Pf7: an open dataset of genome variation in 20,000 worldwide samples.

We describe the MalariaGEN Pf7 data resource, the seventh release of genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.

Assessing the spatiotemporal malaria transmission intensity with heterogeneous risk factors: A modeling study in Cambodia.

Malaria control can significantly benefit from a holistic and precise way of quantitatively measuring the transmission intensity, which needs to incorporate spatiotemporally varying risk factors. In this study, we conduct a systematic investigation to characterize malaria transmission intensity by taking a spatiotemporal network perspective, where nodes capture the local transmission intensities resulting from dominant vector species, the population density, and land cover, and edges describe the cross-region human mobility patterns. The inferred network enables us to accurately assess the transmission intensity over time and space from available empirical observations.

Assessment of Vitamin D status and association with inflammation: Biomarkers Reflecting Inflammation and Nutritional Determinants of Anemia (BRINDA) project.

Background: It is unclear whether 25(OH)D concentrations in children and female adults may be influenced by inflammation and thus require adjustment when estimating the population prevalence of vitamin D deficiency.

Objectives: We examined correlations between inflammation biomarkers, CRP or alpha-1-acid glycoprotein (AGP), and serum 25(OH)D concentrations among preschool children (PSC; 6-59 mo) and nonpregnant females of reproductive age (FRA; 15-49 y).

Methods: We analyzed cross-sectional data from 6 nationally representative nutrition surveys (Afghanistan, Cambodia, Pakistan, UK, USA, and Vietnam) conducted among PSC (n = 9880) and FRA (n = 14,749) from the Biomarkers Reflecting Inflammation and Nutritional Determinants of Anemia project.

Melioidosis in Cynomolgus Macaques ( ) Imported to the United States from Cambodia.

Melioidosis, a potentially fatal infectious disease of humans and animals, including nonhuman primates (NHPs), is caused by the high-consequence pathogen This environmental bacterium is found in the soil and water of tropical regions, such as Southeast Asia, where melioidosis is endemic. The global movement of humans and animals can introduce into nonendemic regions of the United States, where environmental conditions could allow establishment of the organism. Approximately 60% of NHPs imported into the United States originate in countries considered endemic for melioidosis.

Genomic epidemiology of SARS-CoV-2 in Cambodia, January 2020 to February 2021.

The first case of coronavirus disease 2019 (COVID-19) in Cambodia was confirmed on 27 January 2020 in a traveller from Wuhan. Cambodia subsequently implemented strict travel restrictions, and although intermittent cases were reported during the first year of the COVID-19 pandemic, no apparent widespread community transmission was detected. Investigating the routes of severe acute respiratory coronavirus 2 (SARS-CoV-2) introduction into the country was critical for evaluating the implementation of public health interventions and assessing the effectiveness of social control measures.

Benefits and challenges of consolidating public health functions into a National Public Health Institute: a policy analysis.

National Public Health Institutes (NPHIs) around the world vary in composition. Consolidated organizational models can bring together critical functions such as disease surveillance, emergency preparedness and response, public health research, workforce development and laboratory diagnosis within a single focal point. This can lead to enhanced coordination and management of resources and enable more efficient and effective public health operations.

Public health emergency operations center operations and coordination among Thailand, Cambodia, Lao PDR, and Malaysia during the COVID-19 pandemic.

Public Health Emergency Operations Centers (PHEOCs) are the critical units to lead communications, information sharing, and resource mobilisation during national and international health emergencies, and are key components for maintaining global health security. This assessment sought to examine the coordination mechanisms between national and sub-national PHEOCs in Thailand, Cambodia, Lao People's Democratic Republic, and Malaysia (TCLM countries) during the COVID-19 pandemic. Information was collected on PHEOC structures, functions, and cross-border communications in three stages: a literature review of national PHEOC and emergency preparedness capacities; questionnaire responses from stakeholders to describe PHEOC activity at the national level; and meetings with emergency response staff in five border provinces of Thailand to assess communications between sub-national PHEOCs across country borders.

Assembling a global database of child pneumonia studies to inform WHO pneumonia management algorithm: Methodology and applications.

Background: The existing World Health Organization (WHO) pneumonia case management guidelines rely on clinical symptoms and signs for identifying, classifying, and treating pneumonia in children up to 5 years old. We aimed to collate an individual patient-level data set from large, high-quality pre-existing studies on pneumonia in children to identify a set of signs and symptoms with greater validity in the diagnosis, prognosis, and possible treatment of childhood pneumonia for the improvement of current pneumonia case management guidelines.

Methods: Using data from a published systematic review and expert knowledge, we identified studies meeting our eligibility criteria and invited investigators to share individual-level patient data.

Molecular surveillance of artemisinin resistance-related Pfk13 and pfcrt polymorphisms in imported Plasmodium falciparum isolates reported in eastern China from 2015 to 2019.

Background: Artemisinin-based combination therapy (ACT) has been recommended as the first-line treatment by the World Health Organization to treat uncomplicated Plasmodium falciparum malaria. However, the emergence and spread of P. falciparum resistant to artemisinins and their partner drugs is a significant risk for the global effort to reduce disease burden facing the world.

Improving community coverage of Japanese encephalitis vaccination: lessons learned from a mass campaign in Battambang Province, Cambodia.

A mass Japanese encephalitis (JE) immunization campaign for children aged 9 months through 12 years was conducted in 2013 in Battambang province, western Cambodia. Vaccinators working at almost 2,000 immunization posts in approximately 800 villages provided vaccinations to almost 310,000 children using one dose of Chengdu Institute of Biological Products' live, attenuated SA14-14-2 JE vaccine (CD-JEV), achieving a coverage rate of greater than 90%. Lessons learned, in general for mass vaccination campaigns and specifically for vaccination with CD-JEV, are described.

Proactive community case management decreased malaria prevalence in rural Madagascar: results from a cluster randomized trial.

Background: Malaria remains a leading cause of morbidity and mortality worldwide, with progress in malaria control stalling in recent years. Proactive community case management (pro-CCM) has been shown to increase access to diagnosis and treatment and reduce malaria burden. However, lack of experimental evidence may hinder the wider adoption of this intervention.

Emergence of a multidrug-resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13: an international whole-genome sequencing study.

Background: Serotype 24F is one of the emerging pneumococcal serotypes after the introduction of pneumococcal conjugate vaccine (PCV). We aimed to identify lineages driving the increase of serotype 24F in France and place these findings into a global context.

Methods: Whole-genome sequencing was performed on a collection of serotype 24F pneumococci from asymptomatic colonisation (n=229) and invasive disease (n=190) isolates among individuals younger than 18 years in France, from 2003 to 2018.

Entomological Investigation and Detection of Dengue Virus Type 1 in (Skuse) During the 2018-2020 Outbreak in Zhejiang Province, China.

Mosquito-borne diseases are still threats to public health in the Zhejiang province of China. Surveillance of mosquitoes and the mosquito-borne pathogen is a vital approach for early warning, prevention, and control of the infectious disease. In this study, from 2018 to 2020, a total of 141607 female mosquitoes were caught by means of the light trap method.

Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13.

(the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns.

An evaluation of adverse events following an immunization campaign with the live, attenuated SA14-14-2 Japanese encephalitis vaccine in Cambodia.

Introduction: Japanese encephalitis (JE) virus is the most common cause of vaccine-preventable encephalitis in Asia. The SA14-14-2 JE vaccine manufactured by Chengdu Institute of Biological Products has been shown to be safe and effective in clinical trials and childhood routine immunization programs. However, there are few published reports describing results of surveillance for adverse events following immunization (AEFI) when the vaccine is used in mass campaigns.

Molecular Characterization and Phylogenetic Analysis of the 2019 Dengue Outbreak in Wenzhou, China.

In 2019, a dengue outbreak occurred with 290 confirmed cases in Wenzhou, a coastal city in southeast China. To identify the origin of the dengue virus (DENV) from this outbreak, viral RNA was extracted from four serum samples and sequenced for whole genome analysis. Then, phylogenetic analysis, gene mutation, secondary structure prediction, selection pressure analysis, and recombination analysis were performed.

Adverse Childhood Experiences and Intimate Partner Violence Among Youth in Cambodia: A Latent Class Analysis.

Adverse childhood experiences (ACEs) are a global public health problem, including in low- and middle-income country settings, and are associated with increased risk of intimate partner violence (IPV) during young adulthood. However, current measurement of ACEs may underestimate sequelae of different combinations, or classes, of ACEs and mask class-specific associations with adult exposure to IPV. We used data among ever-partnered young women and men aged 18-24 years from the Cambodia Violence Against Children Survey ( = 369; = 298).

Exercising the Sanger Sequencing Strategy for Variants Screening and Full-Length Genome of SARS-CoV-2 Virus during Alpha, Delta, and Omicron Outbreaks in Hiroshima.

This study aimed to exercise the Sanger sequencing strategy for screening of variants among confirmed COVID-19 cases and validate our strategy against NGS strains in Hiroshima retrieved from GISAID. A total of 660 samples from confirmed COVID-19 cases underwent screening for variants by Sanger-based partial sequencing to the targeted spike gene (nt22,735~nt23,532) using an in-house-developed primer set. The identification of variants was done by unique checkpoints of base nucleotide changes in the targeted spike gene.