Non-coding RNAs involved in the molecular pathology of Alzheimer's disease: a systematic review.

Alzheimer's disease (AD) is the leading cause of dementia globally, having a pathophysiology that is complex and multifactorial. Recent findings highlight the significant role of non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and piwi-interacting RNAs (piRNAs) in the molecular mechanisms underlying AD. These ncRNAs are involved in critical biological processes such as cell proliferation, apoptosis, oxidative stress, amyloid-beta aggregation, tau phosphorylation, neuroinflammation, and autophagy, which are pivotal in AD development and progression. This systematic review aims to consolidate current scientific knowledge on the role of ncRNAs in AD, making it the first to encompass the four types of ncRNAs associated with the disease. Our comprehensive search and analysis reveal that ncRNAs not only play crucial roles in the pathogenesis of AD but also hold potential as biomarkers for its early detection and as novel therapeutic targets. Specifically, the findings underscore the significance of miRNAs in regulating genes involved in key AD pathways such as activin receptor signaling pathway, actomyosin contractile ring organization, and advanced glycation endproducts-receptor advanced glycation endproducts (AGE-RAGE) signaling pathway. This review also highlights the potential of ncRNAs in unveiling novel diagnostic and therapeutic strategies, emphasizing the need for further research to validate their clinical utility. Our systematic exploration provides a foundation for future bioinformatic analyses and the development of ncRNA-based precision medicine approaches for AD, offering new insights into the disease's molecular pathology and paving the way for innovative treatment strategies. Systematic review registration: PROSPERO, https://www.crd.york.ac.uk/prospero/, CRD42022355307.

Outbreak of influenza and SARS-CoV-2 at the Armed Forces of the Philippines Health Service Education and Training Center, September 25-October 10, 2023.

In the last week of September 2023, a surge of influenza-like illness was observed among students of the Armed Forces of the Philippines (AFP) Health Service Education and Training Center, where 48 (27 males and 21 females; age in years: mean 33, range 27-41) of 247 military students at the Center presented with respiratory symptoms. Between September 25 and October 10, 2023, all 48 symptomatic students were evaluated with real-time reverse transcription polymerase chain reaction and sequencing for both influenza and SARS-CoV-2. Thirteen (27%) students were found positive for influenza A/H3 only, 6 (13%) for SARS-CoV-2 only, and 4 (8%) were co-infected with influenza A/H3 and SARS-CoV-2. Seventeen influenza A/ H3N2 viruses belonged to the same clade, 3C.2a1b.2a.2a.3a, and 4 SARSCoV-2 sequences belonged to the JE1.1 lineage, indicating a common source outbreak for both. The influenza A/H3N2 circulating virus belonged to a different clade than the vaccine strain for 2023 (3C.2a1b.2a.2a). Only 4 students had received the influenza vaccine for 2023. In response, the AFP Surgeon General issued a memorandum to all military health institutions on October 19, 2023 that mandated influenza vaccination as a prerequisite for enrollment of students at all education and training centers, along with implementation of non-pharmaceutical interventions and early notification and testing of students exhibiting influenza-like-illness.

Predicting COVID-19 Cases in South Korea Using Stringency and Niño Sea Surface Temperature Indices.

Most coronavirus disease 2019 (COVID-19) models use a combination of agent-based and equation-based models with only a few incorporating environmental factors in their prediction models. Many studies have shown that human and environmental factors play huge roles in disease transmission and spread, but few have combined the use of both factors, especially for SARS-CoV-2. In this study, both man-made policies (Stringency Index) and environment variables (Niño SST Index) were combined to predict the number of COVID-19 cases in South Korea. The performance indicators showed satisfactory results in modeling COVID-19 cases using the Non-linear Autoregressive Exogenous Model (NARX) as the modeling method, and Stringency Index (SI) and Niño Sea Surface Temperature (SST) as model variables. In this study, we showed that the accuracy of SARS-CoV-2 transmission forecasts may be further improved by incorporating both the Niño SST and SI variables and combining these variables with NARX may outperform other models. Future forecasting work by modelers should consider including climate or environmental variables (i.e., Niño SST) to enhance the prediction of transmission and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Understanding chaos in COVID-19 and its relationship to stringency index: Applications to large-scale and granular level prediction models.

Understanding the underlying and unpredictable dynamics of the COVID-19 pandemic is important. We supplemented the findings of Jones and Strigul (2020) and described the chaotic behavior of COVID-19 using state space plots which depicted the changes in asymptotic behavior and trajectory brought about by the increase or decrease in the number of cases which resulted from the easing or tightening of restrictions and other non-pharmaceutical interventions instituted by governments as represented by the country's stringency index (SI). We used COVID-19 country-wide case count data and analyzed it using convergent cross-mapping (CCM) and found that the SI influence on COVID-19 case counts is high in almost all the countries considered. When we utilized finer granular geographical data ('barangay' or village level COVID-19 case counts in the Philippines), the effects of SI were reduced as the population density increased. The authors believe that the knowledge of the chaotic behavior of COVID-19 and the effects of population density as applied to finer granular geographical data has the potential to generate more accurate COVID-19 non-linear prediction models. This could be used at the local government level to guide strategic and highly targeted COVID-19 policies which are favorable to public health systems but with limited impact to the economy.

Clinical characterization of COVID-19 breakthrough infections, Philippines.

We clinically characterized PCR detected breakthrough infections among partially/fully vaccinated cases with majority given an inactivated vaccine, CoronaVac. From 1 March to 15 July 2021, we detected 182 SARS-CoV-2 infections among vaccinated cases with 129 classified as breakthrough infections. Majority were male, 30-39 y.o., and were asymptomatic or mildly symptomatic with few severe cases. Alpha, Beta and Delta VOCs were detected from sequenced breakthrough infections. Healthcare workers had significantly lower Ct values(higher viral loads) versus non-HCWs. Our results underscore the importance of regular PCR screening for HCWs due to the risk of SARS-CoV-2 transmission from asymptomatic breakthrough infections and provide evidence supporting administration of a booster dose especially to HCWs.

Performance of a Rapid Diagnostic Test for Influenza in a Tertiary Military Hospital, Philippines.

INTRODUCTION: It is important to evaluate the performance of existing rapid influenza diagnostic tests (RIDTs) and the factors that can affect performance especially when the circulation dynamics of influenza strains change such as the displacement and replacement of the circulating seasonal influenza strains. MATERIALS AND METHODS: Nasal swabs were collected from patients presenting at V Luna Medical Center, Armed Forces of the Philippines Health Service Command, with influenza-like illness (ILI) with one swab tested using Quickvue (QV) influenza A+B RIDT (Quidel) and the other swab tested using the ABI 7500 (Applied Biosystems) real-time reverse transcriptase-polymerase chain reaction. Sensitivity, specificity, positive predictive value, and negative predictive value were estimated. We identified clinical symptoms predictive of influenza subtype and evaluated the independence of QV sensitivity on (1) Cycle threshold (Ct) value, controlling for timing of collection; (2) timing of collection, controlling for Ct value; and (3) Ct value and timing of collection taken together. RESULTS: Between August 2011 and October 2016, patients presenting with ILI (n = 2333) underwent testing. Quickvue sensitivity across all subtypes was significantly correlated with lower Ct values (higher virus titers) (P <.001) and, except for flu A/H3 (P = .974), was also significantly associated with timing of specimen collection (P <.05). No statistically significant difference was noted in QV sensitivity for Flu A/H3 (P = .130), pandemic H1/N1 (P = .207), Flu A/H3 + pandemic H1/N1 (P = .341), and Flu B (P = .103) across different age groups but sensitivity of QV significantly differed (P <.001) across the different influenza subtypes. CONCLUSION: Overall specificity of QV was high across all flu subtypes, but overall sensitivity was low (Flu A/pdm H1) to moderate (Flu A/H3 and Flu B). The findings highlight the need to develop more sensitive influenza RDTs to detect circulating influenza strains and the use of the quadrivalent flu vaccine during the annual influenza vaccination.

Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines.

Here, we report the complete genome sequences of 11 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants from the Philippines. Lineage analysis showed 3 B.1.1.7 and 8 B.1.351 sequences. One B.1.1.7 sequence contained two additional mutations, F318N and V320F, with V320F located in the receptor binding domain of the S1 subunit.

A multi-country field validation of the FluChip-8G Insight Assay.

INTRODUCTION: It is critical to rapidly detect novel and non-seasonal influenza strains. Currently available assays have limited sensitivity in detecting novel influenza subtypes. We performed a multi-country field validation of the FluChip-8G Insight, an assay able to detect and characterize influenza A/B viruses and non-seasonal influenza viruses. MATERIALS AND METHODS: We evaluated the performance of the FluChip-8G Insight on nasal and throat swab clinical samples from Thailand, Philippines and Nepal. Influenza PCR positive and negative samples tested using the US CDC Human Influenza Dx Panel reference standard were selected for testing using the FluChip-8G Influenza Insight. RESULTS: A total of 909 specimens were included in the analysis. The overall sensitivity and specificity of the FluChip-8G Insight to detect combined influenza A+B was 86 % and 100%, respectively. PPV and NPV were estimated at 100 % (95 % CI 99-100) and 73 % (95 % CI 68-78), respectively. Sensitivity across all influenza subtypes was 100% for specimens with <20 and 20-25 Ct values, respectively, but as Ct values increased, sensitivity across all influenza subtypes decreased significantly (p < 0.001) for specimens with Ct values ≥32. CONCLUSION: The FluChip-8G Insight showed good precision and reproducibility among all 3 sites with robust identification of both influenza A and B targets with Ct values <32 and in the absence of co-infection. Positioning this platform in countries considered as hotspots for the emergence of novel/zoonotic influenza strains can increase the lead time in detecting and containing novel influenza strains with pandemic potential.

SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines.

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) belonging to the family Coronaviridae and genus Betacoronavirus is the causative agent of COVID-19 disease and was first identified in Wuhan, China. SARS-CoV-2 spread globally with >28 million cases and 911,000 deaths recorded worldwide as of September 12, 2020. The Philippines reported the first case of community transmission on March 5, 2020, and despite the government imposing one of the longest and strictest lockdowns in Southeast Asia, the number of confirmed COVID-19 cases still surged with >250,000 cases and 4,000 deaths reported as of September 12, 2020. It is important to estimate the burden and impact of SARS-CoV-2 on the military population since this can affect the military readiness. MATERIALS AND METHODS: Nasopharyngeal and oropharyngeal swabs were collected and SARS-CoV-2 real-time RT-PCR testing was performed on the samples. Phylogenetic analysis was performed using sequences from 23 SARS-CoV-2-positive specimens from this study and sequences retrieved from GenBank and GISAID databases. RESULTS: From April 14 to August 15, 2020, a total of 12,432 specimens were tested with 763 (6%) unique individuals testing positive for SARS-CoV-2 by rRT-PCR. In the military population, majority of the patients who were tested (80%) and those who tested positive for SARS-CoV-2 (86%) were male. Military and civilian status was available for 7,672 patients with 515/5,042 (10%) positive among military patients and 248/2,630 (9%) positive among civilian patients. Both military and civilian populations had the highest case counts of SARS-CoV-2-positive cases in the 21- to 30- and 31- to 40-year-old age groups, while the 71- to 80-year-old age group had the highest proportion (18%) of SARS-CoV-2-positive cases. Sequencing analysis showed 19 different variants in the 23 genomes. Twenty of the 23 genomes were classified under clade GR/B1.1, 2 genomes were classified under clade GR/B1.1.28, and 1 genome was classified under Clade O/B.6. Twenty-two of the 23 sequences collected after June 25, 2020, contained the D614G mutation. CONCLUSION: We describe here the results of SARS-CoV-2 testing for military and civilian patients and personnel. The 21- to 30- and 31- to 40-year-old age groups had the highest case counts of SARS-CoV-2-positive cases. Sequencing results showed the presence of the D614G mutation in the spike protein in a majority of specimens collected from the end of June to July 2020.

Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines.

Here, we report the coding-complete genome sequences of 23 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) samples from the Philippines. Sequences were obtained from nasopharyngeal and oropharyngeal swabs from coronavirus disease 2019 (COVID-19)-positive patients. Mutation analysis showed the presence of the D614G mutation in the spike protein in 22 of 23 genomes.

First report of the mcr-1 colistin resistance gene identified in two Escherichia coli isolates from clinical samples, Philippines, 2018.

OBJECTIVES: The first report of a plasmid-borne colistin resistance gene (mcr-1) detected in an Escherichia coli isolate from China heralded the emergence of pandrug-resistant bacteria. Since then, the mcr-1 gene has been detected worldwide, but to date it has not been reported in the Philippines. METHODS: In this study, 123 antimicrobial-resistant isolates collected from January-June 2018 from patients admitted to a tertiary hospital in Manila, Philippines, were characterised. Biochemical identification and antimicrobial susceptibility testing were performed using a BD Phoenix™ M50 system with NMIC/ID-95 panel. Conventional PCR was performed to detect the genes mcr-1 to mcr-5, and short- and long-read whole-genome sequencing was performed. RESULTS: Two mcr-1-positive E. coli clinical isolates from separate patients harboured mcr-1 on an IncI2 plasmid. One isolate was shown to carry 12 antimicrobial resistance genes (ARGs) in addition to mcr-1, including the extended-spectrum ß-lactamase blaCTX-M-55, whilst the other E. coli isolate carried 6 ARGs in addition to mcr-1. CONCLUSION: Both patients had no prior colistin treatment recorded in their medical history and no travel history outside of the country within the past 6 months from the date of hospital admission, indicating local transmission and acquisition of the colistin-resistant strain from either community or hospital settings within the Philippines. This report should serve as a signal to local public-health officials of the need to intensify surveillance efforts and to increase vigilance and implementation of antimicrobial stewardship programmes to contain and slow the spread of antimicrobial resistance.

Multidrug Resistant Mycobacterium tuberculosis Among Military and Civilian Personnel seen at a Tertiary Military Hospital, Manila, Philippines (2015-2018).

INTRODUCTION: About one third of the world population is estimated to be infected with Mycobacterium tuberculosis (MTB), and this proportion is expected to be higher in countries with a high tuberculosis (TB) burden. The Philippines is both a high tuberculosis burden and a high multidrug resistant tuberculosis (MDR-TB) burden country. Though TB has been extensively described in the civilian population, there is limited data on TB in the military population. The objectives are: (1) To determine MTB/MDR-TB prevalence among military and civilian patients in the Philippines presenting with clinically suspected TB in a tertiary military hospital and (2) To determine performance of direct sputum smear microscopy (DSSM) using Ziehl-Neelsen (ZN) staining compared to Xpert MTB/RIF real-time reverse transcriptase polymerase chain reaction. MATERIALS AND METHODS: Sputum samples were obtained from patients, clinically suspected with TB, and/or with TB associated signs/symptoms. Sputum specimens were tested using DSSM with ZN staining and Xpert MTB/RIF assay (Cepheid, Sunnyvale, California) and patient demographic and clinical data were collected. RESULTS: From March 2015 to December 2018, a total of 795 (173 military personnel [164 active duty and 9 retired]; 618 civilians; and 4 with no data on military/civilian status) patients with TB associated symptoms or clinically suspected with TB were tested. Overall, MTB prevalence was 81/795 (10%). MTB prevalence among active duty and retired military personnel were 27/164 (16%) and 4/9 (44%), respectively while MTB prevalence for civilian patients was 50/618 (8%) (p value = 0.0003; OR = 2.48 [95% C.I. 1.5-4]). Among active and retired military personnel who tested positive for MTB, rifampin resistance was 4/27 (15%) and 1/4 (25%), respectively, while rifampin resistance for civilian patients was 9/50 (18%) (p value = 1; OR = 0.88 [95% C.I. 0.26-2.90]). For active duty military personnel, average MTB prevalence (based on Xpert MTB/RIF) covering years 2015-2018 was 21% and ranged from 13% to 35%, while average rifampin resistance among MTB positive active duty military personnel was 15% and ranged from 0% to 25%. Overall sensitivity and specificity of DSSM compared to Xpert MTB/RIF were 70% and 96%, respectively. Positive and negative predictive values of DSSM to accurately categorize MTB in symptomatic cases (with Xpert MTB/RIF as "true positive" reference) were 74% and 95%, respectively. Performance of DSSM varied according to MTB load detected by Xpert MTB/RIF with increasing DSSM sensitivity observed as the MTB load detected by Xpert MTB/RIF increased (p = 0.02). CONCLUSION: This report describes high MTB and MDR-TB prevalence rates among symptomatic military patients with military personnel having higher odds of MTB infection compared to the civilian patients in the study. Since DSSM (ZN) sensitivity greatly varied depending on MTB load, the Xpert MTB/RIF should be used as a first-line diagnostic tool to identify MTB and detect rifampin resistance among presumptive TB cases instead of DSSM (ZN) microscopy.

Comparison of Carbapenem-Resistant Microbial Pathogens in Combat and Non-combat Wounds of Military and Civilian Patients Seen at a Tertiary Military Hospital, Philippines (2013-2017).

INTRODUCTION: Bacterial wound infections are a danger to both military and civilian populations. The nature of injury and infection associated with combat related wounds are important in guiding antibiotic prophylaxis and empiric treatment guidelines. MATERIALS AND METHODS: The isolates were screened for drug-resistance by the MicroScan Walkaway Plus System using either the Negative Breakpoint Combo Panel (NBCP) 30 or 34 or Positive Breakpoint Combo Panel (PBPC) 20 or 23. Isolates with a minimum inhibitory concentration (MIC) of ≥8 µg/mL to imipenem and/or meropenem were tested for both carbapenemase production using the CarbaNP test and real-time PCR to determine molecular resistance mechanisms. Plasmid conjugation analysis was performed to define potential for horizontal gene transfer. RESULTS: We characterized 634 bacterial wound isolates collected from September 2013 to December 2017 from patients seen at a Philippine military tertiary hospital presenting with combat or non-combat injuries [354 (military) and 280 (civilians)]. Staphylococcus aureus was the most predominant bacterial species isolated from wounds in both populations (104/634, 16%). A variety of Gram-negative bacterial species comprised 442/634 (70%) of the isolates identified, with the most prevalent shown to be Pseudomonas aeruginosa, Enterobacter cloacae, Klebsiella pneumoniae, Escherichia coli, and Acinetobacter sp. Carbapenemase production was detected in 34/442 (8%) Gram-negative isolates. Testing for molecular resistance mechanisms showed 32/34 (17 military, 15 civilian) wound isolates were blaNDM positive and 2 were blaVIM positive, with the two blaVIM isolates found in the civilian population. Plasmid conjugation of 14 blaNDM and 2 blaVIM positive wound isolates representatives showed 2/16 (13%) produced E. coli J53 transconjugants (E. coli from a civilian; E. cloacae from a military). CONCLUSION: We describe in this study the wound bacterial and antibiotic resistance profile in the military (combat vs non-combat associated) and civilian population. We observed that, with the exception of Acinetobacter sp., resistance of prevalent Gram-negative bacterial species to imipenem or meropenem were not significantly different between the military and civilian populations. We also presented data on the prevalent bacterial species isolated from both combat and non-combat wounds in a military tertiary care hospital setting as well as the carbapenemase-encoding gene primarily responsible for carbapenem resistance as well as evidence of horizontal transfer via mobile genetic elements. Clinicians may use this information to guide empiric antibiotic coverage for the predominant organisms if wound culture results are not readily available.A prospective, longitudinal evaluation of the wound bacterial profile documenting the changing bacterial flora using higher resolution molecular strategies can provide a more comprehensive understanding of the diversity, composition, and abundance of bacterial composition of the wound microbial community from the time of injury, during the course of evacuation from the field to higher level of care facilities, and up to wound resolution.

Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010-2013.

BACKGROUND: Emerging and re-emerging respiratory pathogens represent an increasing threat to public health. Etiological determination during outbreaks generally relies on clinical information, occasionally accompanied by traditional laboratory molecular or serological testing. Often, this limited testing leads to inconclusive findings. The Armed Forces Research Institute of Medical Sciences (AFRIMS) collected 12,865 nasopharyngeal specimens from acute influenza-like illness (ILI) patients in five countries in South/South East Asia during 2010-2013. Three hundred and twenty-four samples which were found to be negative for influenza virus after screening with real-time RT-PCR and cell-based culture techniques demonstrated the potential for viral infection with evident cytopathic effect (CPE) in several cell lines. OBJECTIVE: To assess whether whole genome next-generation sequencing (WG-NGS) together with conventional molecular assays can be used to reveal the etiology of influenza negative, but CPE positive specimens. STUDY DESIGN: The supernatant of these CPE positive cell cultures were grouped in 32 pools containing 2-26 supernatants per pool. Three WG-NGS runs were performed on these supernatant pools. Sequence reads were used to identify positive pools containing viral pathogens. Individual samples in the positive pools were confirmed by qRT-PCR, RT-PCR, PCR and Sanger sequencing from the CPE culture and original clinical specimens. RESULTS: WG-NGS was an effective way to expand pathogen identification in surveillance studies. This enabled the identification of a viral agent in 71.3% (231/324) of unidentified surveillance samples, including common respiratory pathogens (100/324; 30.9%): enterovirus (16/100; 16.0%), coxsackievirus (31/100; 31.0%), echovirus (22/100; 22.0%), human rhinovirus (3/100; 3%), enterovirus genus (2/100; 2.0%), influenza A (9/100; 9.0%), influenza B, (5/100; 5.0%), human parainfluenza (4/100; 4.0%), human adenovirus (3/100; 3.0%), human coronavirus (1/100; 1.0%), human metapneumovirus (2/100; 2.0%), and mumps virus (2/100; 2.0%), in addition to the non-respiratory pathogen herpes simplex virus type 1 (HSV-1) (172/324; 53.1%) and HSV-1 co-infection with respiratory viruses (41/324; 12.7%).

Carbapenemase-Producing Enterobacteriaceae and Nonfermentative Bacteria, the Philippines, 2013-2016.

During 2013-2016, we isolated blaNDM- and blaVIM-harboring Enterobacteriaceae and nonfermentative bacteria from patients in the Philippines. Of 130 carbapenem-resistant isolates tested, 45 were Carba NP-positive; 43 harbored blaNDM, and 2 harbored blaVIM. Multidrug-resistant microbial pathogen surveillance and antimicrobial drug stewardship are needed to prevent further spread of New Delhi metallo-ß-lactamase variants.

Detection of Diarrhea Etiology Among U.S. Military Personnel During Exercise Balikatan 2014, Philippines, Using TaqMan Array Cards.

BACKGROUND: Military personnel are vulnerable to diarrhea. Diarrheal disease is common when deployed for operations or exercise in developing countries. Although diarrheal disease is transient, cumulative time lost and medical asset can have a significant impact on military operations. Currently, diagnostics of diarrheal etiology typically relies on a mixture of conventional bacteriology, enzyme-linked immunosorbent assay, and polymerase chain reaction (PCR)-based methods including real-time PCR. These methods, however, can be time and labor intensive, although the identification of diarrheal etiology needs to be informative and rapid for treatment and prevention. Real-time PCR has been increasingly used to identify pathogens. Real-time PCR panels of common diarrheal pathogens have been developed, but several diarrheal pathogens are not included in the panel. An expanded and customizable panel to detect diarrhea etiology has been developed employing TaqMan Array Card (TAC) technology. TAC performs 384 real-time PCR reactions simultaneously. As currently configured for diarrheal disease by the University of Virginia, a maximum of 8 samples can be tested simultaneously with approximately 48 target pathogens per sample including bacteria, fungi, helminths, protozoan parasites, and viruses. TAC diarrheal disease panels have been successfully applied to detect pathogens in acute diarrheal stool samples from young children in several international multicenter diarrhea studies. METHODS: In this study, TAC was applied to stool samples collected under an approved human use protocol from military personnel with acute diarrhea participating in the annual joint military exercise, Balikatan, between the Republic of the Philippines and the United States in 2014. Several established pathogen-specific real-time PCR detection assays were also performed in parallel for comparative purposes. FINDINGS: TAC was applied to 7 stool samples. Campylobacter spp. was the most common diarrheal disease pathogen detected. Results from TAC matched 5 out of 6 pathogen specific real-time PCR assays. TAC required a total of 5-6 hours to complete all the procedures from nucleic acid extraction and data analysis, whereas a minimum of 18 hours and 4 hours are required for conventional bacteriology and enzyme-linked immunosorbent assay, respectively, per pathogen. DISCUSSION: With TAC, pathogen load can be estimated from the amount of nucleic acid present for each pathogen, which can be analyzed further to better determine pathogen attribution and to compare pathogen load between case and control samples. Unfortunately, such correlative analysis was not possible because of the limited sample size available in this study. A larger sample size is needed for further evaluation of TAC on a specific population set, including military personnel. Regardless, TAC was found to be a useful and functional diagnostic platform that is less time-consuming, easy to use with high reproducibility, and costs less per sample compared to the current typically employed methods. The successful application of TAC in acute diarrhea stool samples from a US military population in the Philippines demonstrates its versatility as a potential candidate for a next-generation diagnostics platform.

Incidence of Dengue Virus Infection in Adults and Children in a Prospective Longitudinal Cohort in the Philippines.

BACKGROUND: The mean age of dengue has been increasing in some but not all countries. We sought to determine the incidence of dengue virus (DENV) infection in adults and children in a prospective cohort study in the Philippines where dengue is hyperendemic. METHODOLOGY/PRINCIPAL FINDINGS: A prospective cohort of subjects ≥6 months old in Cebu City, Philippines, underwent active community-based surveillance for acute febrile illnesses by weekly contact. Fever history within the prior seven days was evaluated with an acute illness visit followed by 2, 5, and 8-day, and 3-week convalescent visits. Blood was collected at the acute and 3-week visits. Scheduled visits took place at enrolment and 12 months that included blood collections. Acute samples were tested by DENV PCR and acute/convalescent samples by DENV IgM/IgG ELISA to identify symptomatic infections. Enrolment and 12-month samples were tested by DENV hemagglutination inhibition (HAI) assay to identify subclinical infections. Of 1,008 enrolled subjects, 854 completed all study activities at 12 months per-protocol undergoing 868 person-years of surveillance. The incidence of symptomatic and subclinical infections was 1.62 and 7.03 per 100 person-years, respectively. However, in subjects >15 years old, only one symptomatic infection occurred whereas 27 subclinical infections were identified. DENV HAI seroprevalence increased sharply with age with baseline multitypic HAIs associated with fewer symptomatic infections. Using a catalytic model, the historical infection rate among dengue naïve individuals was estimated to be high at 11-22%/year. CONCLUSIONS/SIGNIFICANCE: In this hyperendemic area with high seroprevalence of multitypic DENV HAIs in adults, symptomatic dengue rarely occurred in individuals older than 15 years. Our findings demonstrate that dengue is primarily a pediatric disease in areas with high force of infection. However, the average age of dengue could increase if force of infection decreases over time, as is occurring in some hyperendemic countries such as Thailand.

Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission.

Proper understanding of the long-term epidemiology of chikungunya has been hampered by poor surveillance. Outbreak years are unpredictable and cases often misdiagnosed. Here we analyzed age-specific data from 2 serological studies (from 1973 and 2012) in Cebu, Philippines, to reconstruct both the annual probability of infection and population-level immunity over a 60-year period (1952-2012). We also explored whether seroconversions during 2012-2013 were spatially clustered. Our models identified 4 discrete outbreaks separated by an average delay of 17 years. On average, 23% (95% confidence interval [CI], 16%-37%) of the susceptible population was infected per outbreak, with >50% of the entire population remaining susceptible at any point. Participants who seroconverted during 2012-2013 were clustered at distances of <230 m, suggesting focal transmission. Large-scale outbreaks of chikungunya did not result in sustained multiyear transmission. Nevertheless, we estimate that >350 000 infections were missed by surveillance systems. Serological studies could supplement surveillance to provide important insights on pathogen circulation.

Region-wide synchrony and traveling waves of dengue across eight countries in Southeast Asia.

Dengue is a mosquito-transmitted virus infection that causes epidemics of febrile illness and hemorrhagic fever across the tropics and subtropics worldwide. Annual epidemics are commonly observed, but there is substantial spatiotemporal heterogeneity in intensity. A better understanding of this heterogeneity in dengue transmission could lead to improved epidemic prediction and disease control. Time series decomposition methods enable the isolation and study of temporal epidemic dynamics with a specific periodicity (e.g., annual cycles related to climatic drivers and multiannual cycles caused by dynamics in population immunity). We collected and analyzed up to 18 y of monthly dengue surveillance reports on a total of 3.5 million reported dengue cases from 273 provinces in eight countries in Southeast Asia, covering ∼ 10(7) km(2). We detected strong patterns of synchronous dengue transmission across the entire region, most markedly during a period of high incidence in 1997-1998, which was followed by a period of extremely low incidence in 2001-2002. This synchrony in dengue incidence coincided with elevated temperatures throughout the region in 1997-1998 and the strongest El Niño episode of the century. Multiannual dengue cycles (2-5 y) were highly coherent with the Oceanic Niño Index, and synchrony of these cycles increased with temperature. We also detected localized traveling waves of multiannual dengue epidemic cycles in Thailand, Laos, and the Philippines that were dependent on temperature. This study reveals forcing mechanisms that drive synchronization of dengue epidemics on a continental scale across Southeast Asia.