Publications (35)90.99 Total impact
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Article: Genetic characterization of human respiratory syncytial virus detected in hospitalized children in the Philippines from 2008 to 2012.
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ABSTRACT: BACKGROUND: Human respiratory syncytial virus (HRSV) is the leading cause of acute lower respiratory tract infection in infants and young children. However, molecular characteristic of HRSV is still unknown in the Philippines. OBJECTIVE: To describe the molecular epidemiology of circulating HRSV detected in the Philippines. STUDY DESIGN: From May 2008 to April 2012, nasopharyngeal swabs were collected from infants and children aged between 7 days and 14 years who were hospitalized with severe pneumonia. HRSV was detected by nested PCR targeting M2 gene, and C-terminus of the G gene was sequenced for phylogenetic analysis. RESULT: Out of total 2150 samples, 19.3% (n=415) were positive for HRSV, and 65.0% of them (n=270) were identified as HRSV-A and 35.0% (n=145) as HRSV-B. There were two major HRSV outbreaks: between June 2008 and February 2009, and between June and March 2012. Majority of HRSV strains detected during the former outbreak were HRSV-A (97.5%, 203/208) whereas during the later outbreak, both HRSV-A (54/158, 34.2%) and HRSV-B (104/158, 65.8%) were detected. All HRSV-A strains were classified as genotype NA1 and all HRSV-B as genotype BA, which had 60-nucleotide duplication in secondary hypervariable region of the G gene. Among HRSV-B positive samples, there were 2 distinct clusters with unique amino acid changes and low homology in compared to other strains in BA, suggesting emergence of new variant of HRSV-B. CONCLUSION: The study provides an overview of the genetic variation in circulating HRSV viruses in the Philippines along with identification of possibly a novel variant of HRSV-B.Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology 01/2013; · 3.12 Impact Factor -
Article: Respiratory viruses from hospitalized children with severe pneumonia in the Philippines.
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ABSTRACT: BACKGROUND: Pneumonia remains a leading cause of child death in developing countries. The viruses in severe pneumonia remain poorly defined. METHODS: The study was conducted at the Eastern Visayas Regional Medical Center in Tacloban City, Philippines from May 2008 to May 2009. Patients aged 8 days to 13 years old who were admitted to the Department of Pediatrics with severe pneumonia were enrolled for the study. Upon admission, polymerase chain reaction was performed using nasopharyngeal swabs and blood cultures to detect respiratory viruses and bacteria, respectively. Result Among the 819 patients enrolled, at least one virus was detected in 501 cases (61.2%). In addition, 423 cases were positive for a single virus while bacteria were detected in the blood culture sample of 31 cases. The most commonly detected viruses were human rhinoviruses (n = 189), including types A (n = 103), B (n = 17), and C (n = 69,), and respiratory syncytial virus (RSV) (n = 165). Novel viruses such as human metapneumovirus, human coronavirus NL63, human bocavirus, and human polyomaviruses WU and KI were also detected. There were 70 deaths, and one or more viruses were detected in 35 (50%) of these cases. Positivity only for influenza A virus (OR = 4.3, 95% CI = 1.3-14.6) was significantly associated with fatal outcome. From the blood culture, Burkholderia cepacia group (n = 9), Streptococcus pneumoniae (n = 4), Staphylococcus aureus (n = 4), Haemophilus influenzae (n = 1), and Salmonella C1 (n = 1) were also isolated. CONCLUSION: Viruses were commonly detected in children with severe pneumonia in the Philippines. Hence, viral etiologies should be considered while developing better effective strategies to reduce child pneumonia-related deaths in developing countries.BMC Infectious Diseases 10/2012; 12(1):267. · 3.12 Impact Factor -
Article: Detection and serotyping of human adenoviruses from patients with influenza-like illness in mongolia.
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ABSTRACT: Human adenoviruses (HAdVs) are responsible for approximately 5%-10% of acute respiratory infections. The serotypes of commonly detected respiratory HAdV in Asian countries are diverse. However, there are no well-documented reports of circulating HAdV serotypes in Mongolia. Between January 2010 and May 2011, 1,950 influenza-negative samples from patients with influenza-like illness, including eye swabs from patients with eye symptoms, were screened for HAdV, and 40 samples (2.1%) were positive for HAdVs. Among these 40 samples, 31 samples were positive for the hexon gene used in phylogenetic analysis, as determined by PCR. We identified 7 different serotypes. We constructed the phylogenetic trees of HAdV-B7 and HAdV-B3, the 2 most commonly detected serotypes in this study. All detected HAdV-B7 and -B3 Mongolian strains had identical sequences. HAdV-D8, known to be associated with epidemic keratoconjunctivitis (EKC), was detected from nasopharyngeal and eye swabs. There was no difference between the amino acid sequences of the hexon and fiber genes that may affect tissue tropism in Mongolian strains and those in EKC-causing strains.Japanese journal of infectious diseases. 07/2012; 65(4):289-94. -
Article: Genetic diversity and molecular characterization of enteroviruses from sewage-polluted urban and rural rivers in the Philippines.
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ABSTRACT: Despite the vast distribution and expansive diversity of enteroviruses reported globally, indicators defining a complete view of the epidemiology of enteroviruses in tropical countries such as the Philippines are yet to be established. Detection of enteroviruses in the environment has been one of the markers of circulating viruses in a community. This study aimed to bridge the gap in the epidemiology of enteroviruses in the Philippines by providing an overview of the occurrence of enteroviruses in both urban and rural rivers. Molecular detection directed at the VP1 region of the enterovirus genome was performed on 44 grab river water samples collected from April to December 2009. The majority of the enterovirus serotypes detected were clustered with human enterovirus C species (HEV-C; 21/42), followed by HEV-B (12/42) and HEV-A (9/42). Porcine enterovirus 9 was also found in 12 out of 44 water samples. Phylogenetic analysis indicated that the viruses detected were closely related, if not all forming a monophyletic clade, with those enteroviruses detected previously from acute flaccid paralysis cases in the country. The clustering of environmental and human enterovirus strains implies that the circulation of these strains were associated with river contamination. This study gives further evidence of the environmental persistence of enteroviruses once they are shed in feces and likewise, provides additional data which may help in understanding the epidemiology of enteroviruses in humans, highlighting the need for more studies on the potential public health risks linked with enteroviruses found in the environment and their eventual clinical consequences in the country.Virus Genes 06/2012; 45(2):207-17. · 1.85 Impact Factor -
Article: Detection of non-polio enteroviruses from 17 years of virological surveillance of acute flaccid paralysis in the Philippines.
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ABSTRACT: Acute flaccid paralysis (AFP) surveillance has been conducted as part of the World Health Organization (WHO) strategy on poliomyelitis eradication. Aside from poliovirus, which is the target pathogen, isolation, and identification of non-polio enteroviruses (NPEVs) is also done by neutralization test using pools of antisera which can only identify limited number of NPEVs. In the Philippines, despite the significant number of isolated NPEVs, no information is available with regard to its occurrence, diversity, and pattern of circulation. In this study, a total of 790 NPEVs isolated from stool samples submitted to the National Reference Laboratory from 1992 to 2008 were analyzed; neutralization test was able to type 55% (442) of the isolates. Of the remaining 356 isolates, which were untyped by using neutralization test, 348 isolates were analyzed further by RT-PCR targeting the VP1 gene. A total of 47 serotypes of NPEV strains were identified using neutralization test and molecular typing, including 28 serotypes of human enterovirus B (HEV-B), 12 serotypes of HEV-A, and 7 of HEV-C. The HEV-B group (625/790; 79%) constituted the largest proportion of isolates, followed by HEV-C (108/790; 13.7%), HEV-A (57/790; 7.2%), and no HEV-D. Coxsackievirus (CV) B, echovirus (E)6, E11, and E13 were the most frequent isolates. E6, E11, E13, E14, E25, E30, E33, CVA20, and CVA24 were considered as endemic strains, some NPEVs recurred and few serotypes existed only for 1-3 years during the study period. Despite some limitations in this study, plural NPEVs with multiple patterns of circulation in the Philippines for 17 years were identified.Journal of Medical Virology 04/2012; 84(4):624-31. · 2.82 Impact Factor -
Article: Cumulative incidence of pandemic influenza A (H1N1) 2009 by a community-based serological cohort study in Selenghe Province, Mongolia.
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ABSTRACT: Please cite this paper as: Burmaa et al. (2012) Cumulative incidence of pandemic influenza A (H1N1) 2009 by a community-based serological cohort study in Selenghe Province, Mongolia. Influenza and Other Respiratory Viruses 6(601), e97-e104. Background Large community outbreaks of pandemic A (H1N1) 2009 occurred between October and December 2009 in Mongolia. A serological study was conducted among the general population by testing paired sera collected before and after the first wave of pandemic in Selenghe province, Mongolia. None of the study participants had been vaccinated for pandemic A (H1N1) 2009 before the second samples were collected. Objective The objective of this study was to estimate cumulative incidence of pandemic A (H1N1) 2009 in different age-groups of Selenghe province residents. Methods After informed consent was obtained from apparently healthy volunteers, the paired sera and background information were collected. Antibody titers were measured using hemagglutinin inhibition (HI) and microneutralization (MN) assays for A/California/07/2009pdm. A fourfold rise in antibody titers was regarded as the evidence of infection. Results The overall cumulative incidences in the study group for all ages were 28·8% (76/264) by HI, 35·2% (93/264) by MN, and 25·0% (66/264) by both HI and MN. Cumulative incidences of infection varied among age-groups, with children aged 2-4 and 5-9 years having high cumulative incidence of infection. Overall cumulative incidences of infection in the whole population were estimated to be 23·0% (4946/21 460) by HI, 30·2% (6473/21 460) by MN, and 18·8% (4036/21 460) by both HI and MN. Conclusions This study indicates that about one-fourth of the total population in Selenghe province was infected with pandemic A (H1N1) 2009 virus during the first wave of the pandemic.Influenza and Other Respiratory Viruses 02/2012; 6(6):e97-e104. · 4.16 Impact Factor -
Article: Monitoring of influenza viruses in the aftermath of the great East Japan earthquake.
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ABSTRACT: Influenza has a significant impact on public health when a natural disaster occurs during the influenza season. However, the epidemiological characteristics of influenza following natural disasters have not been well documented due to the difficulty of implementing laboratory-based influenza surveillance in such situations. The Great East Japan Earthquake occurred on March 11, 2011, when influenza was already circulating. Since routine influenza surveillance was not performed in Miyagi Prefecture, we initiated an ad hoc laboratory-based monitoring system immediately after the earthquake. From March 15 to May 19, we tested 277 samples for influenza virus collected around Sendai City and from evacuation centers in Miyagi Prefecture. Influenza A (H3N2) was detected in 112 cases, influenza A (H1N1) 2009 in one case, and influenza B in 92 cases. The H3N2 virus was dominant until the 14th week. However, a sudden increase in the number of influenza B cases occurred after schools were reopened. According to phylogenetic analysis, a major clade switch of the H3N2 virus took place after the earthquake. The Yamagata lineage of influenza B was detected in one patient from western Japan, indicating the importing of viruses into the affected area.Japanese journal of infectious diseases. 01/2012; 65(6):542-4. -
Article: Influenza transmission in a community during a seasonal influenza A(H3N2) outbreak (2010-2011) in Mongolia: a community-based prospective cohort study.
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ABSTRACT: Knowledge of how influenza viruses spread in a community is important for planning and implementation of effective interventions, including social distancing measures. Households and schools are implicated as the major sites for influenza virus transmission. However, the overall picture of community transmission is not well defined during actual outbreaks. We conducted a community-based prospective cohort study to describe the transmission characteristics of influenza in Mongolia. A total of 5,655 residents in 1,343 households were included in this cohort study. An active search for cases of influenza-like illness (ILI) was performed between October 2010 and April 2011. Data collected during a community outbreak of influenza A(H3N2) were analyzed. Total 282 ILI cases occurred during this period, and 73% of the subjects were aged <15 years. The highest attack rate (20.4%) was in those aged 1-4 years, whereas the attack rate in those aged 5-9 years was 10.8%. Fifty-one secondary cases occurred among 900 household contacts from 43 households (43 index cases), giving an overall crude household secondary attack rate (SAR) of 5.7%. SAR was significantly higher in younger household contacts (relative risk for those aged <1 year: 9.90, 1-4 years: 5.59, and 5-9 years: 6.43). We analyzed the transmission patterns among households and a community and repeated transmissions were detected between households, preschools, and schools. Children aged 1-4 years played an important role in influenza transmission in households and in the community at large. Working-age adults were also a source of influenza in households, whereas elderly cases (aged ≥ 65 years) had no link with household transmission. Repeated transmissions between households, preschools, and schools were observed during an influenza A(H3N2) outbreak period in Mongolia, where subjects aged 1-4 years played an important role in influenza transmission.PLoS ONE 01/2012; 7(3):e33046. · 4.09 Impact Factor -
Article: Enterovirus 68 among children with severe acute respiratory infection, the Philippines.
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ABSTRACT: Enterovirus 68 (EV68) is a rare enterovirus associated with respiratory illness that, unlike other enteroviruses, has been identified only from respiratory specimens. We identified EV68 from respiratory specimens of children hospitalized with a diagnosis of severe pneumonia in Leyte, Republic of the Philippines. Twenty-one samples showed high similarity with EV68 by sequencing of 5' nontranslated region; 17 of these samples were confirmed as EV68 by sequencing of viral protein 1 capsid coding region. Most previously reported EV68 cases had been identified as sporadic cases. All 21 patients we identified had severe illness, and 2 died, possibly the first reported fatal cases associated with EV68 infection. Our study suggests that EV68 may be a possible causative agent of severe respiratory illnesses.Emerging Infectious Diseases 08/2011; 17(8):1430-5. · 6.79 Impact Factor -
Article: Interruption of the circulation of an indigenous measles genotype and the introduction of other genotypes after a mass vaccination campaign in the Philippines.
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ABSTRACT: Molecular analysis of measles viruses in the Philippines was conducted from 2000 to 2008. No confirmed measles cases were detected in the surveillance in 2005 after the mass vaccination campaign in 2004. However, a re-emergence of measles cases occurred in 2007, which was caused by other genotypes and the previous circulating genotype had disappeared.Journal of Medical Virology 08/2011; 83(8):1424-7. · 2.82 Impact Factor -
Article: Viruses that cross borders: factors responsible for global dissemination of viral infections.
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ABSTRACT: Pandemic viral infections as emerging infectious diseases are of a great global concern. However, for some viruses, particular strains are endemic to specific areas and can be genetically distinguished from strains in other regions. In contrast, for some other viruses, genetically similar strains can spread and circulate all over the world. This study addresses global dissemination of various viral infections. We classified 34 viruses as per their ability to cross borders by review. We also described factors responsible for and the dynamics of global dissemination. We examined biological characteristics of viruses, manners or routes of transmission, host responses and epidemiological factors. Factors required for viruses to cross borders include 'non-blood infection', 'short incubation period', 'short infectious period', 'frequent re-infection', 'small basic reproductive number (R(0))' and 'high annual incidence'. Knowing the factors responsible for global dissemination of pathogens is useful for controlling and/or containing both classic and emerging infectious diseases.Intervirology 01/2011; 54(5):246-52. · 2.34 Impact Factor -
Article: Detection of human rhinovirus C viral genome in blood among children with severe respiratory infections in the Philippines.
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ABSTRACT: Human rhinovirus (HRV) C was recently identified as the third species of HRV using a molecular technique. Infections caused by previously identified HRVs (A and B) are thought to be limited to the respiratory tract; however, pathogenesis of HRVC is still largely unknown. A total of 816 nasopharyngeal swabs from hospitalized children with severe respiratory infections in the Philippines (May 2008-May 2009) were tested for HRV by reverse transcription polymerase chain reaction (RT-PCR), and 243 samples (29.8%) were positive for HRV. Among these patients, serum samples were also tested to determine whether specific HRV species were associated with viremia. Only 30 serum samples (12.3%) were positive for HRV. However, the HRV positive rates were different among HRV species, 3% (4/135) for HRVA, 0% (0/25) for HRVB, and 31% (26/83) for HRVC, and were the highest on 2 days after the onset of symptoms. These results suggest that HRVC may have a different pathogenicity and can more commonly cause viremia than HRVA and HRVB. Serum positive rates for HRV are affected by age, i.e., higher positive rates for those aged 1 year or more. HRVC that were detected from serum exhibited the same level of sequence diversity as those positive only for nasopharyngeal samples in phylogenetic analysis. However, all HRVA which were detected from serum were clustered in a monophyletic clade based on their 5' non-coding region (NCR) sequences, which is closely related with a certain HRVC genotype (A2) in 5'-NCR. This finding suggests that the 5'NCR region may be associated with viremia.PLoS ONE 01/2011; 6(11):e27247. · 4.09 Impact Factor -
Article: Simplified screening method for detecting oseltamivir resistant pandemic influenza A (H1N1) 2009 virus by a RT-PCR/restriction fragment length polymorphism assay.
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ABSTRACT: The sudden emergence of the pandemic influenza A (H1N1) 2009 virus in early 2009 has resulted in a rapid transmission of this virus worldwide. Within a short time span, sporadic cases infected with this virus that shows oseltamivir resistance have also been reported. These resistant viruses have an amino acid change from histidine to tyrosine at position 275 (H275Y) of the neuraminidase gene. In this study, a reverse transcriptase PCR/restriction fragment length polymorphism (RT-PCR/RFLP) assay was developed to detect the H275Y mutation. Resistant and sensitive viruses could be differentiated using the RFLP patterns. This RT-PCR/RFLP assay is a simple method and also very specific and sensitive for detecting the H275Y mutation of pandemic influenza A (H1N1) 2009 viruses, and can be used in resource-limited settings.Journal of virological methods 12/2010; 170(1-2):165-8. · 2.13 Impact Factor -
Article: Comparison of selection pressures on the HA gene of pandemic (2009) and seasonal human and swine influenza A H1 subtype viruses.
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ABSTRACT: The 2009 human pandemic influenza (H1N1) virus possesses the HA gene of the H1 subtype. The evolutionary process of the 2009 H1N1 virus remains to be defined. We performed genetic analyses of the HA gene by comparing the 2009 H1N1 virus with seasonal human and swine viruses. We analyzed sequences of 116 2009 H1N1 viruses, and obtained 1457 seasonal H1N1, 365 swine H1, and 1332 2009 H1N1 viruses from the database. Selection pressure for the 2009 H1N1 virus was higher than that for the swine virus and equivalent to that for the seasonal virus. Positions 206 and 264 were found to be positively selected sites. We also identified sites under different selection pressures from the seasonal or swine virus that may be involved in imparting significant biological characteristics. The evolutionary characteristics of the H1 gene of the 2009 H1N1 virus differed from those of seasonal and swine viruses.Virology 09/2010; 405(2):314-21. · 3.35 Impact Factor -
Article: [Influenza infection].
Nippon rinsho. Japanese journal of clinical medicine 08/2010; 68 Suppl 8:531-4. -
Article: Differentiation of human influenza A viruses including the pandemic subtype H1N1/2009 by conventional multiplex PCR.
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ABSTRACT: April 2009 witnessed the emergence of a novel H1N1 influenza A virus infecting the human population. Currently, pandemic and seasonal influenza viruses are co-circulating in human populations. Understanding the course of the emerging pandemic virus is important. It is still unknown how the novel virus co-circulates with or outcompetes seasonal viruses. Sustainable and detailed influenza surveillance is required throughout the world including developing countries. In the present study, a multiplex PCR using four primers was developed, which was designed to differentiate the pandemic H1N1 virus from the seasonal H1N1 and H3N2 viruses, to obtain amplicons of different sizes. Multiplex PCR analysis could clearly differentiate the three subtypes of human influenza A virus. This assay was performed using 206 clinical samples collected in 2009 in Japan. Between February and April, four samples were subtyped as seasonal H1N1 and four as seasonal H3N2. All samples collected after July were subtyped as pandemic H1N1. Currently, pandemic viruses seem to have replaced seasonal viruses almost completely in Japan. This is a highly sensitive method and its cost is low. Influenza surveillance using this assay would provide significant information on the epidemiology of both pandemic and seasonal influenza.Journal of virological methods 05/2010; 168(1-2):94-7. · 2.13 Impact Factor -
Article: Detection of novel respiratory viruses from influenza-like illness in the Philippines.
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ABSTRACT: Several novel viruses have been recently identified in respiratory samples. However, the epidemiology of these viruses in tropical countries remains unclear. The aim of the present study was to provide an overview of the epidemiology of novel respiratory viruses, including human metapneumovirus, human bocavirus, new subtypes of human coronavirus (NL63 and HKU1), KI virus, WU virus, and Melaka virus in the Philippines, a tropical country. Nasopharyngeal aspirates from 465 patients with influenza-like illness were collected in 2006 and 2007. Reverse transcription polymerase chain reaction (RT-PCR) and PCR were performed to detect viruses from culture-negative specimens. Human metapneumovirus, human bocavirus, human coronavirus HKU1, KI virus, and WU virus were detected for the first time in the Philippines; Melaka virus was not found.Journal of Medical Virology 05/2010; 82(6):1071-4. · 2.82 Impact Factor -
Article: Reassortment between swine influenza A viruses increased their adaptation to humans in pandemic H1N1/09.
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ABSTRACT: In April 2009, pandemic H1N1/09 influenza, which originated from swine influenza, appeared in North America, and it has since spread globally among humans. It is important to know how swine influenza A virus broke the host barrier to cause a pandemic. We analyzed 673 strains of human, avian, and swine influenza viruses and assessed the internal genes PB2, PB1, PA, NP, M, and NS. Here we found accumulation of mutations in segments that were retained as well as introduced due to genetic reassortment of viruses. The retained segments may have to mutate to accommodate new segments. The mutations caused by interaction among segments retained and introduced due to reassortment between swine influenza viruses may have increased the adaptation of the virus to humans, leading to pandemic H1N1/09. We indicate the sites that probably contributed to the acquisition of efficient human-to-human transmission.Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 05/2010; 10(4):569-74. · 3.22 Impact Factor -
Article: Origin of measles virus: divergence from rinderpest virus between the 11th and 12th centuries.
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ABSTRACT: Measles, caused by measles virus (MeV), is a common infection in children. MeV is a member of the genus Morbillivirus and is most closely related to rinderpest virus (RPV), which is a pathogen of cattle. MeV is thought to have evolved in an environment where cattle and humans lived in close proximity. Understanding the evolutionary history of MeV could answer questions related to divergence times of MeV and RPV. We investigated divergence times using relaxed clock Bayesian phylogenetics. Our estimates reveal that MeV had an evolutionary rate of 6.0-6.5 x 10(-4) substitutions/site/year. It was concluded that the divergence time of the most recent common ancestor of current MeV was the early 20th century. And, divergence between MeV and RPV occurred around the 11th to 12th centuries. The result was unexpected because emergence of MeV was previously considered to have occurred in the prehistoric age. MeV may have originated from virus of non-human species and caused emerging infectious diseases around the 11th to 12th centuries. In such cases, investigating measles would give important information about the course of emerging infectious diseases.Virology Journal 03/2010; 7:52. · 2.34 Impact Factor -
Article: Origin of measles virus: divergence from rinderpest virus between the 11<sup>th </sup>and 12<sup>th </sup>centuries
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ABSTRACT: Abstract Measles, caused by measles virus (MeV), is a common infection in children. MeV is a member of the genus Morbillivirus and is most closely related to rinderpest virus (RPV), which is a pathogen of cattle. MeV is thought to have evolved in an environment where cattle and humans lived in close proximity. Understanding the evolutionary history of MeV could answer questions related to divergence times of MeV and RPV. We investigated divergence times using relaxed clock Bayesian phylogenetics. Our estimates reveal that MeV had an evolutionary rate of 6.0 - 6.5 × 10<sup>-4 </sup>substitutions/site/year. It was concluded that the divergence time of the most recent common ancestor of current MeV was the early 20<sup>th </sup>century. And, divergence between MeV and RPV occurred around the 11<sup>th </sup>to 12<sup>th </sup>centuries. The result was unexpected because emergence of MeV was previously considered to have occurred in the prehistoric age. MeV may have originated from virus of non-human species and caused emerging infectious diseases around the 11<sup>th </sup>to 12<sup>th </sup>centuries. In such cases, investigating measles would give important information about the course of emerging infectious diseases.Virology Journal. 01/2010;
Top co-authors
Top Journals
Institutions
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2008–2009
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Tohoku University
- • Graduate School of Medicine
- • Department of Urology
Sendai-shi, Miyagi-ken, Japan
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2005
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Sendai City Hospital
Sendai, Kagoshima-ken, Japan
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