Transforming the health information system using mobile and geographic information technologies, Papua New Guinea.

In the context of declining economic growth, now exacerbated by the coronavirus disease 2019 pandemic, Papua New Guinea is increasing the efficiency of its health systems to overcome difficulties in reaching global health and development targets. Before 2015, the national health information system was fragmented, underfunded, of limited utility and accessed infrequently by health authorities. We built an electronic system that integrated mobile technologies and geographic information system data sets of every house, village and health facility in the country. We piloted the system in 184 health facilities across five provinces between 2015 and 2016. By the end of 2020, the system's mobile tablets were rolled out to 473 facilities in 13 provinces, while the online platform was available in health authorities of all 22 provinces, including church health services. Fractured data siloes of legacy health programmes have been integrated and a platform for civil registration systems established. We discuss how mobile technologies and geographic information systems have transformed health information systems in Papua New Guinea over the past 6 years by increasing the timeliness, completeness, quality, accessibility, flexibility, acceptability and utility of national health data. To achieve this transformation, we highlight the importance of considering the benefits of mobile tools and using rich geographic information systems data sets for health workers in primary care in addition to the needs of public health authorities.

Dans un contexte de déclin de la croissance économique, exacerbé par la pandémie de maladie à coronavirus, la Papouasie-Nouvelle-Guinée a décidé d'augmenter l'efficacité de ses systèmes sanitaires afin de surmonter les difficultés à atteindre les objectifs globaux en matière de santé et de développement. Avant 2015, le système d'information sanitaire national était fragmenté, sous-financé, peu utile et rarement consulté par les autorités sanitaires. Nous avons donc conçu un système électronique intégrant des technologies mobiles et des ensembles de données géographiques provenant de chaque ménage, de chaque village et de chaque établissement de soins du pays. Entre 2015 et 2016, nous avons piloté le système dans 184 établissements de soins répartis sur cinq provinces. Fin 2020, les tablettes mobiles du système ont été distribuées dans 473 établissements de 13 provinces, tandis que les autorités sanitaires des 22 provinces du pays, y compris les services sanitaires confessionnels, ont pu accéder à la plateforme en ligne. Les silos de données fragmentées des programmes de santé antérieurs y ont été incorporés et une plateforme destinée aux registres d'état civil a été créée. Le présent document se penche sur la manière dont les technologies d'information mobiles et géographiques ont transformé les systèmes d'information sanitaire en Papouasie-Nouvelle-Guinée ces six dernières années en améliorant la ponctualité, l'exhaustivité, la qualité, l'accessibilité, la flexibilité, la recevabilité et l'utilité des données nationales sur la santé. Pour réaliser cette transformation, il est à nos yeux essentiel de tenir compte des avantages que représentent les outils mobiles, et de tirer profit des vastes ensembles de données géographiques non seulement pour les travailleurs des soins de santé primaires, mais aussi pour les besoins des autorités de santé publique.

En el contexto de un crecimiento económico en declive, agravado ahora por la pandemia de la enfermedad por coronavirus, Papúa Nueva Guinea está aumentando la eficiencia de sus sistemas sanitarios para superar las dificultades para alcanzar los objetivos globales de salud y desarrollo. Antes de 2015, el sistema nacional de información sanitaria estaba fragmentado, carecía de fondos suficientes, su utilidad era limitada y las autoridades sanitarias accedían a él con poca frecuencia. Construimos un sistema electrónico que integraba tecnologías móviles y conjuntos de datos del sistema de información geográfica de cada casa, pueblo y centro de salud del país. Entre 2015 y 2016 pusimos a prueba el sistema en 184 centros de salud de cinco provincias. A finales de 2020, las tabletas móviles del sistema se implementaron en 473 centros de 13 provincias, mientras que la plataforma en línea estaba disponible en las autoridades sanitarias de las 22 provincias, incluidos los servicios de salud de las iglesias. Se han integrado los silos de datos fracturados de los programas sanitarios heredados y se ha establecido una plataforma para los sistemas de registro civil. Exponemos cómo las tecnologías móviles y los sistemas de información geográfica han transformado los sistemas de información sanitaria en Papúa Nueva Guinea en los últimos seis años, aumentando la puntualidad, la exhaustividad, la calidad, la accesibilidad, la flexibilidad, la aceptabilidad y la utilidad de los datos sanitarios nacionales. Para lograr esta transformación, destacamos la importancia de tener en cuenta los beneficios de las herramientas móviles y de utilizar conjuntos de datos ricos en sistemas de información geográfica para los trabajadores sanitarios de la atención primaria, además de las necesidades de las autoridades sanitarias públicas.

Progress Toward Regional Measles Elimination - Worldwide, 2000-2020.

In 2012, the World Health Assembly endorsed the Global Vaccine Action Plan,* with the objective of eliminating measles† in five of the six World Health Organization (WHO) regions by 2020 (1). The Immunization Agenda 2021-2030 (IA2030)§ uses measles incidence as an indicator of the strength of immunization systems. The Measles-Rubella Strategic Framework 2021-2030¶ and the Measles Outbreaks Strategic Response Plan 2021-2023** are aligned with the IA2030 and highlight robust measles surveillance systems to document immunity gaps, identify root causes of undervaccination, and develop locally tailored solutions to ensure administration of 2 doses of measles-containing vaccine (MCV) to all children. This report describes progress toward World Health Assembly milestones and measles elimination objectives during 2000-2020 and updates a previous report (2). During 2000-2010, estimated MCV first dose (MCV1) coverage increased globally from 72% to 84%, peaked at 86% in 2019, but declined to 84% in 2020 during the COVID-19 pandemic. All countries conducted measles surveillance, although fewer than one third achieved the sensitivity indicator target of ≥2 discarded†† cases per 100,000 population in 2020. Annual reported measles incidence decreased 88% during 2000-2016, from 145 to 18 cases per 1 million population, rebounded to 120 in 2019, before falling to 22 in 2020. During 2000-2020, the annual number of estimated measles deaths decreased 94%, from 1,072,800 to 60,700, averting an estimated 31.7 million measles deaths. To achieve regional measles elimination targets, enhanced efforts are needed to reach all children with 2 MCV doses, implement robust surveillance, and identify and close immunity gaps.

Surveillance strategies for the detection of disease outbreaks in the Pacific islands: meta-analysis of published literature, 2010-2019.

OBJECTIVE: Due to their tropical location, development status and the limited capacity of health systems, Pacific island counties and territories are particularly susceptible to infectious disease outbreaks; but evidence as to the optimal way in which outbreaks are detected is scarce. In this review, we synthesise evidence from literature about how outbreaks are detected in Pacific island countries and territories and critique factors identified as inhibiting surveillance practice. METHOD: For this systematic review, we searched electronic databases Embase, Global Health, MEDLINE and MEDLINE Epub from 1 January 2010 and 31 March 2019 for reports describing infectious disease outbreaks occurring in the Pacific islands. Reports were included if they reported the method by which an outbreak was detected or the time between an outbreak's onset and its detection. We extracted information about the report type and authors, the outbreak and its method/s of detection, and pertinent issues inhibiting surveillance practice. RESULTS: Of 860 articles identified, 37 reports describing 39 outbreaks met the inclusion criteria. Most outbreaks (n = 30) were identified through formal event-based surveillance; six through syndromic surveillance; and two by ad hoc notification from the community. Barriers to early outbreak detection included population isolation; lack of resources and infrastructure to support surveillance implementation and signal investigation; and broader health system factors such as preparedness planning and availability of laboratory services. CONCLUSION: Most surveillance-related gain in the Pacific islands may be made through building formal event-based surveillance systems and streamlining reporting processes to facilitate outbreak notification. This observation is pertinent given the focus on establishing and expanding syndromic surveillance approaches for outbreak detection in the islands over the last decade.

OBJECTIF: En raison de leur situation tropicale, de leur état de développement et de la capacité limitée des systèmes de santé, les comtés et territoires des îles du Pacifique sont particulièrement sensibles aux épidémies de maladies infectieuses, mais les données quant à la manière optimale de détecter les épidémies sont rares. Dans cette étude, nous synthétisons les données de la littérature sur la manière dont les épidémies sont détectées dans les pays et territoires des îles du Pacifique et les facteurs critiques identifiés comme entravant la pratique de la surveillance. MÉTHODE: Pour cette analyse systématique, nous avons recherché dans les bases de données électroniques Embase, Global Health, MEDLINE et MEDLINE Epub du 1er janvier 2010 et du 31 mars 2019 pour des rapports décrivant les épidémies de maladies infectieuses survenant dans les îles du Pacifique. Les rapports ont été inclus s'ils indiquaient la méthode de détection d'une épidémie ou le délai entre le début d'une épidémie et sa détection. Nous avons extrait les informations sur le type de rapport et les auteurs, l'épidémie et sa ou ses méthodes de détection, ainsi que les problèmes pertinents qui entravent la pratique de la surveillance. RÉSULTATS: Sur les 860 articles identifiés, 37 rapports décrivant 39 ménages ont satisfait aux critères d'inclusion. La plupart des épidémies (n = 30) ont été identifiés suite à une surveillance formelle basée sur les événements, six suite à une surveillance syndromique et deux suite à une notification ad-hoc de la communauté. Les obstacles à la détection précoce des épidémies comprennent l'isolement de la population, le manque de ressources et d'infrastructures pour soutenir la mise en œuvre de la surveillance et l'investigation des signaux, ainsi que des facteurs plus généraux du système de santé tels que la planification de la préparation et la disponibilité des services de laboratoire. CONCLUSION: La plupart des gains liés à la surveillance dans les îles du Pacifique peuvent être réalisés par la mise en place de systèmes de surveillance formels basés sur les événements et l'aiguillage des processus de report pour faciliter la notification des épidémies. Cette observation est pertinente étant donné l'accent mis sur l'établissement et l'expansion des approches de surveillance syndromique pour la détection des épidémies dans les îles au cours de la dernière décennie.

Epidemic surveillance in a low resource setting: lessons from an evaluation of the Solomon Islands syndromic surveillance system, 2017.

BACKGROUND: Solomon Islands is one of the least developed countries in the world. Recognising that timely detection of outbreaks is needed to enable early and effective response to disease outbreaks, the Solomon Islands government introduced a simple syndromic surveillance system in 2011. We conducted the first evaluation of the system and the first exploration of a national experience within the broader multi-country Pacific Syndromic Surveillance System to determine if it is meeting its objectives and to identify opportunities for improvement. METHODS: We used a multi-method approach involving retrospective data collection and statistical analysis, modelling, qualitative research and observational methods. RESULTS: We found that the system was well accepted, highly relied upon and designed to account for contextual limitations. We found the syndromic algorithm used to identify outbreaks was moderately sensitive, detecting 11.8% (IQR: 6.3-25.0%), 21.3% (IQR: 10.3-36.8%), 27.5% (IQR: 12.8-52.3%) and 40.5% (IQR: 13.5-65.7%) of outbreaks that caused small, moderate, large and very large increases in case presentations to health facilities, respectively. The false alert rate was 10.8% (IQR: 4.8-24.5%). Rural coverage of the system was poor. Limited workforce, surveillance resourcing and other 'upstream' health system factors constrained performance. CONCLUSIONS: The system has made a significant contribution to public health security in Solomon Islands, but remains insufficiently sensitive to detect small-moderate sized outbreaks and hence should not be relied upon as a stand-alone surveillance strategy. Rather, the system should sit within a complementary suite of early warning surveillance activities including event-based, in-patient- and laboratory-based surveillance methods. Future investments need to find a balance between actions to address the technical and systems issues that constrain performance while maintaining simplicity and hence sustainability.

Towards effective outbreak detection: a qualitative study to identify factors affecting nurses' early warning surveillance practice in Solomon Islands.

BACKGROUND: Intelligence generated by a surveillance system is dependent on the quality of data that are collected. We investigated the knowledge, attitudes and practices of nurses responsible for outbreak early warning surveillance data collection in Solomon Islands to identify factors that influence their ability to perform surveillance-related tasks with rigour. METHODS: We interviewed 12 purposively selected surveillance nurses and conducted inductive analysis on resulting data. RESULTS: Interviewees were knowledgeable and willing to contribute to the surveillance system. Constraining factors included the perception that surveillance was less important than patient care and could be 'deferred' during busy periods and wide variability in the application of case definitions. Motivating factors were frequent in-clinic training, formal recognition for good performance, incentives and designation of a focal point. Nurses held mixed views about the effect of mobile technologies on surveillance practice. CONCLUSIONS: This study identified several challenges to consistent and accurate data collection and reporting. Engagement of different parts of the health system, including human resources and health facilities' management, is needed to address these challenges.

Contextual factors and health service performance from the perspective of the provincial health administrators in Papua New Guinea.

INTRODUCTION: The Rural Primary Health Services Delivery Project aims to improve the quality and coverage of health services to rural populations in Papua New Guinea. There are limitations in measuring performance of such projects through analysis of health information system data alone due to data quality issues and a multitude of unmeasured factors that affect performance. A mixed methods study was undertaken to understand the contextual factors that affect health service performance. METHODS: A performance assessment framework was developed including service delivery indicators derived from the National Health Information System. Prior to implementation, a baseline analysis of the indicators was undertaken. Subsequently, semi-structured interviews were conducted with health administrators, in which they were asked about factors they perceived to influence health facility performance. During the interviews, key informants were provided with health indicators for their province and asked to interpret the performance of facilities. Interviews were transcribed and inductive thematic analysis performed. RESULTS: Performance indicators varied greatly within and between districts. Key informants cited a number of reasons for this variation. Health facilities accessible by road in urban areas, with competent and/or higher level staff and health services operated by churches or private companies, were cited as contributors to high performance. For high performing districts, key informants also discussed use of health information, planning and targeted strategies to improve performance. Inadequate numbers of staff, poorly skilled staff, funding delays and challenging geography were major contributors noted for poor performance. CONCLUSION: Analysis of quantitative indicators needs to be performed at health facility level in order to understand district level performance. Interpretation of performance through key informant interviews provided useful insight into previously undocumented contextual factors affecting health delivery performance. The sequential explanatory mixed methods design could be applied to evaluations of other health service delivery programs in similar contexts.

Lessons for health program monitoring and evaluation in a low resource setting.

Numerous guidelines outline best practices for health program monitoring and evaluation (M&E). However, health programs are often implemented in less than ideal circumstances where these best practices may not be resourced or feasible. This article describes how M&E has been conducted for a health service delivery improvement program in remote Papua New Guinea and outlines lessons learned. The lessons learned were to integrate M&E into every aspect of the program, strengthen existing health information data, link primary data collection with existing program activities, conduct regular monitoring and feedback for early identification of implementation issues, involve the program team in evaluation, and communicate M&E data through multiple mediums to stakeholders. These lessons could be applied to other health programs implemented in low resource settings.

Health information system strengthening and malaria elimination in Papua New Guinea.

BACKGROUND: The objective of the study was to describe an m-health initiative to strengthen malaria surveillance in a 184-health facility, multi-province, project aimed at strengthening the National Health Information System (NHIS) in a country with fragmented malaria surveillance, striving towards enhanced control, pre-elimination. METHODS: A remote-loading mobile application and secure online platform for health professionals was created to interface with the new system (eNHIS). A case-based malaria testing register was developed and integrated geo-coded households, villages and health facilities. A malaria programme management dashboard was created, with village-level malaria mapping tools, and statistical algorithms to identify malaria outbreaks. RESULTS: Since its inception in 2015, 160,750 malaria testing records, including village of residence, have been reported to the eNHIS. These case-based, geo-coded malaria data are 100% complete, with a median data entry delay of 9 days from the date of testing. The system maps malaria to the village level in near real-time as well as the availability of treatment and diagnostics to health facility level. Data aggregation, analysis, outbreak detection, and reporting are automated. CONCLUSIONS: The study demonstrates that using mobile technologies and GIS in the capture and reporting of NHIS data in Papua New Guinea provides timely, high quality, geo-coded, case-based malaria data required for malaria elimination. The health systems strengthening approach of integrating malaria information management into the eNHIS optimizes sustainability and provides enormous flexibility to cater for future malaria programme needs.

The impact of active surveillance and health education on an Ebola virus disease cluster - Kono District, Sierra Leone, 2014-2015.

BACKGROUND: During December 2014-February 2015, an Ebola outbreak in a village in Kono district, Sierra Leone, began following unsafe funeral practices after the death of a person later confirmed to be infected with Ebola virus. In response, disease surveillance officers and community health workers, in collaboration with local leadership and international partners, conducted 1 day of active surveillance and health education for all households in the village followed by ongoing outreach. This study investigated the impact of these interventions on the outbreak. METHODS: Fifty confirmed Ebola cases were identified in the village between December 1, 2014 and February 28, 2015. Data from case investigations, treatment facility and laboratory records were analyzed to characterize the outbreak. The reproduction number (R) was estimated by fitting to the observed distribution of secondary cases. The impact of the active surveillance and health education was evaluated by comparing two outcomes before and after the day of the interventions: 1) the number of days from symptom onset to case-patient isolation or death and 2) a reported epidemiologic link to a prior Ebola case. RESULTS: The case fatality ratio among the 50 confirmed Ebola cases was 64.0 %. Twenty-three cases occurred among females (46.0 %); the mean age was 39 years (median: 37 years; range: 5 months to 75 years). Forty-three (87.8 %) cases were linked to the index case; 30 (61.2 %) were either at the funeral of Patient 1 or had contact with him while he was ill. R was 0.93 (95 % CI: 0.15-2.3); excluding the funeral, R was 0.29 (95 % CI: 0.11-0.53). The mean number of days in the community after onset of Ebola symptoms decreased from 4.0 days (median: 3 days; 95 % CI: 3.2-4.7) before the interventions to 2.9 days (median: 2 days; 95 % CI: 1.6-4.3) afterward. An epidemiologic link was reported in 47.6 % of case investigations prior to and 100 % after the interventions. CONCLUSIONS: Initial case investigation and contact tracing were hindered by delayed reporting and under-reporting of symptomatic individuals from the community. Active surveillance and health education contributed to quicker identification of suspected cases, interrupting further transmission.

First reported outbreak of locally acquired hepatitis E virus infection in Australia.

OBJECTIVE: To determine the source and extent of a locally acquired hepatitis E virus (HEV) infection outbreak. DESIGN, SETTING AND PARTICIPANTS: A cluster of notified cases of HEV infection linked to a single restaurant (X) was identified in May 2014. People with laboratory-confirmed HEV infection in New South Wales between January 2013 and December 2014 were interviewed about potential risk factors for HEV infection. Co-diners at restaurant X and patients with suspected but unexplained viral hepatitis were retrospectively tested. Foods eaten by the infected persons were compared with those of seronegative co-diners. HEV RNA detected in sera from infected persons was sequenced and genotyped. Implicated foods were traced back to their sources. MAIN OUTCOME MEASURES: Potential sources of infection, including overseas travel and foods eaten, and origin of implicated food products. RESULTS: In 55 serologically confirmed cases of HEV infection, 24 people had not travelled overseas during their incubation periods. Of the 24, 17 reported having eaten at restaurant X, 15 of whom could be interviewed. All reported consuming pork liver pâté, compared with only four of seven uninfected co-diners (P < 0.05). The other seven people with locally acquired infections each reported consuming a pork product during their incubation periods. HEV RNA was detected in 16 of the 24 cases; all were of genotype 3. Sequencing indicated greater than 99% homology among restaurant X isolates. HEV RNA was isolated from pork sausages from a batch implicated in one of the locally acquired infections not linked with restaurant X. The pork livers used for pâté preparation by restaurant X were traced to a single Australian farm. CONCLUSIONS: This is the first reported HEV outbreak in Australia. HEV should be considered in patients presenting with a compatible illness, even without a history of overseas travel. Pork products should be thoroughly cooked before consumption.

Spatio-temporal epidemiology of the cholera outbreak in Papua New Guinea, 2009-2011.

BACKGROUND: Cholera continues to be a devastating disease in many developing countries where inadequate safe water supply and poor sanitation facilitate spread. From July 2009 until late 2011 Papua New Guinea experienced the first outbreak of cholera recorded in the country, resulting in >15,500 cases and >500 deaths. METHODS: Using the national cholera database, we analysed the spatio-temporal distribution and clustering of the Papua New Guinea cholera outbreak. The Kulldorff space-time permutation scan statistic, contained in the software package SatScan v9.2 was used to describe the first 8 weeks of the outbreak in Morobe Province before cholera cases spread throughout other regions of the country. Data were aggregated at the provincial level to describe the spread of the disease to other affected provinces. RESULTS: Spatio-temporal and cluster analyses revealed that the outbreak was characterized by three distinct phases punctuated by explosive propagation of cases when the outbreak spread to a new region. The lack of road networks across most of Papua New Guinea is likely to have had a major influence on the slow spread of the disease during this outbreak. CONCLUSIONS: Identification of high risk areas and the likely mode of spread can guide government health authorities to formulate public health strategies to mitigate the spread of the disease through education campaigns, vaccination, increased surveillance in targeted areas and interventions to improve water, sanitation and hygiene.

A state-wide information campaign during a pertussis epidemic in New South Wales, 2010.

Pertussis notifications increased dramatically in New South Wales in 2008, exceeding the rates in previous epidemic years. A state-wide, multi-faceted campaign was launched in March 2009 to provide information about pertussis prevention. A population-based survey was conducted using a Computer Assisted Telephone Interviewing facility to assess the effectiveness of sending letters to households with young infants. A representative sample of 1,200 adults across all 8 area health services was interviewed between July 2009 and September 2010, with responses weighted against the state population. Many respondents (39.7%) reported receiving the letter, while fewer (29.6%) reported receiving an adult pertussis booster in the last year, mostly in response to General Practitioner advice (40.4%). Letter receipt was associated with the uptake of an adult pertussis booster in the past 12 months by respondents (OR 5.8; 95%CI 4.1, 8.2) and other adults in the household (OR 5.1; 95%CI 3.5, 7.5), as well as knowledge about pertussis prevention. Health providers remain crucial for vaccination decision making; however letters may have contributed to an increased uptake of pertussis booster vaccination and knowledge. Health authorities may consider mailing households in future pertussis epidemics as a component of a wider communication strategy.

Mobile phone-based syndromic surveillance system, Papua New Guinea.

The health care system in Papua New Guinea is fragile, and surveillance systems infrequently meet international standards. To strengthen outbreak identification, health authorities piloted a mobile phone-based syndromic surveillance system and used established frameworks to evaluate whether the system was meeting objectives. Stakeholder experience was investigated by using standardized questionnaires and focus groups. Nine sites reported data that included 7 outbreaks and 92 cases of acute watery diarrhea. The new system was more timely (2.4 vs. 84 days), complete (70% vs. 40%), and sensitive (95% vs. 26%) than existing systems. The system was simple, stable, useful, and acceptable; however, feedback and subnational involvement were weak. A simple syndromic surveillance system implemented in a fragile state enabled more timely, complete, and sensitive data reporting for disease risk assessment. Feedback and provincial involvement require improvement. Use of mobile phone technology might improve the timeliness and efficiency of public health surveillance.

Genomics-based timely detection of Dengue Virus type I genotypes I and V in Uruguay.

We report the first whole-genome sequences of Dengue Virus type I genotypes I and V from Uruguay, including the first cases ever reported in the country. Through timely genomic analysis, identification of these genotypes was possible, aiding in timely public health responses and intervention strategies to mitigate the impact of dengue outbreaks.

Vaccine value profile for Chikungunya.

Chikungunya virus (CHIKV) a mosquito-borne alphavirus is the causative agent of Chikungunya (CHIK), a disease with low mortality but high acute and chronic morbidity resulting in a high overall burden of disease. After the acute disease phase, chronic disease including persistent arthralgia is very common, and can cause fatigue and pain that is severe enough to limit normal activities. On average, around 40% of people infected with CHIKV will develop chronic arthritis, which may last for months or years. Recommendations for protection from CHIKV focus on infection control through preventing mosquito proliferation. There is currently no licensed antiviral drug or vaccine against CHIKV. Therefore, one of the most important public health impacts of vaccination would be to decrease burden of disease and economic losses in areas impacted by the virus, and prevent or reduce chronic morbidity associated with CHIK. This benefit would particularly be seen in Low and Middle Income Countries (LMIC) and socio-economically deprived areas, as they are more likely to have more infections and more severe outcomes. This 'Vaccine Value Profile' (VVP) for CHIK is intended to provide a high-level, holistic assessment of the information and data that are currently available to inform the potential public health, economic and societal value of vaccines in the development pipeline and vaccine-like products.This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public private partnerships, and multi-lateral organizations. All contributors have extensive expertise on various elements of the CHIK VVP and collectively aimed to identify current research and knowledge gaps.The VVP was developed using only existing and publicly available information.

Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil.

Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total of 613,000 confirmed cases as of June 2023. In collaboration with the Central Public Health Laboratory in the capital city of Campo Grande, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate the circulation of the Omicron variant in the region. The study aimed to uncover the genomic landscape and provide valuable insights into the prevalence and transmission patterns of this highly transmissible variant. Our findings revealed an increase in the number of cases within the region during 2022, followed by a gradual decline as a result of the successful impact of the vaccination program together with the capacity of this unpredictable and very transmissible variant to quickly affect the proportion of susceptible population. Genomic data indicated multiple introduction events, suggesting that human mobility played a differential role in the variant's dispersion dynamics throughout the state. These findings emphasize the significance of implementing public health interventions to mitigate further spread and highlight the powerful role of genomic monitoring in promptly tracking and uncovering the circulation of viral strains. Together those results underscore the importance of proactive surveillance, rapid genomic sequencing, and data sharing to facilitate timely public health responses.

Increased interregional virus exchange and nucleotide diversity outline the expansion of the chikungunya virus ECSA lineage in Brazil.

The emergence and reemergence of mosquito-borne diseases in Brazil such as Yellow Fever, Zika, Chikungunya, and Dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus (CHIKV) across the country since its first detection in 2014 in Northeast Brazil. Faced with this scenario, on-site training activities in genomic surveillance carried out in partnership with the National Network of Public Health Laboratories have led to the generation of 422 CHIKV genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These new genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersion dynamics of the CHIKV East-Central-South-African (ECSA) lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C>T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving CHIKV ECSA lineage genetic diversity in Brazil.

Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil.

The emergence and reemergence of mosquito-borne diseases in Brazil such as yellow fever, zika, chikungunya, and dengue have had serious impacts on public health. Concerns have been raised due to the rapid dissemination of the chikungunya virus across the country since its first detection in 2014 in Northeast Brazil. In this work, we carried out on-site training activities in genomic surveillance in partnership with the National Network of Public Health Laboratories that have led to the generation of 422 chikungunya virus genomes from 12 Brazilian states over the past two years (2021-2022), a period that has seen more than 312 thousand chikungunya fever cases reported in the country. These genomes increased the amount of available data and allowed a more comprehensive characterization of the dispersal dynamics of the chikungunya virus East-Central-South-African lineage in Brazil. Tree branching patterns revealed the emergence and expansion of two distinct subclades. Phylogeographic analysis indicated that the northeast region has been the leading hub of virus spread towards other regions. Increased frequency of C > T transitions among the new genomes suggested that host restriction factors from the immune system such as ADAR and AID/APOBEC deaminases might be driving the genetic diversity of the chikungunya virus in Brazil.

Dengue Fever Surveillance in Mato Grosso do Sul: Insights from Genomic Analysis and Implications for Public Health Strategies.

Since its discovery in early 1916, dengue fever, a common vector-borne illness in Brazil, has resulted in extensive urban outbreaks and poses a serious threat to the public's health. Understanding the dynamics of Dengue Virus (DENV) serotypes circulating in different regions of Brazil is essential for implementing effective disease control and prevention measures. In response to this urgent need, we conducted an on-site training program in genomic surveillance in collaboration with the Central Laboratory of Health and the Secretary of Health of the Mato Grosso do Sul state. This initiative resulted in the generation of 177 DENV genome sequences collected between May 2021 and May 2022, a period during which over 11,391 dengue fever cases were reported in the state. Through this approach, we were able to identify the co-circulation of two different dengue serotypes (DENV1 and DENV2) as well as the existence of diverse viral lineages within each genotype, suggesting that multiple introduction events of different viral strains occurred in the region. By integrating epidemiological data, our findings unveiled temporal fluctuations in the relative abundance of different serotypes throughout various epidemic seasons, highlighting the complex and changing dynamics of DENV transmission throughout time. These findings demonstrate the value of ongoing surveillance activities in tracking viral transmission patterns, monitoring viral evolution, and informing public health actions.

A Multiplex Nanopore Sequencing Approach for the Detection of Multiple Arboviral Species.

The emergence and continued geographic expansion of arboviruses and the growing number of infected people have highlighted the need to develop and improve multiplex methods for rapid and specific detection of pathogens. Sequencing technologies are promising tools that can help in the laboratory diagnosis of conditions that share common symptoms, such as pathologies caused by emerging arboviruses. In this study, we integrated nanopore sequencing and the advantages of reverse transcription polymerase chain reaction (RT-PCR) to develop a multiplex RT-PCR protocol for the detection of Chikungunya virus (CHIKV) and several orthoflaviviruses (such as dengue (Orthoflavivirus dengue), Zika (Orthoflavivirus zikaense), yellow fever (Orthoflavivirus flavi), and West Nile (Orthoflavivirus nilense) viruses) in a single reaction, which provides data for sequence-based differentiation of arbovirus lineages.