected and, in the second stage, participants were selected from 120 clusters. Using the mode of the tuberculin reaction sizes (15 mm) and the mirror-image technique, the prevalence and the ARTI were estimated. RESULTS: The prevalence of TB estimated for urban, rural and estate sectors were 13.9%, 2.2% and 2.3%, respectively. The national estimate of the prevalence of TB was 4.2% (95% CI = 1.7-7.2%). ARTI for the urban, rural and estate sectors were 1.4%, 0.2% and 0.2%, respectively, and the national estimate was 0.4% (95% CI = 0.2-0.7%). The estimated annual burden of newly infected or re-infected TB cases with the potential of developing into the active disease (400/100 000 population) was nearly 10-fold higher than the national new case detection rate (48/100 000 population). CONCLUSION: The national estimate of ARTI was lower than the estimates for many developing countries. The high-estimated risk for the urban sector reflected the need for intensified, sector-specific focus on TB control activities. This underscores the need to strengthen case detection. Repeat surveys are essential to determine the annual decline rate of infection.

Integration of leprosy services into the General Health Service in Sri Lanka: overcoming challenges to implementation in a remote district.

Sri Lanka took a policy decision to integrate leprosy services into the general health services (GHS) in 1999. This paper aims to summarize the emergence of new, specific challenges and how they were overcome during the integration of leprosy services to the GHS in a remote, leprosy endemic district in Sri Lanka. In this article, the regional epidemiologist as the team leader describes the principles used for transition to an effective integrated model of leprosy services from a centralized leprosy control model in the district. In addition, rationale for integration is viewed from the epidemiological and operational perspectives. National and district leprosy epidemiological data from secondary sources are also reviewed for corroborating the effectiveness of integration. Challenges surfaced were mainly related to the transfer of ownership of the programme, selection of appropriate service providing institutions easily accessible to clients, sustainability of leprosy services at the GHS, ensuring participation of all stakeholders in capacity building programmes and co-ordination of patient care in the absence of a dermatologist in the district. An empowered district team leader with specified roles and responsibilities, his sound technical and managerial know how and ability to translate 'team work' concept to practice were found to be essential for successful implementation of integration. Decision-making powers at the district level and flexibility to introduce new, area-specific changes to the centrally prepared core activities of integration were also vital to overcome locally surfaced challenges.

Was there a disparity in age appropriate infant immunization uptake in the theatre of war in the North of Sri Lanka at the height of the hostilities?: a cross-sectional study in resettled areas in the Kilinochchi district.

BACKGROUND: It was long speculated that there could be under-immunized pockets in the war affected Northern part of Sri Lanka relative to other areas. With the cessation of hostilities following the military suppression of the rebellion, opportunities have arisen to appraise the immunization status of children in areas of re-settlement in former war ravaged districts. METHODS: We conducted a cross-sectional study to describe the coverage and age appropriateness of infant vaccinations in a former conflict district during the phase of re-settlement. The target population comprised all children of re-settled families in the age group of 12 - 23 months in the district. We selected a study sample of 300 children from among the target population using the WHO's 30 cluster EPI survey method. Trained surveyors collected data using a structured checklist. The infant vaccination status was ascertained by reviewing vaccination records in the Child Health Development Record or any other alternative documentary evidence. RESULTS: The survey revealed that the proportion of fully vaccinated children in the district was 91%. For individual vaccines, it ranged from 92% (measles) to 100% (BCG, DPT/OPV1). However, the age appropriateness of vaccination was less than 50% for all antigens except for BCG (94%). The maximum number of days of delay of vaccinations ranged from 21 days for BCG to 253 days for measles. Age appropriate vaccination rates significantly differed for DPT/OPV1-3 and measles during the conflict and post-conflict stages while it did not for the BCG. Age appropriate vaccination rates were significantly higher for DPT/OPV1-3 during the conflict while for the measles it was higher in the post conflict stage. CONCLUSIONS: Though the vaccination coverage for infant vaccines in the war affected Kilinochchi district was similar to other districts in the country, it masked a disparity in terms of low age-appropriateness of infant immunizations given in field settings. This finding underscores the need for investigation of underlying reasons and introduction of remedial measures in the stage of restoring Primary Health Care services in the ex-conflict zone.

Participatory decision-making through the Advisory Committee on Communicable Diseases: the Sri Lankan experience.

The paper describes how the Advisory Committee on Communicable Diseases (ACCD) in Sri Lanka addresses new challenges by ensuring participatory, collective and transparent decision-making through a broad representation of stakeholders. The Committee, which is more than 40 years old, differs from many other national immunization advisory committees, since it has a broad mandate to deal with all communicable diseases, including those for which there are no vaccines, and addresses such areas as disease surveillance and health system improvements, in addition to vaccination-related issues. The Committee has 38 members. Unlike in some countries, ACCD recommendations are legally binding for all public sector health providers. The paper provides several examples of recent recommendations and factors that influenced the Committee's decision-making, and concludes with ways the Committee can be improved.