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Human enterovirus D68 (EV-D68) is a causative agent for acute respiratory infections and potentially central nervous system illnesses with increasing epidemiological significance. Recent studies have highlighted the role of sialic acids as a functional receptor for EV-D68 in vitro. However, further investigations are required to reveal its significance in actual infections in human.

Background: The incidence of antimicrobial resistance has been increasing worldwide in the past decades, which includes resistance to bacteria that cause common childhood illnesses, such as acute respiratory infections and diarrhea. Numerous children with those common illnesses are treated with antibiotics. However, in such cases, antibiotic treatment is not required. Community-based studies focusing on antibiotic use among children are still limited. This study aimed to identify the prevalence of antibiotic use for common childhood illnesses and to investigate factors associated with antibiotic use in children under 5 years old as well as female caregivers in a rural community in Indonesia., Methods: A cross-sectional study of 334 children in three villages of Banten Province, located in the western part of Java Island, was conducted in May 2018. Female caregivers who were responsible for providing medications to children were interviewed. We obtained information such as demographic data, any common clinical illness within the last 30 days, and antibiotic usage during an episode of illness. We excluded children with underlying disease that require a regular follow-up and children who were hospitalized in the last 30 days in the analysis. Antibiotic use answered by female caregivers was verified by checking its package or showing photos of various antibiotics to the female caregivers. Crushed antibiotics were confirmed with health professionals., Results: A total of 203 children had clinical symptoms, and the most common symptom was fever and respiratory symptoms. In total, 49.3% received antibiotics, and 66% of them were prescribed by private health professionals. Only two children received antibiotics without a prescription. The most common antibiotic used among children was amoxicillin., Conclusions: The high prevalence of antibiotic use was observed in children under 5 years of age, and the major source to obtain antibiotics was to consult health professionals. Training on appropriate antibiotic use must be conducted for health professionals in not only public but also private sectors., Competing Interests: Competing interestsThe authors declare that they have no competing interests.

The 5' untranslated region (UTR) of the RNA genomes of enteroviruses possesses an internal ribosome entry site (IRES) that directs translation of the mRNA by binding to ribosomes. Infection with enterovirus D68 causes respiratory symptoms and is sometimes associated with neurological disorders. The number of reports of the viral infection and neurological disorders has increased in 2010s, although the reason behind this phenomenon remains unelucidated. In this study, we investigated the evolutionary and functional diversity of the 5' UTR of recently circulating strains of the virus. Genomic sequences of 374 viral strains were acquired and subjected to phylogenetic analysis. The IRES activity of the viruses was measured using a luciferase reporter assay. We found a highly conserved sequence in the 5' UTR and also identified the location of variable sites in the predicted RNA secondary structure. IRES activities differed among the strains in some cell lines, including neuronal and respiratory cells, and were especially high in strains of a major lineage from the recent surge. The effect of mutations in the 5' UTR should be studied further in the future for better understanding of viral pathogenesis.

Background: Respiratory syncytial virus (RSV) is one of the main viral causes of lower respiratory tract illness (LRTI), especially in young children. RSV vaccines, including maternal and infant vaccines, are under development; however, more epidemiological studies are needed to develop effective vaccination strategies., Objectives: To estimate detailed age-specific incidence rates and severity of RSV-associated LRTI (RSV-LRTI) using data from a community-based prospective cohort study in the Philippines., Patients/methods: Cohort children who visited health facilities due to acute respiratory symptoms were identified, and nasopharyngeal swabs were collected to detect RSV. The severity of RSV-LRTI was assessed using the severity definition proposed by the World Health Organization. Risk factors for developing RSV-LRTI and contribution of SpO 2 measurement were also evaluated., Results: A total of 395 RSV episodes which occurred in children aged 2-59 months were categorised as 183 RSV-LRTI, 72 as severe RSV-LRTI and 29 as very severe RSV-LRTI. Children aged 3-5 months had the highest incidence rate of RSV-LRTI, at 207.4 per 1000 child-years (95% CI: 149.0-279.5). Younger age group, place of living and low educational level of caregivers were associated with developing RSV-LRTI. Clinical manifestations had low levels of agreement with hypoxaemia as measured by pulse oximeter., Conclusion: The highest burden of RSV was observed in young infants aged 3-5 months, whereas the burden was also high in those aged 12-20 months. Future vaccination strategies should consider the protection of older children, especially those aged one year, as well as young infants., (© 2019 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)

A prospective matched case-control study was conducted to evaluate associations between dietary histories, including consumption of bivalves, diarrhea, and norovirus positive diarrhea in adult ambulatory patients at an outpatient clinic of a hospital in Tokyo, Japan. Ambulatory cases with diarrhea were matched with nondiarrheal control patients, who visited the same clinic. A standardized questionnaire was used to obtain patients' information, including histories of food consumption and clinical information. Norovirus infection was confirmed using real-time reverse transcription polymerase chain reaction. A total of 207 patients, including 69 diarrheal cases and 138 nondiarrheal cases were included in the analysis. Among them, 60 (29.0%) participants reported consuming bivalves. Norovirus was detected in 35% (24/69) of diarrheal cases. Of those, 10 (41.7%) reported consumption of bivalves and of those, 6 (60.0%) consumed raw bivalves. The proportion of those who consumed raw bivalves was significantly higher in norovirus-positive diarrheal cases than in norovirus-negative diarrheal cases (25.0% vs 6.7%; odds ratio [OR], 4.67; 95% confidence interval [CI], 1.1-20.7) and matched nondiarrheal controls (25.0% vs 6.3%, OR: 5.00; 95% CI, 1.1-22.2). The attributable fraction of consuming raw bivalves for norovirus-associated diarrhea to matched nondiarrheal controls was 20.0%. Consuming raw bivalves was substantially attributed to norovirus-associated diarrhea in adult ambulatory patients and preventive measures for reducing the risk associated with consumption of raw bivalves could decrease the incidence of norovirus-associated diarrhea., (© 2019 Wiley Periodicals, Inc.)

Background: Several inactivated enterovirus-A71 (EV-A71) vaccines are currently licensed in China; however, the development of additional EV-A71 vaccines is ongoing, necessitating extensive analysis of the molecular epidemiology of the virus worldwide. Until 2012, laboratory confirmation of EV-A71 for hand, foot, and mouth disease (HFMD) and other associated diseases had not occurred in the Philippines. Because EV-A71 has been linked with cases of acute flaccid paralysis (AFP), AFP surveillance is one strategy for documenting its possible circulation in the country. To expand current knowledge on EV-A71, molecular epidemiologic analysis and genetic characterization of EV-A71 isolates were performed in this study., Methods: A retrospective study was performed to identify and characterize nonpolio enteroviruses (NPEVs) associated with AFP in the Philippines, and nine samples were found to be EV-A71-positive. Following characterization of these EV-A71 isolates, the complete viral protein 1 (VP1) gene was targeted for phylogenetic analysis., Results: Nine EV-A71 isolates detected in 2000 (n = 2), 2002 (n = 4), 2005 (n = 2), and 2010 (n = 1) were characterized using molecular methods. Genomic regions spanning the complete VP1 region were amplified and sequenced using specific primers. Phylogenetic analysis of the full-length VP1 region identified all nine EV-A71 Philippine isolates as belonging to the genogroup C lineage, specifically the C2 cluster. The result indicated a genetic linkage with several strains isolated in Japan and Taiwan, suggesting that strains in the C2 cluster identified in the Asia-Pacific region were circulating in the Philippines., Conclusion: The study presents the genetic analysis of EV-A71 in the Philippines. Despite some limitations, the study provides additional genetic data on the circulating EV-A71 strains in the Asia-Pacific region, in which information on EV-A71 molecular epidemiology is incomplete. Considering that EV-A71 has a significant public health impact in the region, knowledge of its circulation in each country is important, especially for formulating vaccines covering a wide variety of strains.

Objective: Pneumonia remains the leading cause of hospitalisations and deaths among children aged <5 years. Diverse respiratory pathogens cause acute respiratory infections, including pneumonia. Here, we analysed viral and bacterial pathogens and risk factors associated with death of hospitalised children., Design: A 9-year case series study., Setting: Two secondary-care hospitals, one tertiary-care hospital and one research centre in the Philippines., Participants: 5054 children aged <5 years hospitalised with severe pneumonia., Methods: Nasopharyngeal swabs for virus identification, and venous blood samples for bacterial culture were collected. Demographic, clinical data and laboratory findings were collected at admission time. Logistic regression analyses were performed to identify the factors associated with death., Results: Of the enrolled patients, 57% (2876/5054) were males. The case fatality rate was 4.7% (238/5054), showing a decreasing trend during the study period (p<0.001). 55.0% of the patients who died were either moderately or severely underweight. Viruses were detected in 61.0% of the patients, with respiratory syncytial virus (27.0%) and rhinovirus (23.0%) being the most commonly detected viruses. In children aged 2-59 months, the risk factors significantly associated with death included age of 2-5 months, sensorial changes, severe malnutrition, grunting, central cyanosis, decreased breath sounds, tachypnoea, fever (≥38.5°C), saturation of peripheral oxygen <90%, infiltration, consolidation and pleural effusion on chest radiograph.Among the pathogens, adenovirus type 7, seasonal influenza A (H1N1) and positive blood culture for bacteria were significantly associated with death. Similar patterns were observed between the death cases and the aforementioned factors in children aged <2 months., Conclusion: Malnutrition was the most common factor associated with death and addressing this issue may decrease the case fatality rate. In addition, chest radiographic examination and oxygen saturation measurement should be promoted in all hospitalised patients with pneumonia as well as bacteria detection to identify patients who are at risk of death., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: To develop a more effective vaccination strategy for reducing the impact of respiratory syncytial virus (RSV) infection, especially in young infants (<6 months old), it is necessary to understand the transmission dynamics of RSV., Methods: We conducted a community-based prospective cohort study from 2014 to 2016 in Biliran Province, the Philippines, on children <5 years old. We collected nasopharyngeal swabs from symptomatic children with acute respiratory infection (ARI) during household visits and at health facilities. In households (n = 181) with RSV-positive ARI cases (RSV-ARI), we also identified ARI episodes among other children <5 years old in the same household. In addition, we determined the serial interval to estimate the basic reproduction number ( R 0 ), the average number of secondary cases generated by a single primary case., Results: In the 181 households analyzed, we found 212 RSV-ARI in 152 households with a single case and 29 households with multiple cases, which included 29 1st RSV-ARI and 31 2nd RSV-ARI. We also found possible index cases among children <5 years old in the same household for 29.0% (18 of 62) of young infants with RSV-ARI. The estimated mean serial interval was 3.2 days, and R 0 was estimated to be 0.92-1.33 for RSV-A and 1.04-1.76 for RSV-B, which varied between different times (2014 and 2015) and places., Conclusions: Young infants are likely to acquire RSV infection from older children in the same household. Therefore, vaccination targeting older children might protect infants from RSV infection.

Background: Community-acquired pneumonia (CAP) is a common cause of morbidity and mortality among adults worldwide. However, the distribution of the etiology of CAP varies from one country to another, with limited data from rural areas., Methods: A prospective hospital-based study on adult CAP was conducted in Leyte, Central Philippines from May 2010 to May 2012. Blood, sputum, and nasopharyngeal samples obtained from patients were used to identify pathogens using standard microbiological culture methods and PCR., Results: Of the 535 patients enrolled, 38% were younger than 50 years old. More than half of the patients had an underlying disease, including pulmonary tuberculosis (22%). The detection rate was higher for bacteria (40%) than viruses (13%). Haemophilus influenzae (12%) was the most commonly detected bacterium and influenza virus (5%) was the most commonly detected virus. The proportion of CAP patients with Mycobacterium tuberculosis infection was higher in the younger age group than in the older age group. Among CAP patients, 14% died during hospitalization, and drowsiness on admission and SpO 2 <90% were independent risk factors for mortality., Conclusions: Bacterial infections contribute substantially to the number of hospitalizations among CAP patients in rural Philippines. This study also highlights the importance of treatment of tuberculosis in reducing the burden of adult CAP in the country., (Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The Hajj is an annual pilgrimage that 1-2 million Muslims undertake in the Kingdom of Saudi Arabia (KSA), which is the largest mass gathering event in the world, as the world's most populous Muslim nation, Indonesia holds the largest visa quota for the Hajj. All Hajj pilgrims under the quota system are registered in the Indonesian government's Hajj surveillance database to ensure adherence to the KSA authorities' health requirements. Performance of the Hajj and its rites are physically demanding, which may present health risks. This report provides a descriptive overview of mortality in Indonesian pilgrims from 2004 to 2011. The mortality rate from 2004 to 2011 ranged from 149 to 337 per 100,000 Hajj pilgrims, equivalent to the actual number of deaths ranging between 501 and 531 cases. The top two mortality causes were attributable to diseases of the circulatory and respiratory systems. Older pilgrims or pilgrims with comorbidities should be encouraged to take a less physically demanding route in the Hajj. All pilgrims should be educated on health risks and seek early health advice from the mobile medical teams provided., Competing Interests: The authors have no conflicts of interest to declare., (© Atlantis Press International B.V.)

Norovirus (NoV) and sapovirus (SaV) are recognized as the causative agents of acute gastroenteritis, and NoV is one of the leading pathogens reported worldwide. This study reports on the distribution of NoV and SaV genotypes in children hospitalized with acute gastroenteritis in Chiang Mai, Thailand, from January 2015 to February 2017. From a total of 843 stool samples, 170 (20.2%) and 16 (1.9%) were identified as having NoV and SaV infections, respectively. Two samples (0.2%) were positive for both NoV and SaV. Of these, NoV GII.4 (57.2%) was the dominant genotype, followed by GII.2, GII.3, GII.17, GII.6, GII.7, GII.13, GII.14, GII.15, GII.21, GI.6, and GI.5. Among the NoV GII.4 variants, Sydney 2012 was the dominant variant during the period 2015-2016, while the other variants detected in this study were Asia 2003 and New Orleans 2009. Interestingly, an increase of NoV GII.2 was observed in 2016 and 2017. Characterization of partial RNA-dependent RNA polymerase and VP1 nucleotide sequences of GII.2 strains revealed that more than half of the GII.2 strains circulating in 2016 and 2017 were recombinant strains of GII.P16/GII.2. For SaV, the majority of strains belonged to GI.1 (55.6%) and GI.2 (33.3%), while GII.5 accounted for 11.1%. In conclusion, this study demonstrates the diversity of NoV and SaV, and the emergence of NoV GII.P16/GII.2 recombinant strains in 2016 and 2017 in Chiang Mai, Thailand., (© 2018 Wiley Periodicals, Inc.)

Hepatitis A virus (HAV) is a common infectious etiology of acute hepatitis worldwide. The Philippines remains highly endemic for hepatitis A, but there is still a lack of information about HAV in the country. To evaluate the HAV contamination in environmental water in the Philippines, we conducted the detection and genetic analyses of HAV RNA in samples from river water. Twelve water samples were collected at 6 sampling sites of 3 rivers in Metro Manila, in both the dry and wet seasons in 2012 and 2013. The HAV RNA was detected in all the 6 samples collected in the dry season, and in one sample from the wet season. Phylogenetic analysis confirmed that the HAV strains detected in the river water included multiple sequences belonging to subgenotypes IA and IIIA. This indicates that at least 2 genotypes of the HAV strains are circulating in the environment in the Philippines, posing a risk of HAV infection to not only residents, but also tourists, especially in the dry season.

Background: Acute respiratory infection (ARI) is of great concern in public health. It remains unclear whether viral infections can affect the host's susceptibility to subsequent ARIs., Methods: A prospective cohort study on ARIs of children below 5 years old was conducted in the Philippines from 2014 to 2016. The respiratory symptoms were recorded daily, and nasopharyngeal swabs were collected at both household and health facilities. The specimens were tested for respiratory viruses. We then determined whether viral etiology was associated with the severity of the present ARI and whether previous viral infections was associated with subsequent ARIs., Results: A total of 3851 children and 16337 ARI episodes were enrolled and recorded, respectively. Samples were collected from 24% of all ARI episodes; collection rate at the healthcare facilities was 95%. Enterovirus D68, rhinovirus species C, and respiratory syncytial virus were significantly associated with severe ARIs. The risk for subsequent ARIs was significantly enhanced after infections with adenovirus, influenza A virus, parainfluenza virus type 4, and rhinovirus species C., Conclusions: This study revealed that viral etiology plays a significant role in the severity of the present ARI and that viral infection affects the host's susceptibility to subsequent ARIs.

Complete genome sequences were determined for 12 human respiratory syncytial virus strains collected from nasopharyngeal samples obtained from children with repeated subgroup B infections. Eight common amino acid polymorphisms in the G, F, and L proteins were identified between the viruses detected in initial and subsequent infections.

Objectives: Pneumonia remains a primary cause of death for under-five children. It is possible to reduce the mortality impact from childhood pneumonia if caregivers recognise the danger signs of pneumonia and obtain appropriate healthcare. Among caregivers, research on fathers' healthcare-seeking behaviours and perceptions are limited, whereas research on mothers is available. This study aims to reveal fathers' roles and perspectives with respect to the selection of care and treatment for children with pneumonia in a remote island of the Philippines., Design: A qualitative research was carried out using semistructured interviews., Setting and Participants: The interviews were conducted with 12 fathers whose children had pneumonia-like episodes in the 6 months prior to the interview. Data analysis was performed using the concept analysis method to identify codes which were merged into subcategories and categories. Finally, the themes were identified., Results: Three themes were identified as part of fathers' roles, and two were identified as fathers' perspectives on various treatment options. Fathers took care of their sick children by not entrusting care only to mothers because they considered this as part of their role. Notably, fathers considered that arranging money for the child's treatment was a matter of prime importance. They selected a particular treatment based on their experiences and beliefs, including herbal medicine, home treatment, and visiting traditional healers and health facilities. Their decision was influenced by not only their perception of the severity of illness but also cultural beliefs on the cause of illness. Visiting health facilities, particularly during hospital admissions, causes significant financial burden for the family which was the main concern of fathers., Conclusion: It is crucial to consider the cultural background and also imperative to address issues related to medical cost and the credibility of health facilities to improve fathers' healthcare-seeking behaviour., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2018. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Human respiratory syncytial virus (RSV) is the leading cause of severe acute respiratory infection in infants and young children, which is characterized by repeated infections. However, the role of amino acid substitutions in repeated infections remains unclear. Hence, this study aimed to elucidate the genetic characteristics of RSV in children with repeated infections using molecular analyses of F and G genes., Methods: We conducted a cohort study of children younger than 5 years in the Philippines. We collected nasopharyngeal swabs from children with acute respiratory symptoms and compared F and G sequences between initial and subsequent RSV infections., Results: We examined 1802 children from May 2014 to January 2016 and collected 3471 samples. Repeated infections were observed in 25 children, including 4 with homologous RSV-B reinfections. Viruses from the 4 pairs of homologous reinfections had amino acid substitutions in the G protein mostly at O-glycosylation sites, whereas changes in the F protein were identified at antigenic sites V (L173S) and θ (Q209K), considered essential epitopes for the prefusion conformation of the F protein., Conclusions: Amino acid substitutions in G and F proteins of RSV-B might have led to antigenic changes, potentially contributing to homologous reinfections observed in this study.

Background: Sapovirus is one of the primary viral causes of acute gastroenteritis (AGE), especially where rotavirus vaccination has been implemented. The characteristics and impact of natural infection at the community level, however, have not been well documented., Methods: Stool samples were analyzed from 100 children randomly selected from a community-based birth cohort study in Peru. All diarrheal and 1 nondiarrheal stools collected trimonthly from children up to age 2 years (n = 1669) were tested for sapovirus detection. Viral shedding duration was determined by testing additional weekly samples (n = 440) collected before and after a sapovirus-positive sample., Results: The incidence of sapovirus infection in the first and second years of life was 4.3 and 11.1 per 100 child-months, respectively. By age 2 years, 82% of children had at least 1 sapovirus infection, and 64% had at least 1 sapovirus-associated diarrhea episode. The median shedding period was 18.5 days. In 112 of 175 infections, 14 genotypes from 4 genogroups (GI, GII, GIV, and GV) were determined. Among genogroups, GI were more frequently found in symptomatic infections than in asymptomatic infections (odds ratio, 3.1; 95% confidence interval, 1.3-7.4). Fifty-nine children had serial sapovirus infections, but only 3 had repeated infection of the same genotype., Conclusions: Sapovirus was frequently detected in children with AGE at the community level during the first 2 years of life. Serial sapovirus infections by multiple genotypes in a child suggest genotype-specific immunity from each infection, which needs to be taken into account for vaccine development.

Background: In the autumn of 2015, we experienced a surge in the number of pediatric cases of wheeze in our hospital, which was suspected to be caused by enterovirus (EV)-D68 transmission in the community. Thus, we implemented an ad hoc retrospective surveillance for EV-D68., Methods: Patients <15 years of age with acute respiratory infection were eligible for inclusion in this study. All enrolled patients underwent virus detection test. Additionally, neutralization tests (NTs) were performed using the stored serum samples of the enrolled patients to compare the antigenicity of the virus isolated in this study with that isolated in 2010 and evaluate the anti-EV-D68 antibody prevalence., Results: Respiratory syncytial virus (RSV) was the most commonly detected virus (35%), followed by EV-D68 (19%) and non-EV-D68 enteroviruses/human rhinoviruses (14%). Patients with EV-D68 infection had higher median age than those with RSV infection (P < 0.05). Moreover, patients with EV-D68 infection showed a higher expiratory wheeze prevalence than those with non-EV-D68 enterovirus/rhinovirus and RSV infections. The antigenicity of the isolate from the current study was similar to the virus that circulated in 2010. At the early study phase, children in our community did not have high NT titers, but the median log NT titer increased from 1.5 to 5 over time (P < 0.05)., Conclusion: This study showed the concurrent circulation of EV-D68 with non-EV-D68 enteroviruses/rhinoviruses and RSV in infants and children in our community and captured the early stage of EV-D68 transmission.

Complete genome sequences of 13 human respiratory syncytial virus strains were determined from samples obtained from children hospitalized in the Philippines between 2012 and 2013 because of acute respiratory infection. We identified amino acid polymorphisms between the NA1 and ON1 genotypes in the P, G, F, and L proteins., (Copyright © 2018 Malasao et al.)

We report here two complete coding genome sequences of novel genotype GII.8 sapovirus strains identified in diarrhea samples collected from two Peruvian children. The complete coding genome sequences of both GII.8 variants were determined using the Sanger sequencing method.

Background: We have previously estimated that respiratory syncytial virus (RSV) was associated with 22% of all episodes of (severe) acute lower respiratory infection (ALRI) resulting in 55 000 to 199 000 deaths in children younger than 5 years in 2005. In the past 5 years, major research activity on RSV has yielded substantial new data from developing countries. With a considerably expanded dataset from a large international collaboration, we aimed to estimate the global incidence, hospital admission rate, and mortality from RSV-ALRI episodes in young children in 2015., Methods: We estimated the incidence and hospital admission rate of RSV-associated ALRI (RSV-ALRI) in children younger than 5 years stratified by age and World Bank income regions from a systematic review of studies published between Jan 1, 1995, and Dec 31, 2016, and unpublished data from 76 high quality population-based studies. We estimated the RSV-ALRI incidence for 132 developing countries using a risk factor-based model and 2015 population estimates. We estimated the in-hospital RSV-ALRI mortality by combining in-hospital case fatality ratios with hospital admission estimates from hospital-based (published and unpublished) studies. We also estimated overall RSV-ALRI mortality by identifying studies reporting monthly data for ALRI mortality in the community and RSV activity., Findings: We estimated that globally in 2015, 33·1 million (uncertainty range [UR] 21·6-50·3) episodes of RSV-ALRI, resulted in about 3·2 million (2·7-3·8) hospital admissions, and 59 600 (48 000-74 500) in-hospital deaths in children younger than 5 years. In children younger than 6 months, 1·4 million (UR 1·2-1·7) hospital admissions, and 27 300 (UR 20 700-36 200) in-hospital deaths were due to RSV-ALRI. We also estimated that the overall RSV-ALRI mortality could be as high as 118 200 (UR 94 600-149 400). Incidence and mortality varied substantially from year to year in any given population., Interpretation: Globally, RSV is a common cause of childhood ALRI and a major cause of hospital admissions in young children, resulting in a substantial burden on health-care services. About 45% of hospital admissions and in-hospital deaths due to RSV-ALRI occur in children younger than 6 months. An effective maternal RSV vaccine or monoclonal antibody could have a substantial effect on disease burden in this age group., Funding: The Bill & Melinda Gates Foundation., (Copyright © 2017 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 license. Published by Elsevier Ltd.. All rights reserved.)

An outbreak of Ebola virus disease (EVD) in Liberia began in March 2014 and ended in January 2016. Epidemiological information on the EVD cases was collected and managed nationally; however, collection and management of the data were challenging at the time because surveillance and reporting systems malfunctioned during the outbreak. EVD diagnostic laboratories, however, were able to register basic demographic and clinical information of patients more systematically. Here we present data on 16,370 laboratory samples that were tested between April 4, 2014 and March 29, 2015. A total of 10,536 traceable individuals were identified, of whom 3,897 were confirmed cases (positive for Ebola virus RNA). There were significant differences in sex, age, and place of residence between confirmed and suspected cases that tested negative for Ebola virus RNA. Age (young children and the elderly) and place of residence (rural areas) were the risk factors for death due to the disease. The case fatality rate of confirmed cases decreased from 80% to 63% during the study period. These findings may help support future investigations and lead to a fuller understanding of the outbreak in Liberia.

Background: Estimation of the incidences of influenza and respiratory syncytial virus (RSV) infection is important for disease control. Previous estimate in the city showed a substantial burden of influenza in both outpatients and inpatients while it did not account for individuals who do not seek medical attention nor RSV., Patients/methods: A total of 17 674 influenza-like illness (ILI) and 13 242 severe acute respiratory illness (SARI) cases were recruited, and samples were collected from 6267 and 2962 of ILI and SARI cases, respectively. RT-PCR assays were performed to detect influenza and RSV in the samples. A health-seeking behavior survey was conducted from February 2014 to April 2014 to estimate the fraction of infected individuals who did not seek medical attention between rainy and dry season., Results: Average influenza and RSV incidence rates in outpatients were 1.6 and 1.4 per 1000 individuals, respectively, and the highest incidence rate for both viruses was found in the of 6-23 month age group. Average influenza and RSV hospitalization incidence rates were 1.7 and 1.9 per 1000 individuals, respectively. Further, we estimated that the incidence rates of influenza and RSV in individuals who did not seek medical attention were threefold and 1.6-fold those in the medically attended population., Conclusions: Respiratory syncytial virus and influenza pose a substantial disease burden, particularly in hospitalized cases. The implementation of either a community-based approach or an enhanced surveillance system in combination with a community survey will allow a better understanding of the disease burdens of RSV and influenza in the Philippines., (© 2017 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.)

Sewage samples have been investigated to study the norovirus concentrations in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for 3 years, 2013 to 2016. We performed cross-correlation analysis of the concentrations of norovirus GI or GII in sewage samples collected weekly and the reported number of gastroenteritis cases. Norovirus genotypes in sewage were also analyzed by pyrosequencing and compared with those identified in stool samples. The cross-correlation analysis found the peak coefficient ( R = 0.51) at a lag of zero, indicating that the variation in the GII concentration, expressed as the log 10 number of copies per milliliter, was coincident with that in the gastroenteritis cases. A total of 15 norovirus genotypes and up to 8 genotypes per sample were detected in sewage, which included all of the 13 genotypes identified in the stool samples except 2. GII.4 was most frequently detected in both sample types, followed by GII.17. Phylogenetic analysis revealed that a strain belonging to the GII.17 Kawasaki 2014 lineage had been introduced into the study area in the 2012-2013 season. An increase in GI.3 cases was observed in the 2015-2016 season, and sewage monitoring identified the presence of GI.3 in the previous season (2014-2015). Our results demonstrated that monitoring of noroviruses in sewage is useful for sensitive detection of epidemic variants in human populations. IMPORTANCE We obtained statistical evidence of the relationship between the variation in the norovirus GII concentration in sewage and that of gastroenteritis cases during the 3-year study period. Sewage sample analysis by a pyrosequencing approach enabled us to understand the temporal variation in the norovirus genotypes circulating in human populations. We found that a strain closely related to the GII.17 Kawasaki 2014 lineage had been introduced into the study area at least 1 year before its appearance and identification in clinical cases. A similar pattern was observed for GI.3; cases were reported in the 2015-2016 season, and closely related strains were found in sewage in the previous season. Our observation indicates that monitoring of noroviruses in sewage is useful for the rapid detection of an epidemic and is also sensitive enough to study the molecular epidemiology of noroviruses. Applying this approach to other enteric pathogens in sewage will enhance our understanding of their ecology., (Copyright © 2017 American Society for Microbiology.)

Although there have been many epidemiological reports of the inter-country transmission of measles, systematic analysis of the global transmission dynamics of the measles virus (MV) is limited. In this study, we applied phylogeographic analysis to characterize the global transmission dynamics of the MV using large-scale genetic sequence data (obtained for 7456 sequences) from 115 countries between 1954 and 2015. These analyses reveal the spatial and temporal characteristics of global transmission of the virus, especially in Australia, China, India, Japan, the UK, and the USA in the period since 1990. The transmission is frequently observed, not only within the same region but also among distant and frequently visited areas. Frequencies of export from measles-endemic countries, such as China, India, and Japan are high but decreasing, while the frequencies from countries where measles is no longer endemic, such as Australia, the UK, and the USA, are low but slightly increasing. The world is heading toward measles eradication, but the disease is still transmitted regionally and globally. Our analysis reveals that countries wherein measles is endemic and those having eliminated the disease (apart from occasional outbreaks) both remain a source of global transmission in this measles elimination era. It is therefore crucial to maintain vigilance in efforts to monitor and eradicate measles globally.

Background: The clinical effectiveness of monovalent influenza A(H1N1)pdm09 vaccines has not been comprehensively summarised. We undertook a systematic review and meta-analysis to assess vaccine effectiveness (VE) for adjuvanted and unadjuvanted vaccines., Methods: We searched healthcare databases and grey literature from 11 June 2009 to 12 November 2014. Two researchers independently assessed titles and abstracts to identify studies for full review. Random effects meta-analyses estimated the pooled effect size of vaccination compared to placebo or no vaccination for crude and adjusted odds ratios (OR) to prevent laboratory confirmed influenza illness (LCI) and related hospitalization. VE was calculated as (1-pooled OR)∗100. Narrative synthesis was undertaken where meta-analysis was not possible., Results: We identified 9229 studies of which 38 at moderate risk of bias met protocol eligibility criteria; 23 were suitable for meta-analysis. Pooled adjusted VE against LCI with adjuvanted and unadjuvanted vaccines both reached statistical significance (adjuvanted: VE=80%; 95% confidence interval [CI] 59-90%; unadjuvanted: VE=66%; 95% CI 47-78%); in planned secondary analyses, VE in adults often failed to reach statistical significance and pooled point estimates were lower than observed in children. Overall pooled adjusted VE against hospitalization was 61% (95% CI 14-82%); in planned secondary analyses, adjusted VE attained statistical significance in adults aged 18-64years and children for adjuvanted vaccines. Adjuvanted vaccines were significantly more effective in children compared to adults for both outcomes., Conclusions: Adjuvanted and unadjuvanted monovalent influenza A(H1N1)pdm09 vaccines were both effective in preventing LCI. Overall, the vaccines were also effective against influenza-related hospitalization. For both outcomes adjuvanted vaccines were more effective in children than in adults., (Copyright © 2017. Published by Elsevier Ltd.)

Introduction: The seasonality of influenza and respiratory syncytial virus (RSV) is well known, and many analyses have been conducted in temperate countries; however, this is still not well understood in tropical countries. Previous studies suggest that climate factors are involved in the seasonality of these viruses. However, the extent of the effect of each climate variable is yet to be defined., Materials and Methods: We investigated the pattern of seasonality and the effect of climate variables on influenza and RSV at three sites of different latitudes: the Eastern Visayas region and Baguio City in the Philippines, and Okinawa Prefecture in Japan. Wavelet analysis and the dynamic linear regression model were applied. Climate variables used in the analysis included mean temperature, relative and specific humidity, precipitation, and number of rainy days. The Akaike Information Criterion estimated in each model was used to test the improvement of fit in comparison with the baseline model., Results: At all three study sites, annual seasonal peaks were observed in influenza A and RSV; peaks were unclear for influenza B. Ranges of climate variables at the two Philippine sites were narrower and mean variables were significantly different among the three sites. Whereas all climate variables except the number of rainy days improved model fit to the local trend model, their contributions were modest. Mean temperature and specific humidity were positively associated with influenza and RSV at the Philippine sites and negatively associated with influenza A in Okinawa. Precipitation also improved model fit for influenza and RSV at both Philippine sites, except for the influenza A model in the Eastern Visayas., Conclusions: Annual seasonal peaks were observed for influenza A and RSV but were less clear for influenza B at all three study sites. Including additional data from subsequent more years would help to ascertain these findings. Annual amplitude and variation in climate variables are more important than their absolute values for determining their effect on the seasonality of influenza and RSV., Competing Interests: The authors have declared that no competing interests exist.

In recent years, emerging infectious diseases such as Ebola virus disease (EVD) and se- vere acute respiratory syndrome (SARS) have been an issue of global concern. With global- ization, the risk of emergence of new diseases is increasing since humans have more chan- ces to be exposed to new pathogens. Also, the risk of international spread of infectious diseases is increasing because of increased international travel. International organizations including World Health Organization have been trying to establish better global systenM to respond to emerging infectious diseases. But SARS outbreak in 2003 and EVD outbreak in West Africa in 2014 highlighted that the current global system is still not fully functioning. The risk of emerging infectious diseases also exists in Japan. It is urgent to strengthen ca- pacity to detect and respond to such outbreaks in Japan.

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics., Competing Interests: The authors declare no conflict of interest.

Introduction: Typhoon Yolanda (Haiyan) hit the central part of the Philippines on November 8, 2013. To identify possible outbreaks of communicable diseases after the typhoon, nasopharyngeal swabs, stool and blood samples were collected from patients who visited the Eastern Visayas Regional Medical Center due to acute respiratory infection (ARI), acute gastroenteritis (AGE) or other febrile illness (OFI) including suspected dengue fever, between November 28, 2013 and February 5, 2014.   Methods: Samples were tested on-site for selected pathogens using rapid diagnostic tests. Confirmation and further analysis were conducted at the Research Institute for Tropical Medicine (RITM) in Manila using polymerase chain reaction (PCR) and sequencing. Residues of the rapid diagnostic tests and samples collected in the filter papers (FTATM card) were transported to Manila under suboptimal conditions. PCR results were compared between the kit residues and the filter papers.   Results: A total of 185 samples were collected. Of these, 128 cases were ARI, 17 cases were AGE and 40 cases were OFI. For nasopharyngeal swab samples, detection rates for enterovirus and rhinovirus residues were higher than the filter papers. For stool samples, rotavirus positive rate for the filter paper was higher than the kit residues. We also managed to obtain the sequence data from some of the kit residues and filter papers.   Discussion: Our results confirmed the importance of PCR for the laboratory diagnosis of infectious diseases in post-disaster situations when  diagnostic options are limited.

Background: Seasonal influenza causes annual epidemics by the accumulation of antigenic changes. Pandemic influenza occurs through a major antigenic change of the influenza A virus, which can originate from other hosts. Although new antigenic variants of the influenza A virus replace formerly circulating seasonal and pandemic viruses, replacement mechanisms remain poorly understood., Methods: A stochastic individual-based SEIR (susceptible-exposed-infectious-recovered) model with two viral strains (formerly circulating old strain and newly emerged strain) was developed for simulations to elucidate the replacement mechanisms., Results: Factors and conditions of virus and host populations affecting the replacement were identified. Replacement is more likely to occur in tropical regions than temperate regions. The magnitude of the ongoing epidemic by the old strain, herd immunity against the old strain, and timing of appearance of the new strain are not that important for replacement. It is probable that the frequency of replacement by a pandemic virus is higher than a seasonal virus because of the high initial susceptibility and high basic reproductive number of the pandemic virus., Conclusions: The findings of this study on replacement mechanisms could lead to a better understanding of virus transmission dynamics and may possibly be helpful in establishing an effective strategy to mitigate the impact of seasonal and pandemic influenza., (Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Since influenza C virus was first isolated in 1947, the virus has been only occasionally isolated by cell culture; there are only four strains for which complete genome sequences are registered. Here, we analyzed a total of 106 complete genomes, ranging from the first isolate from 1947 to recent isolates from 2014, to determine the genetic lineages of influenza C virus, the reassortment events, and the rates of nucleotide substitution. The results showed that there are six lineages, named C/Taylor, C/Mississippi, C/Aichi, C/Yamagata, C/Kanagawa, and C/Sao Paulo. They contain both antigenic and genetic lineages of the hemagglutinin-esterase (HE) gene, and the internal genes PB2, PB1, P3, NP, M, and NS are divided into two major lineages, a C/Mississippi/80-related lineage and a C/Yamagata/81-related lineage. Reassortment events were found over the entire period of 68 years. Several outbreaks of influenza C virus between 1990 and 2014 in Japan consisted of reassortant viruses, suggesting that the genomic constellation is related to influenza C virus epidemics. The nucleotide sequences were highly homologous to each other. The minimum percent identity between viruses ranged from 91.1% for the HE gene to 96.1% for the M gene, and the rate of nucleotide substitution for the HE gene was the highest, at 5.20 × 10(-4) substitutions/site/year. These results indicate that reassortment is an important factor that increases the genetic diversity of influenza C virus, resulting in its ability to prevail in humans. IMPORTANCE Influenza C virus is a pathogen that causes acute respiratory illness in children and results in hospitalization of infants. We previously demonstrated (Y. Matsuzaki et al., J Clin Virol 61:87-93, 2014, http://dx.doi.org/10.1016/j.jcv.2014.06.017) that periodic epidemics of this virus occurred in Japan between 1996 and 2014 and that replacement of the dominant antigenic group occurred every several years as a result of selection by herd immunity. However, the antigenicity of the HE glycoprotein is highly stable, and antigenic drift has not occurred for at least 30 years. Here, we analyzed a total of 106 complete genomes spanning 68 years for the first time, and we found that influenza C viruses are circulating worldwide while undergoing reassortment as well as selection by herd immunity, resulting in an increased ability to prevail in humans. The results presented in this study contribute to the understanding of the evolution, including reassortment events, underlying influenza C virus epidemics., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Selecting the best quantitative PCR assay is essential to detect human norovirus genome effectively from clinical and environmental samples because no cell lines have been developed to propagate this virus. The real-time PCR methods for noroviruses GI (4 assays) and GII (3 assays) were evaluated using wastewater (n = 70) and norovirus-positive stool (n = 77) samples collected in Japan between 2012 and 2013. Standard quantitative PCR assays recommended by the U.S. Environmental Protection Agency, International Organization for Standardization, and Ministry of Health, Labour and Welfare, Japan, together with recently reported assays were included. Significant differences in positive rates and quantification cycles were observed by non-parametric analysis. The present study identifies the best assay for norovirus GI and GII to amplify norovirus genomes efficiently.

Background: Human respiratory syncytial virus (HRSV) is a leading viral etiologic agent of pediatric lower respiratory infections, including bronchiolitis and pneumonia. Two antigenic subgroups, HRSV-A and B, each contain several genotypes. While viral load may vary among HRSV genotypes and affect the clinical course of disease, data are scarce regarding the actual differences among genotypes. Therefore, this study estimated and compared viral load among NA1 and ON1 genotypes of HRSV-A and BA9 of HRSV-B. ON1 is a newly emerged genotype with a 72-nucleotide duplication in the G gene as observed previously with BA genotypes in HRSV-B., Findings: Children <5 years of age with an initial diagnosis of severe or very severe pneumonia at a hospital in the Philippines from September 2012 to December 2013 were enrolled. HRSV genotypes were determined and the viral load measured from nasopharyngeal swabs (NPS). The viral load of HRSV genotype NA1 were significantly higher than those of ON1 and BA9. Regression analysis showed that both genotype NA1 and younger age were significantly associated with high HRSV viral load., Conclusions: The viral load of NA1 was higher than that of ON1 and BA9 in NPS samples. HRSV genotypes may be associated with HRSV viral load. The reasons and clinical impacts of these differences in viral load among HRSV genotypes require further evaluation.

Since the initial discovery of RSV-A ON1 in Canada in 2010, ON1 has been reported worldwide, yet information regarding its clinical impact and severity has been controversial. To investigate the clinical relevance of RSV-A ON1,acute respiratory infection (ARI) cases enrolled to our population-based prospective pediatric ARI surveillance at Khanh Hoa General Hospital, Central Vietnam from January 2010 through December 2012 were studied. Clinical-epidemiological information and nasopharyngeal samples were collected. Multiplex PCR assays were performed for screening 13 respiratory viruses. RSV-positive samples were further tested for subgroups (A/B) and genotypes information by sequencing the G-glycoprotein 2nd hypervariable region. Statistical analysis was performed to evaluate the clinical-epidemiological characteristics of RSV-A ON1. A total of 1854 ARI cases were enrolled and 426 (23.0%) of them were RSV-positive. During the study period, RSV-A and B had been co-circulating. NA1 was the predominant RSV-A genotype until the appearance of ON1 in 2012. RSV-related ARI hospitalization incidence significantly increased after the emergence of ON1. Moreover, multivariate analysis revealed that risk of lower respiratory tract infection was 2.26 (95% CI: 1.37-3.72) times, and radiologically-confirmed pneumonia was 1.98 (95% CI: 1.01-3.87) times greater in ON1 compared to NA1 cases. Our result suggested that ON1 ARI cases were clinically more severe than NA1.

Human sapovirus has been shown to be one of the most important etiologies in pediatric patients with acute diarrhea. However, very limited data are available about the causative roles and epidemiology of sapovirus in community settings. A nested matched case-control study within a birth cohort study of acute diarrhea in a peri-urban community in Peru from 2007 to 2010 was conducted to investigate the attributable fraction (AF) and genetic diversity of sapovirus. By quantitative reverse transcription-real-time PCR (qPCR) sapovirus was detected in 12.4% (37/299) of diarrheal and 5.7% (17/300) of nondiarrheal stools (P = 0.004). The sapovirus AF (7.1%) was higher in the second year (13.2%) than in the first year (1.4%) of life of children. Ten known genotypes and one novel cluster (n = 5) within four genogroups (GI, GII, GIV, and GV) were identified by phylogenetic analysis of a partial VP1 gene. Further sequence analysis of the full VP1 gene revealed a possible novel genotype, tentatively named GII.8. Notably, symptomatic reinfections with different genotypes within the same (n = 3) or different (n = 5) genogroups were observed in eight children. Sapovirus exhibited a high attributable burden for acute gastroenteritis, especially in the second year of life, of children in a Peruvian community. Further large-scale studies are needed to understand better the global burden, genetic diversity, and repeated infections of sapovirus., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

During 2011-2013, a nationwide outbreak of chikungunya virus infection occurred in the Philippines. The Asian genotype was identified as the predominant genotype; sporadic cases of the East/Central/South African genotype were detected in Mindanao. Further monitoring is needed to define the transmission pattern of this virus in the Philippines.

The local and global transmission dynamics of influenza B virus is not completely understood mainly because of limited epidemiological and sequence data for influenza B virus. Here we report epidemiological and molecular characteristics of influenza B viruses from 2010 to 2013 in Leyte Island, Philippines. Phylogenetic analyses showed global dissemination of the virus among both neighboring and distant areas. The analyses also suggest that southeast Asia is not a distributor of influenza B virus and can introduce the virus from other areas. Furthermore, we found evidence on the local persistence of the virus over years in the Philippines. Taken together, both local persistence and global dissemination play a significant role in the circulation of influenza B virus., (Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.)

Unlabelled: The Epstein-Barr virus (EBV) is etiologically linked to approximately 10% of gastric cancers, in which viral genomes are maintained as multicopy episomes. EBV-positive gastric cancer cells are incompetent for progeny virus production, making viral DNA cloning extremely difficult. Here we describe a highly efficient strategy for obtaining bacterial artificial chromosome (BAC) clones of EBV episomes by utilizing a CRISPR/Cas9-mediated strand break of the viral genome and subsequent homology-directed repair. EBV strains maintained in two gastric cancer cell lines (SNU719 and YCCEL1) were cloned, and their complete viral genome sequences were determined. Infectious viruses of gastric cancer cell-derived EBVs were reconstituted, and the viruses established stable latent infections in immortalized keratinocytes. While Ras oncoprotein overexpression caused massive vacuolar degeneration and cell death in control keratinocytes, EBV-infected keratinocytes survived in the presence of Ras expression. These results implicate EBV infection in predisposing epithelial cells to malignant transformation by inducing resistance to oncogene-induced cell death., Importance: Recent progress in DNA-sequencing technology has accelerated EBV whole-genome sequencing, and the repertoire of sequenced EBV genomes is increasing progressively. Accordingly, the presence of EBV variant strains that may be relevant to EBV-associated diseases has begun to attract interest. Clearly, the determination of additional disease-associated viral genome sequences will facilitate the identification of any disease-specific EBV variants. We found that CRISPR/Cas9-mediated cleavage of EBV episomal DNA enabled the cloning of disease-associated viral strains with unprecedented efficiency. As a proof of concept, two gastric cancer cell-derived EBV strains were cloned, and the infection of epithelial cells with reconstituted viruses provided important clues about the mechanism of EBV-mediated epithelial carcinogenesis. This experimental system should contribute to establishing the relationship between viral genome variation and EBV-associated diseases., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Norovirus is a leading etiological agent of viral gastroenteritis. Because of relatively mild disease symptoms and frequent asymptomatic infections, information on the ecology of this virus is limited. Our objective was to examine the genetic diversity of norovirus circulating in the human population by means of genotyping the virus in municipal wastewater. We investigated norovirus genogroups I and II (GI and GII) in municipal wastewater in Japan by pyrosequencing and quantitative PCR (qPCR) from November 2012 to March 2013. Virological surveillance for gastroenteritis cases was concurrently conducted in the same area. A total of fourteen distinct genotypes in total (GI.1, 3, 4, 6, 7, GII.2, 4, 5, 6, 7, 12, 13, 14, and 17), with up to eight genotypes detected per sample, were observed in wastewater using pyrosequencing; only four genotypes (GI.6, GII.4, 5, and 14) were obtained from clinical samples. Seventy-eight percent of norovirus-positive stool samples contained GII.4, but this genotype was not dominant in wastewater. The norovirus GII.4 Sydney 2012 variant, which appeared and spread during our study period, was detected in both the wastewater and clinical samples. These results suggest that an environmental approach using pyrosequencing yields a more detailed distribution of norovirus genotypes/variants. Thus, wastewater monitoring by pyrosequencing is expected to provide an effective analysis of the distribution of norovirus genotypes causing symptomatic and asymptomatic infections in human populations., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Rabies is endemic in the Philippines and dog bites are a major cause of rabies cases in humans. The rabies control program has not been successful in eliminating rabies because of low vaccination coverage among dogs. Therefore, more effective and feasible strategies for rabies control are urgently required in the country. To control rabies, it is very important to know if inter-island transmission can occur because rabies can become endemic once the virus is introduced in areas that previously had no reported cases. Our molecular epidemiological study suggests that inter-island transmission events can occur; therefore, we further investigated these inter-island transmission using phylogenetic and modeling approaches. We investigate inter-island transmission between Luzon and Tablas Islands in the Philippines. Phylogenetic analysis and mathematical modeling demonstrate that there was a time lag of several months to a year from rabies introduction to initial case detection, indicating the difficulties in recognizing the initial rabies introductory event. There had been no rabies cases reported in Tablas Island; however, transmission chain was sustained on this island after the introduction of rabies virus because of low vaccination coverage among dogs. Across the islands, a rabies control program should include control of inter-island dog transportation and rabies vaccination to avoid viral introduction from the outside and to break transmission chains after viral introduction. However, this program has not yet been completely implemented and transmission chains following inter-island virus transmission are still observed. Local government units try to control dog transport; however, it should be more strictly controlled, and a continuous rabies control program should be implemented to prevent rabies spread even in rabies-free areas., (Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)

Background: Pregnant women and infants under 6 months are at risk of influenza-related complications. Limited information exists on their community burden of respiratory viruses., Methods and Findings: This prospective, observational open cohort study was conducted in Baganuur district, Ulaanbaatar, Mongolia during 2013/14 and 2014/15 influenza seasons. Influenza-like illness (ILI) and severe acute respiratory infection (sARI) were identified by follow-up calls twice a week. For those identified, influenza and respiratory syncytical virus (RSV) were tested by point-of-care test kits. We calculated overall and stratified (by trimester or age group) incidence rates (IR) and used Cox proportional hazard regression for risk factor analyses. Among 1260 unvaccinated pregnant women enrolled, overall IRs for ILI, sARI and influenza A were 11.8 (95% confidence interval (C.I):11.2-12.4), 0.1 (95%C.I:0.0-0.4), and 1.7 (95%C.I:1.5-1.9) per 1,000person-days, respectively. One sARI case was influenza A positive. IRs and adjusted hazard ratios (Adj.HR) for ILI and influenza A were lowest in the third trimester. Those with co-morbidity were 1.4 times more likely to develop ILI [Adj.HR:1.4 (95%C.I:1.1-1.9)]. Among 1304 infants enrolled, overall ILI and sARI IRs were 15.2 (95%C.I:14.5-15.8) and 20.5 (95%C.I:19.7-21.3) per 1,000person-days, respectively. From the tested ILI (77.6%) and sARI (30.6%) cases, the overall positivity rates were 6.3% (influenza A), 1.1% (influenza B) and 9.3% (RSV). Positivity rates of influenza A and RSV tend to increase with age. sARI cases were 1.4 times more likely to be male [Adj.HR:1.4 (95%C.I:1.1-1.8)]. Among all influenza A and RSV positive infants, 11.8% and 68.0% were respectively identified among sARI hospitalized cases., Conclusion: We observed low overall influenza A burden in both groups, though underestimation was likely due to point-of-care tests used. For infants, RSV burden was more significant than influenza A. These findings would be useful for establishing control strategies for both viruses in Mongolia.

Introduction: Pregnant and postpartum women are especially vulnerable to natural disasters. These women suffer from increased risk of physical and mental issues including pregnant related problems. Typhoon Haiyan (Yolanda), which hit the Philippines affected a large number of people and caused devastating damages. During and after the typhoon, pregnant women were forced to live in particularly difficult circumstances. The purpose of this study was to determine concerns and problems regarding public health needs and coping mechanisms among pregnant women during and shortly after the typhoon., Methods: This study employed a cross-sectional design utilizing focus group discussions (FGDs). Participants were 53 women (mean age: 26.6 years old; 42 had children) from four affected communities who were pregnant at the time of the typhoon. FGDs were conducted 4 months after the typhoon, from March 19 to 28, 2014, using semi-structured interviews. Data were analyzed using the qualitative content analysis., Result: Three themes were identified regarding problems and concerns during and after the typhoon: 1) having no ideas what is going to happen during the evacuation, 2) lacking essentials to survive, and 3) being unsure of how to deal with health concerns. Two themes were identified as means of solving issues: 1) finding food for survival and 2) avoiding diseases to save my family. As the pregnant women already had several typhoon experiences without any major problems, they underestimated the catastrophic nature of this typhoon. During the typhoon, the women could not ensure their safety and did not have a strong sense of crisis management. They suffered from hunger, food shortage, and poor sanitation. Moreover, though the women had fear and anxiety regarding their pregnancy, they had no way to resolve these concerns. Pregnant women and their families also suffered from common health problems for which they would usually seek medical services. Under such conditions, the pregnant woman cooperated with others for survival and used their knowledge of disease prevention., Discussion: Pregnant women experienced difficulties with evacuation, a lack of minimum survival needs, and attending to their own health issues. Pregnant women were also concerned about needs and health issues of their families, particular, when they had small children. Collecting accurate information regarding the disaster and conducting self-sustainable preparation prior to the disaster among pregnant women will help them to protect their pregnancy status, thereby improving their families' chance of survival during and after disasters.

The lack of vaccine and limited antiviral options against respiratory syncytial virus (RSV) highlights the need for novel therapeutic strategies. One alternative is to develop drugs that target host factors required for viral replication. Several microarray and proteomics studies had been published to identify possible host factors that are affected during RSV replication. In order to obtain a comprehensive understanding of RSV-host interaction, we integrated available proteome and transcriptome datasets and used it to construct a virus-host interaction network. Then, we interrogated the network to identify host factors that are targeted by the virus and we searched for drugs from the DrugBank database that interact with these host factors, which may have potential applications in repositioning for future treatment options of RSV infection.

Human respiratory syncytial virus (HRSV) is a major cause of acute lower respiratory tract infections in infants and children worldwide. We performed molecular analysis of HRSV among infants and children with clinical diagnosis of severe pneumonia in four study sites in the Philippines, including Biliran, Leyte, Palawan, and Metro Manila from June 2012 to July 2013. Nasopharyngeal swabs were collected and screened for HRSV using real-time polymerase chain reaction (PCR). Positive samples were tested by conventional PCR and sequenced for the second hypervariable region (2nd HVR) of the G gene. Among a total of 1,505 samples, 423 samples were positive for HRSV (28.1%), of which 305 (72.1%) and 118 (27.9%) were identified as HRSV-A and HRSV-B, respectively. Two genotypes of HRSV-A, NA1 and ON1, were identified during the study period. The novel ON1 genotype with a 72-nucleotide duplication in 2nd HVR of the G gene increased rapidly and finally became the predominant genotype in 2013 with an evolutionary rate higher than the NA1 genotype. Moreover, in the ON1 genotype, we found positive selection at amino acid position 274 (p<0.05) and massive O- and N-glycosylation in the 2nd HVR of the G gene. Among HRSV-B, BA9 was the predominant genotype circulating in the Philippines. However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains. These findings suggest that HRSV is an important cause of severe acute respiratory infection among children in the Philippines and revealed the emergence and subsequent predominance of the ON1 genotype and the sporadic detection of the GB2 genotype. Both genotypes were detected for the first time in the Philippines.

Infection due to the Middle East respiratory syndrome coronavirus (MERS-CoV) is widespread. The present study was performed to assess the protocols used for the molecular diagnosis of MERS-CoV by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern Asia in 2015. Although the diagnostic protocols were established only 2 years ago, mismatches between the sequences of primers/probes and viruses were found for several of the assays. Such mismatches could lead to a lower sensitivity of the assay, thereby leading to false-negative diagnosis. A slight modification in the primer design is suggested. Protocols for the molecular diagnosis of viral infections should be reviewed regularly after they are established, particularly for viruses that pose a great threat to public health such as MERS-CoV., (Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Malaria is a major health problem in many developing countries including Indonesia. The purpose of this study was to investigate the socio-demographic characteristics and geographic distribution of malaria cases in Bangka District, Bangka-Belitung Island Province, Indonesia. Bangka District is a malaria endemic area of Indonesia. We analyzed the epidemiological data of all reported malaria cases during 2008-2012 in Bangka District. Of the 4,756 malaria-confirmed cases reported during the study period, 3,234 (68. 0%) were among persons aged ≥ 15 years, 1,024 (21.5%) were among persons aged 5-14 years and 498 (10.5%) were among persons aged < 5 years. Malaria cases were primarily located along the sea coast and less frequently in inland. Malaria cases were found not only among the local population but also among migrant workers. The monthly incidence of reported malaria cases in the study population ranged from 0.06 to 1.06 per 1,000 person-months. The cases were mostly due to Plasmodium vivax (57.1%) followed by Plasmodiumfalciparum (40.2%). Plasmodiumfalciparum was more common among migrant workers while Plasmodium vivax was more common among the local population (Odds ratio 1.2; p = 0.03). The main transmission vector found in the coastal area was Anopheles sundaicus. An. letifer and An. barbirostris were found inland. We identified "malaria hot-spots" in the study area using a Geographic Information System. The results of this study will contribute to the malaria control program.

Background: Households are one of the major settings of influenza transmission in the community and transmission is frequently initiated by school-aged children. We surveyed households with primary school (PS) and/ or junior high school (JH) children for the 2012-13 influenza season in Odate, Japan then characterized the epidemiology of influenza household transmission as well as estimated the serial intervals., Methods: We delivered a self-reported questionnaire survey to households with PS and/or JH school children in Odate City, Japan. Influenza A (H3N2) virus predominantly circulated during the 2012-13 influenza season. We investigated the epidemiological characteristics of within-household transmission and calculated the serial intervals (SI). SIs were drew by a non-parametric model and compared with parametric models by the Akaike Information Criterion. The covariable contributions were investigated by the accelerated failure model., Results: Household influenza transmission was identified in 255 out of 363 household respondents. Primary school (PS) children accounted for 45.1 % of primary cases, and disease transmission was most commonly observed between PS children and parents, followed by transmission from PS children to siblings. In primary cases of PS or JH children, younger age and longer absence from school were significantly associated with household transmission events. The mean SI was estimated as 2.8 days (95 % confidence interval 2.6-3.0 days) in the lognormal model. The estimated acceleration factors revealed that while secondary school age and the absence duration > 7 days were associated with shorter and longer SIs, respectively, antiviral prescriptions for primary cases made no contribution., Conclusions: High frequencies of household transmission from primary school with shorter SI were found. These findings contribute to the development of future mitigation strategies against influenza transmission in Japan.

Background: Human sapovirus (SaV) is a causative agent of acute gastroenteritis. Recently, SaV detection has been increasing worldwide due to the emerging SaV genotype I.2. However, SaV infection has not been reported in the Philippines., Objectives: To evaluate the prevalence and genetic diversity of SaV in hospitalized children aged less than 5 years with acute gastroenteritis., Study Design: Stool samples were collected from children with acute gastroenteritis at three hospitals in the Philippines from June 2012 to August 2013. SaV was detected by reverse transcription real-time PCR, and the polymerase and capsid gene sequences were analyzed. Full genome sequencing and recombination analysis were performed on possible recombinant viruses., Results: SaV was detected in 7.0% of the tested stool samples (29/417). In 10 SaV-positive cases, other viruses were also detected, including rotavirus (n=6), norovirus (n=2), and human astrovirus (n=2). Four known SaV genotypes (GI.1 [7], GI.2 [2], GII.1 [12], and GV [2]) and one novel recombinant (n=3) were identified by polymerase and capsid gene sequence analysis. Full genome sequencing revealed that the 5' nontranslated region (NTR) and nonstructural protein region of the novel recombinant were closely related to the GII.1 Bristol/98/UK variant, whereas the structural protein region and 3' NTR were closely related to the GII.4 Kumamoto6/Mar2003/JPN variant., Discussion and Conclusions: SaV was regularly detected in hospitalized children due to acute gastroenteritis during the study period. A novel recombinant, SaV GII.1/GII.4, was identified in three cases at two different study sites., (Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.)