Sex: Male
Education:
- Diploma in Tropical Medicine and Hygiene, Liverpool School of Tropical Medicine, 2015
- Master of Science in Clinical Trials, University of London
- Post Graduate Diploma in Clinical Trials, University of London
- Master of Science in Public Health, University of the Philippines
- Doctor of Medicine, University of the Philippines
- Bachelor of Science in Biology, University of the Philippines
Field of Specialization:
Emerging Infectious Diseases
Influenza
Virus
Incidence
Epidemiologic Studies
Medical & Health Education
Researches:
Article title: Coding-Complete Genome Sequences of 11 SARS-CoV-2 B.1.1.7 and B.1.351 Variants from Metro Manila, Philippines
Authors: John Mark Velasco, Piyawan Chinnawirotpisan, Maria Theresa Valderama, Khajohn Joonlasak, Wudtichai Manasatienkij, Angkana Huang, Paula Corazon Diones, , Fatima Claire Navarro, Vicente Vila II, Henry Tabinas Jr., Domingo Chua Jr., Stefan Fernandez, Anthony Jones, Chonticha Klungthong
Publication title: Microbiology Resource Announcements 10(28), July 2021
Abstract:
Here, we report the complete genome sequences of 11 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.
Full text available upon request to the author
Article title: A multi-country field validation of the FluChip-8G Insight Assay
Authors: John Mark Velasco, Sanjaya Shrestha, Maria Theresa Valderama, Jasmin Shrestha, Binob Shrestha, Paula Corazon Diones Susie Leonardia, Yongyuth Poolpanichupatam, Kittinun Hussem, Domingo Chua Jr., Fatima Claire Navarro, Maribel Develos, Louis Macareo, Damon Ellison, Stefan Fernandez, Chonticha Klungthong
Publication title: Journal of Virological Methods 289:114029, March 2021
Abstract:
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.
Full text available upon request to the author
Article title: Performance of a Rapid Diagnostic Test for Influenza in a Tertiary Military Hospital, Philippines
Authors: John Mark Velasco, MD, MPH, MSc, DTM&H, Maria Theresa Valderama, RMT, MPH, Paula Corazon Diones, MD, MOH, COL Fatima Claire Navarro, MC, GSC, CPT Maribel Develos, MC, (Inact), COL Ma. Nila Lopez, MC, (GSC) (Ret.), LTC Cynthia Liao, MC, LTC Domingo Chua, Jr., MC, COL Louis Macareo, MC, USA (Ret.), LTC Stefan Fernandez, MS, USA
Publication title: Military Medicine 187(3), January 2021
Abstract:
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.
Full text link https://tinyurl.com/mtvd6dck
Article title: SARS-CoV-2 Among Military and Civilian Patients, Metro Manila, Philippines
Authors: John Mark Velasco, MD, MPH, MSc, DTM&H, COL Fatima Claire Navarro, MC, GSC, Paula Corazon Diones, MD, MOH, MAJ Vicente Villa, II, MC; Maria Theresa Valderama, RMT, MPH, MAJ Henry Tabinas, Jr., MD, LTC Domingo Chua, Jr., MC, LTC Romulo Dela Rosa, MC, Ma. Melissa Monica Turao-Agoncillo, MD, FPCP, DPSMID, CPT John Carlo Timbol, MC, Susie Leonardia, RMT, Maria Leanor Timbol, RMT, Chonticha Klungthong, PhD, Piyawan Chinnawirotpisan, PhD, Khajohn Joonlasak, Wudtichai Manasatienkij, PhD, Angkana Huang, MAJ Anthony Jones, PhD, LTC Stefan Fernandez, PhD
Publication title: Military Medicine 186(8), November 2020
Abstract:
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.
Full text link https://tinyurl.com/5y53xjex
Article title: Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines
Authors: John Mark Velasco, Piyawan Chinnawirotpisan, Khajohn Joonlasak, Wudtichai Manasatienkij, Angkana Huang, Maria Theresa Valderama, Paula Corazon Diones, , Susie Leonardia, Maria Leanor Timbol, Fatima Claire Navarro, Vicente Villa II, Henry Tabinas Jr., Domingo Chua Jr., Stefan Fernandez, Anthony Jones, Chonticha Klungthong
Publication title: Microbiology Resource Announcements 9(43), October 2020
Abstract:
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.
Full text link https://tinyurl.com/4uwyjp29
Article title: Multidrug Resistant Mycobacterium tuberculosis Among Military and Civilian Personnel seen at a Tertiary Military Hospital, Manila, Philippines (2015–2018)
Authors: John Mark Velasco, MD, MPH, MSc, DTM&H, Noel Gaurano, MC, GSC, Maria Theresa Valderama, RMT, MPH, Kathyleen Nogrado, MSPH, Paula Corazon Diones, MD, MOH, Ma Nila Lopez, COL, MC (GSC) (Ret.), Cynthia Liao, LTC, MC, Domingo Chua, LTC, MC, Maribel Develos, CPT, MC (Inact), Stefan Fernandez, LTC, MS, USA, Louis Macareo, COL, MC, USA, Brett Swierczewski, LTC, MS, USA
Publication title: Military Medicine 185(8), January 2020
Abstract:
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.
Full text available upon request to the author
Article title: First Report of Colistin Resistance Gene mcr-1 identified in two Escherichia coli from Clinical Samples, Philippines, 2018
Authors: John Mark S. Velasco, Ma. Theresa G. Valderama, Katie R. Margulieux, Paula Corazon S. Diones, Angeli Mae B .Reyes, Susie G. Leonardia, Cynthia P. Liao, Domingo A. Chua, Jr, Fatima Claire S. Navarro, Sirigade Ruekit, Stefan Fernandez, Louis R. Macareo, John M. Crawford, Brett E. Swierczewski
Publication title: Journal of Global Antimicrobial Resistance 21:291-293, June 2020
Abstract:
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 β-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.
Full text available upon request to the author
Article title: 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)
Authors: John Mark Velasco, Ma Theresa Valderama, Katie Margulieux, Paula Corazon Diones, Trent Peacock, MS USAR, Fatima Claire Navarro, MC GSC, Cynthia Liao, MC, Domingo Chua, Jr. MC, Louis Macareo, MC USA, John Crawford, VC USA, Brett Swierczewski, MS USA
Publication title: Military Medicine 185(8), June 2019
Abstract:
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.
Full text available upon request to the author
Article title: Carbapenemase-Producing Enterobacteriaceae and Nonfermentative Bacteria, the Philippines, 2013–2016
Authors: John Mark Velasco, Maria Theresa Valderama, Trent Peacock, Nirdnoy Warawadee, Kathyleen Nogrado, Fatima Claire Navarro, Domingo Chua, Jr., Srijan Apichai, Ruekit Sirigade, Louis R. Macareo, Brett Swierczewski
Publication title: Emerging Infectious Diseases 23(9), September 2017
Abstract:
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-β-lactamase variants.
Full text link https://tinyurl.com/mt3dae2e
Article title: 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 2010-13
Authors: Wiriya Rutvisuttinunt, Chonticha Klungthonga, Butsaya Thaisomboonsuka,Piyawan Chinnawirotpisan, Chuanpis Ajariyakhajorn, Wudtichai Manasatienkij,Thipwipha Phonpakobsin, Chanthap Lon, David Saunders, Sonam Wangchuk,Sanjaya K. Shrestha, John Mark S. Velasco, Maria Theresa P. Alera, Sriluck Simasathien,Darunee Buddhari, Richard G. Jarman, Louis R Macareo, In-Kyu Yoon, Stefan Fernandez
Publication title: Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 94(Suppl. 1), July 2017
Abstract:
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 but 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 to 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 ways 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%).
Full text link https://tinyurl.com/5d82hrda
Article title: Detection of Diarrhea Etiology Among U.S. Military Personnel During Exercise Balikatan 2014, Philippines, Using TaqMan Array Cards
Authors: Paphavee Lertsethtakarn, PhD, Kaewkanya Nakjarung, MS, Sasikorn Silapong, BS, Pimmnapar Neesanant, PhD Pimmada Sakpaisal, MS Ladaporn Bodhidatta, MD Jie Liu, PhD, Eric Houpt, MD, John Mark Velasco, MD, COL Louis R. Macareo, MC USA, MAJ Brett E. Swierczewski, MS USA, COL Carl J. Mason, MC USA (Ret.)
Publication title: Military Medicine 181(11):e1669-e1674, November 2016
Abstract:
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.
Full text link https://tinyurl.com/4y7dvsc5
Article title: Resolution of a Chikungunya Outbreak in a Prospective Cohort, Cebu, Philippines, 2012–2014
Authors: Anon Srikiatkhachorn, Maria Theresa Alera, Catherine B. Lago, Ilya A. Tac-An, Daisy Villa, Stefan Fernandez, Butsaya Thaisomboonsuk, Chonticha Klungthong, Jens W. Levy, John Mark Velasco, Vito G. Roque, Jr., Ananda Nisalak, Louis R. Macareo, In-Kyu Yoon
Publication title: Emerging Infectious Diseases 22(10), October 2016
Abstract:
Chikungunya is a reemerging, mosquitoborne infectious disease caused by chikungunya virus (CHIKV). Its classic manifestations include fever and joint inflammation, which can develop into chronic joint disease. Infections in immunocompromised persons can lead to severe organ involvement and death. Chikungunya outbreaks appear to occur in 2 patterns: 1) spatially and temporally restricted outbreaks in endemic areas (1,2); and 2) large epidemics that occur periodically every 40–50 years affecting multiple geographic areas (3). The mechanisms associated with the initiation of these large outbreaks are not well understood. An A226V amino acid substitution in the virus envelope, which enhances replication in Aedes albopictus, a mosquito vector for CHIKV, and expansion of vectors into areas with previously immunologically naive populations are thought to be responsible for some recent epidemics (4). In chikungunya-endemic areas, environmental factors such as changes in rainfall and vector densities have been implicated in smaller scale outbreaks. The mechanisms underlying outbreak resolution are not well understood. Herd immunity afforded by exposed persons might play an important role in preventing ongoing virus transmission. Reported seroprevalence rates in affected areas have ranged from 10% to ≈40% after an outbreak (5–7).
Full text link https://tinyurl.com/4kcjmpvt
Article title: Complete Genome Sequences of Zika Virus Strains Isolated from the Blood of Patients in Thailand in 2014 and the Philippines in 2012
Authors: D. W. Ellison, J. T. Ladner, R. Buathong, M. T. Alera, M. R. Wiley, L. Hermann, W. Rutvisuttinunt, C. Klungthong, P. Chinnawirotpisan, W. Manasatienkij, M. C. Melendrez, I. Maljkovic Berry, B. Thaisomboonsuk, P. Ong-ajchaowlerd, W. Kaneechit, J. M. Velasco, I. A. Tac-An, D. Villa, C. B. Lago, V. G. Roque, Jr., T. Plipat,A. Nisalak, A. Srikiatkhachorn, S. Fernandez, I. K. Yoon, A. D. Haddow, G. F. Palacios, R. G. Jarman, L. R. Macareo
Publication title: Genome Announcements 4(3):e00359-16, June 2016
Abstract:
Here, we present the complete genome sequences of two Zika virus (ZIKV) strains, Zika virus/ Homo sapiens -tc/THA/2014/SV0127-14 and Zika virus/ H. sapiens -tc/PHL/2012/CPC-0740, isolated from the blood of patients collected in Thailand, 2014, and the Philippines, 2012, respectively. Sequencing and phylogenetic analysis showed that both strains belong to the Asian lineage.
Full text link https://tinyurl.com/5n7p37bd
Article title: Incidence of Dengue Virus Infection in Adults and Children in a Prospective Longitudinal Cohort in the Philippines
Authors: Maria Theresa Alera, Anon Srikiatkhachorn, John Mark Velasco, Ilya A. Tac-An,Catherine B. Lago, Hannah E. Clapham, Stefan Fernandez, Jens W. Levy,Butsaya Thaisomboonsuk, Chonticha Klungthong, Louis R. Macareo, Ananda Nisalak,Laura Hermann, Daisy Villa, In-Kyu Yoon
Publication title: PLoS Neglected Tropical Diseases 10(2):e0004337, February 2016
Abstract:
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.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.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.
Full text link https://tinyurl.com/ytrw45rr
Article title: Region-wide synchrony and traveling waves of dengue across eight countries in Southeast Asia
Authors: Willem G. van Panhuis, Marc Choisy, Xin Xiong, Nian Shong Chok, Pasakorn Akarasewi, Sopon Iamsirithaworn,Sai K. Lam, Chee K. Chong, Fook C. Lam, Bounlay Phommasak, Phengta Vongphrachanh,Khamphaphongphane Bouaphanh, Huy Rekol, Nguyen Tran Hien, Pham Quang Thai, Tran Nhu Duong,Jen-Hsiang Chuang, Yu-Lun Liu, Lee-Ching Ng, Yuan Shi, Enrique A. Tayag, Vito G. Roque Jr., Lyndon L. Lee Suy, Richard G. Jarman, Robert V. Gibbons, John Mark S. Velasco, In-Kyu Yoon, Donald S. Burke,and Derek A. T. Cummings
Publication title: Proceedings of the National Academy of Sciences 112(42), October 2015
Abstract:
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.
Full text link https://tinyurl.com/y4n36rt7
Article title: Chikungunya Virus Infections Among Dengue-Like Illness Patients at a Tertiary Care Hospital in the Philippines, 2012-2013
Authors: John Mark Velasco, Maria Theresa Valderama, Maria Nila Lopez, Domingo Chua Jr., Rene Latog II, Vito Roque Jr.,June Corpuz, Chonticha Klungthong, Prinyada Rodpradit, Kittinun Hussem, Yongyuth Poolpanichupatam,Louis Macareo, Stefan Fernandez, and In-Kyu Yoon
Publication title: The American journal of tropical medicine and hygiene 93(6), September 2015
Abstract:
Chikungunya virus (CHIKV) often co-circulates with dengue virus (DENV). A cross-sectional surveillance study was conducted at a tertiary hospital in Manila, Philippines, to describe the prevalence and characteristics of DENV and CHIKV infections among patients seeking care for dengue-like illness. Acute blood samples from patients ≥ 6 months of age clinically diagnosed with dengue from November 2012 to December 2013 underwent reverse transcriptase polymerase chain reaction (RT-PCR) to detect DENV and CHIKV RNA. A total of 118 patients with clinically diagnosed dengue (age range = 1-89 years, mean = 22 years; male-to-female ratio = 1.51) were tested by DENV RT-PCR; 40 (34%) were DENV PCR-positive (age range = 1-45 years, mean = 17 years). All DENV serotypes were detected: 11 (28%) DENV-1, six (15%) DENV-2, six (15%) DENV-3, and 17 (42%) DENV-4. Of 112 patients clinically diagnosed with dengue and tested by CHIKV RT-PCR, 11 (10%) were CHIKV PCR-positive (age range = 2-47 years, mean = 20.3 years). No coinfections were detected. Presenting signs/symptoms did not differ between DENV- and CHIKV-positive cases. Sequencing of envelope 1 gene from two CHIKV PCR-positive samples showed Asian genotype. This study highlights the potential for misdiagnosis of medically attended CHIKV infections as DENV infection and the difficulty in clinically differentiating dengue and chikungunya based on presenting signs/symptoms alone. This underscores the necessity for diagnostic laboratory tests to distinguish CHIKV infections in the background of actively co-circulating DENV.
Full text link https://tinyurl.com/2p8z6tbh
Article title: Reconstruction of 60 Years of Chikungunya Epidemiology in the Philippines Demonstrates Episodic and Focal Transmission
Authors: Henrik Salje, Simon Cauchemez, Maria Theresa Alera, Isabel Rodriguez-Barraquer, Butsaya Thaisomboonsuk, Anon Srikiatkhachorn, Catherine B. Lago, Daisy Villa6, Chonticha Klungthong, Ilya A. Tac-An, Stefan Fernandez, John Mark Velasco, Vito G. Roque, Jr., Ananda Nisalak, Louis R. Macareo, Jens W. Levy, Derek Cummings, In-Kyu Yoon
Publication title: The Journal of Infectious Diseases 213(4), September 2015
Abstract:
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 two 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 four discrete outbreaks separated by an average delay of 17 years. On average, 23% (95% 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 <230m suggesting focal transmission. Large-scale outbreaks of chikungunya did not result in sustained multi-year transmission. Nevertheless, we estimate >350,000 infections were missed by surveillance systems. Serological studies could supplement surveillance to provide important insights on pathogen circulation.
Full text link https://tinyurl.com/54aykthf
Article title: Diarrheal and Respiratory Illness Surveillance During US-RP Balikatan 2014
Authors: John Mark Velasco, MD, MPH, MSc; Maria eresa Valderama, RMT, MPH; Kathyleen Nogrado, MSPH; Tippa Wongstitwilairoong, RMT, MS; Brett Swierczewski, PhD (MAJ, MS, USA); Ladaporn Bodhidatta, MD; Paphavee Lertsethtakarn, PhD; Chonticha Klungthong, PhD; Stefan Fernandez, PhD (LTC, MS, USA); Carl Mason, MD (COL, MC, USA); In-Kyu Yoon, MD (COL, MC, USA); Louis Macareo, MD (COL, MC, USA)
Publication title: Medical Surveillance Monthly Report (MSMR) 22(6):20-23, June 2015
Abstract:
Diarrheal and respiratory illness surveillance was conducted during the 2014 Republic of the Philippines-U.S. Exercise Balikatan in the Philippines. Seven stool and three respiratory specimens that met the inclusion criteria were collected. Diarrhea stool specimens were tested with commercial enzyme-linked immunosorbent assay kits and real-time polymerase chain reaction (PCR) for 12 viral, bacterial, and protozoan pathogens. Campylobacter, enterotoxigenic Escherichia coli (ETEC), and enteropathogenic Escherichia coli (EPEC) were detected in four of seven (57%), two of seven (29%), and four of seven (57%) specimens, respectively. There were co-infections of EPEC and ETEC in two cases and EPEC and Campylobacter spp. in one case. Respiratory samples were tested using RT-PCR. One of three samples was positive for influenza B. Laboratory-based surveillance is important in determining causative agents for illnesses experienced by military personnel during deployment. Development of vaccines for enteric diseases should be expedited to mitigate their impact on operational readiness.
Full text link https://tinyurl.com/2p8nk7kw
Article title: High Rate of Subclinical Chikungunya Virus Infection and Association of Neutralizing Antibody with Protection in a Prospective Cohort in The Philippines
Authors: In-Kyu Yoon, Maria Theresa Alera, Catherine B. Lago, Ilya A. Tac-An, Daisy Villa, Stefan Fernandez, Butsaya Thaisomboonsuk, Chonticha Klungthong, Jens W. Levy,John Mark Velasco, Vito G. Roque, Jr., Henrik Salje, Louis R. Macareo, LauraL. Hermann, Ananda Nisalak, Anon Srikiatkhachorn
Publication title: PLoS Neglected Tropical Diseases 9(5):e0003764, May 2015
Abstract:
Chikungunya virus (CHIKV) is a globally re-emerging arbovirus for which previous studies have indicated the majority of infections result in symptomatic febrile illness. We sought to characterize the proportion of subclinical and symptomatic CHIKV infections in a prospective cohort study in a country with known CHIKV circulation.A prospective longitudinal cohort of subjects ≥6 months old underwent community-based active surveillance for acute febrile illness in Cebu City, Philippines from 2012-13. Subjects with fever history were clinically evaluated at acute, 2, 5, and 8 day visits, and at a 3-week convalescent visit. Blood was collected at the acute and 3-week convalescent visits. Symptomatic CHIKV infections were identified by positive CHIKV PCR in acute blood samples and/or CHIKV IgM/IgG ELISA seroconversion in paired acute/convalescent samples. Enrollment and 12-month blood samples underwent plaque reduction neutralization test (PRNT) using CHIKV attenuated strain 181/clone25. Subclinical CHIKV infections were identified by ≥8-fold rise from a baseline enrollment PRNT titer 50 years old. Baseline CHIKV PRNT titer ≥10 was associated with 100% (95%CI: 46.1, 100.0) protection from symptomatic CHIKV infection. Phylogenetic analysis demonstrated Asian genotype closely related to strains from Asia and the Caribbean.Subclinical infections accounted for a majority of total CHIKV infections. A positive baseline CHIKV PRNT titer was associated with protection from symptomatic CHIKV infection. These findings have implications for assessing disease burden, understanding virus transmission, and supporting vaccine development.
Full text link https://tinyurl.com/49jt2yyz
Article title: Zika Virus Infection, Philippines, 2012
Authors: Maria Theresa Alera, Laura Hermann, Ilya A. Tac-An, Chonticha Klungthong, Wiriya Rutvisuttinunt, Wudtichai Manasatienkij, Daisy Villa, Butsaya Thaisomboonsuk, John Mark Velasco, Piyawan Chinnawirotpisan, Catherine B. Lago, Vito G. Roque, Jr., Louis R. Macareo, Anon Srikiatkhachorn, Stefan Fernandez, In-Kyu Yoon
Publication title: Emerging Infectious Diseases 21(4):722-724, April 2015
Abstract:
No abstract
Full text link https://tinyurl.com/2ws9zwk9
Article title: Prediction of High Incidence of Dengue in the Philippines
Authors: Anna L. Buczak, Benjamin Baugher, Steven M. Babin, Liane C. Ramac-Thomas, Erhan Guven,Yevgeniy Elbert, Phillip T. Koshute, John Mark S. Velasco, Vito G. Roque, Jr., Enrique A. Tayag, In-Kyu Yoon, Sheri H. Lewis
Publication title: PLoS Neglected Tropical Diseases 8(4):e2771, April 2014
Abstract:
Accurate prediction of dengue incidence levels weeks in advance of an outbreak may reduce the morbidity and mortality associated with this neglected disease. Therefore, models were developed to predict high and low dengue incidence in order to provide timely forewarnings in the Philippines. Model inputs were chosen based on studies indicating variables that may impact dengue incidence. The method first uses Fuzzy Association Rule Mining techniques to extract association rules from these historical epidemiological, environmental, and socio-economic data, as well as climate data indicating future weather patterns. Selection criteria were used to choose a subset of these rules for a classifier, thereby generating a Prediction Model. The models predicted high or low incidence of dengue in a Philippines province four weeks in advance. The threshold between high and low was determined relative to historical incidence data. Model accuracy is described by Positive Predictive Value (PPV), Negative Predictive Value (NPV), Sensitivity, and Specificity computed on test data not previously used to develop the model. Selecting a model using the F0.5 measure, which gives PPV more importance than Sensitivity, gave these results: PPV = 0.780, NPV = 0.938, Sensitivity = 0.547, Specificity = 0.978. Using the F3 measure, which gives Sensitivity more importance than PPV, the selected model had PPV = 0.778, NPV = 0.948, Sensitivity = 0.627, Specificity = 0.974. The decision as to which model has greater utility depends on how the predictions will be used in a particular situation. This method builds prediction models for future dengue incidence in the Philippines and is capable of being modified for use in different situations; for diseases other than dengue; and for regions beyond the Philippines. The Philippines dengue prediction models predicted high or low incidence of dengue four weeks in advance of an outbreak with high accuracy, as measured by PPV, NPV, Sensitivity, and Specificity.
Full text link https://tinyurl.com/5n6nscty
Article title: Demographic, clinical and laboratory findings among adult and pediatric patients hospitalized with dengue in the Philippines
Authors: John Mark S. Velasco, Ma Theresa P. Alera, Charity Ann Ypil-Cardenas, Efren M. Dimaano, Richard G. Jarman, Piyawan Chinnawirotpisan, Butsaya Thaisomboonsuk, In-Kyu Yoon, Derek A. Cummings and Mammen P. Mammen Jr.
Publication title: The Southeast Asian journal of tropical medicine and public health 45(2):337-45, March 2014
Abstract:
We evaluated the differences in demographic, clinical, and laboratory findings between adult and pediatric patients hospitalized with dengue fever. Ninety patients with dengue infection admitted at San Lazaro Hospital (SLH), Manila from September 2005 to January 2006 were included in the study. The cases were laboratory-confirmed to have dengue infection. The majority of dengue cases (92%) had secondary dengue infection (median age = 18, age range: 2-37) while the remainder (8%) had a primary dengue infection (median age = 12, age range: 7-22). Nearly all the patients (99%) had dengue hemorrhagic fever (DHF). Sixty-five of the cases (72%) had serotype data: 2 (3%) were dengue virus serotype 1 (DENV-1) (median age = 17), 12 (18%) had DENV-2 (median age = 17.5), 38 (59%) had DENV-3 (median age = 16) and 13 (20%) had DENV-4 (median age = 18). The initial signs, symptoms and laboratory results except hematocrit (p = 0.02) and hemoglobin (p = 0.02) did not differ significantly between adults and children. During the study period, half the cases were adults (218 years; n = 45) and half were children (<18 years; n = 45). The ages of cases ranged from 2 to 37 years (median = 17 years) and the peak incidence was 15-19 years. Dengue is often considered as a pediatric disease. Additional studies are needed to determine if an age shift is occurring and where.
Full text link https://tinyurl.com/2p8u8w4t
Article title: Hospital-based surveillance of Japanese encephalitis at a tertiary hospital in Manila
Authors: Ma Theresa P. Alera , John Mark S. Velasco, Charity Ann Ypil-Cardenas, Richard G. Jarman, Ananda N. Nisalak, Butsaya Thaisomboonsuk, Robert V. Gibbons, Efren M. Dimaano, In-Kyu Yoon
Publication title: The Southeast Asian journal of tropical medicine and public health 44(5):791-8, September 2013
Abstract:
Japanese encephalitis virus (JEV) is endemic in the Philippines but the incidence and burden of disease are not well established. We conducted a prospective hospital-based study at San Lazaro Hospital, a tertiary level hospital in Manila, from September 2005 to December 2006. Cases were determined using an in-house dengue and Japanese encephalitis (JE) enzyme-linked immunosorbent assay in order to detect the proportion of JE cases among the acute encephalitis syndrome (AES) cases admitted to our hospital. Fifteen patients were found to have AES, of whom 6 (40%) had confirmed JE. Of the JE cases, 4 were females and 2 were males with an age range of 3-14 years. Three of the 6 JE cases occurred during July. The most common signs and symptoms on admission among JE cases were: fever, headache, loss of appetite, neck rigidity and altered sensorium. JE likely comprises a significant proportion of hospitalized AES cases among children from Manila and nearby provinces. Further studies on the nation-wide prevalence and distribution of JE in the Philippines are needed to guide health authorities in disease control and prevention strategies.
Full text link https://tinyurl.com/3wabyjxs
Article title: Tweeting Fever: Are Tweet Extracts a Valid Surrogate Data Source for Dengue Fever?
Authors: Jacqueline S. Coberly, Clayton R. Fink, Eugene Elbert, In-Kyu Yoon, John M. Velasco, Agnes Tomayo, V. Roque, S. Ygano, Durinda Macasoco, and Sheri Lewis
Publication title: Online Journal of Public Health Informatics 5(1)
Abstract:
Objective: To determine whether Twitter data contains information on dengue-like illness and whether the temporal trend of such data correlates with the incidence dengue or dengue-like illness as identified by city and national health authorities. Introduction Dengue fever is a major cause of morbidity and mortality in the Republic of the Philippines (RP) and across the world. Early identification of geographic outbreaks can help target intervention campaigns and mitigate the severity of outbreaks. Electronic disease surveillance can improve early identification but, in most dengue endemic areas data pre-existing digital data are not available for such systems. Data must be collected and digitized specifically for electronic disease surveillance. Twitter, however, is heavily used in these areas; for example, the RP is among the top 20 producers of tweets in the world. If social media could be used as a surrogate data source for electronic disease surveillance, it would provide an inexpensive pre-digitized data source for resource-limited countries. This study investigates whether Twitter extracts can be used effectively as a surrogate data source to monitor changes in the temporal trend of dengue fever in Cebu City and the National Capitol Region surrounding Manila (NCR) in the RP. Methods We obtained two sources of ground truth incidence for dengue. The first was daily dengue fever incidence for Cebu City and the NCR taken from the Philippines Integrated Disease Surveillance and Response System (PIDSR). The second ground truth source was fever incidence from Cebu City for 2011. The Cebu City Health Office (CCHO) has monitored fever incidence as a surrogate for dengue fever since the 1980s. Tweets from Cebu City, and the NCR were collected prospectively thru Twitter’s public application program interface. The Cebu City fever ground truth data set was smoothed with a seven day moving average to facilitate comparison to the PIDSR and Twitter data. A vocabulary of words and phrases describing fever and dengue fever in the tweets collected were identified and used to mark relevant tweets. A subset of these ‘fever’ tweets that mentioned fever related to a medical situation were identified. The incidence and the temporal pattern of these medically-relevant tweets were compared with the incidence and pattern of fever and dengue fever in the two ground truth data sets. Pearson correlation coefficient was used to compare the correlation among the different data sets. Noted lag periods were adjusted by moving the data in time and re-computing the correlation coefficient. Results 26,023,103 tweets were collected from the two geographic regions: 10,303,366 from Cebu City and 15,719,767 tweets from the NCR. 8,814 (0.02%) Tweets contained the word fever and 4099 (0.01% of total) mentioned fever in a medically-relevant context, for example. “…I have a fever…” vs. “…football fever….” The medically-relevant tweets were compared with both ground truth data sets. The correlation between the Tweets and each of the incidence data sets is shown below.
Conclusions: Tweets containing medically-relevant fever references were correlated (p<0.0001) with both fever and dengue fever incidence in the ground truth data sets. The signal indicating fever in the medically-related tweets led the incidence data significantly: by 6 days for the Cebu City fever incidence; and by 12 days for the PIDSR dengue fever incidence. Temporal adjustment to account for observed lag periods increased the correlation coefficient by about one-third in both cases. This was a limited pilot study, but it suggests that Twitter extracts may provide a valid and timely surrogate data source to monitor dengue fever in this population. Further study of the correlation of Twitter and dengue in other areas, and of Twitter with other illnesses is warranted.
Full text link https://tinyurl.com/2s3aar7c
Article title: Implementation of SMS fever surveillance in the Philippines
Authors: A. Tomayao, I.-K. Yoon, I. Tac-an, D. Macasocol, D. Obidas, S. Ygona, J. Coberly, R. Wojcik, M.T. Alera, J.M. Velasco, T. Fernandez
Publication title: International journal of infectious diseases: IJID: official publication of the International Society for Infectious Diseases 16(1):e147
Abstract:
Background:The Cebu City Health Department (CHD) established paper-based fever surveillance for dengue in year 2000. CHD utilized health volunteers to identify fever cases in their neighborhood and refer cases to Barangay Health Centers (BHCs). An aggregate report was submitted to CHD on a weekly to monthly basis. However, this resulted in identification of outbreaks only several weeks after onset. We assisted in modifying the existing paper-based fever monitoring into a short message service (SMS)-based fever surveillance system. We describe challenges in implementation and its preliminary results.
Methods: Providers at BHCs sent fever cases daily via SMS to CHD hotline. Texted variables included clinic date, age, sex and fever syndromes which are coded. Providers received an auto-reply for successful transmission. An auto-reply for erroneous data prompted providers to resend in prescribed format or provide complete data.
The SMS Fever Surveillance system was implemented in all of the 80 BHCs that comprised the CHD. In 2011, the surveillance system was based on data collected from seventy-five (75) out of 80 BHCs. All 50 urban BHCs in the lowlands and 30 rural BHCs in mountain areas participated in the surveillance. The surveillance was representative of the city's population of about 822,628 people. Data, collected on a daily basis between July 15, 2010 and December 29, 2011 from the 75 BHCs corresponded to 7694 fever cases. Valid one-time texts made up 82% of all texts. Data was transmitted within 24 hours of clinic visit in 62% of cases, 48 hours in 8% of cases and 72 hours in 4% of cases.
Conclusion: This is the first city-wide SMS-based fever syndromic surveillance established in the Philippines. Mobile phone SMS is an effective tool to rapidly transmit cases for near “real-time” data analyses to detect outbreaks. An auto-reply may increase timeliness, accuracy and completeness of data. In addition, SMS-based fever surveillance in conjunction with hospital-based reporting can detect health events of international importance. Future interventions might include rapid laboratory testing for selected pathogens to determine etiologies of acute febrile illness.
Full text link https://tinyurl.com/5n8v6bnt