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Yuki Matsushima,
Hideaki Shimizu,
Atsuko Kano,
Etsuko Nakajima,
Yoko Ishimaru, Shuvra Kanti Dey,
Yuki Watanabe,
Fuyuka Adachi,
Kohnosuke Mitani,
Tsuguto Fujimoto,
Tung Gia Phan,
Hiroshi Ushijima
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ABSTRACT: A novel virus of the species human adenovirus D, HAdV-67 (P-New/H9/F25), was first isolated from diarrheal feces of six children in Dhaka City, Bangladesh. The genome of this novel virus may be composed of multiple recombinations among HAdV-9, HAdV-25, HAdV-26, HAdV-33, HAdV-46, and an unknown human adenovirus D which was an origin of HAdV-67.
Genome announcements. 01/2013; 1(1).
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ABSTRACT: A total of 463 fecal specimens from human patients were tested for the presence of Camphylobacter by a commercial immunochromatography kit (ImmunoCard STAT! CAMPY), polymerase chain reaction (PCR) and conventional bacteriological (CB) methods. Using culture as the standard of reference, the ImmunoCard STAT! CAMPY assay had a sensitivity of 86% and a specificity of 100%. On the other hand, using PCR as the standard of reference, ImmunoCard STAT! CAMPY assay had a sensitivity of 90.5% and a specificity of 100%.
Journal of microbiological methods 10/2012; · 2.43 Impact Factor
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Yuki Matsushima,
Hideaki Shimizu,
Atsuko Kano,
Etsuko Nakajima,
Yoko Ishimaru, Shuvra Kanti Dey,
Yuki Watanabe,
Fuyuka Adachi,
Keiichiro Suzuki,
Kohnosuke Mitani,
Tsuguto Fujimoto,
Tung Gia Phan,
Hiroshi Ushijima
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ABSTRACT: We report a novel human adenovirus D (HAdV-65) isolated from feces of 4 children in Bangladesh who had acute gastroenteritis. Corresponding genes of HAdV-65 were related to a hexon gene of HAdV-10, penton base genes of HAdV-37 and HAdV-58, and a fiber gene of HAdV-9. This novel virus may be a serious threat to public health.
Emerging Infectious Diseases 05/2012; 18(5):846-8. · 6.79 Impact Factor
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ABSTRACT: Recombination of RNA viruses plays an important part in molecular epidemiological study, virus evolution, vaccine design, and viral control programs. Sapovirus, a member of the family Caliciviridae, is one of the major causative agents of viral gastroenteritis affecting all age groups.
Sapovirus capsid and polymerase regions were amplified by PCR using specific primers. PCR products were sequenced directly and sequence analysis was performed using CLUSTAL X, SimPlot, and MEGA 4 software package.
Based on the genetic analysis, a novel, naturally occurring recombinant sapovirus strain was identified in Bangladesh. Breakpoint analysis of the recombinant sapovirus showed that the recombination site was at the open reading frame ORF1/ORF2 overlap.
We described the genetic characterization of a novel, naturally occurring recombinant sapovirus and provided the first evidence of recombination in sapovirus in Bangladesh.
Clinical laboratory 01/2011; 57(1-2):91-4. · 0.90 Impact Factor
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ABSTRACT: Noroviruses (NoV) are important causes of acute gastroenteritis in infants and young children. This study investigated the prevalence of NoV infections in infants and children with acute gastroenteritis in Japan from July 2006 to June 2007.
A total of 628 fecal specimens were collected from infants and children with acute gastroenteritis in five different places (Maizuru, Tokyo, Sapporo, Saga and Osaka), Japan during the period of July 2006 to June 2007. All fecal specimens were examined for NoV by reverse transcription-polymerase chain reaction. Molecular analysis of NoV was carried out by sequencing methods.
From 628 fecal specimens tested, 15.6% (99 of 628) were positive for NoV. Of these, NoV GII most predominant, with a prevalence of 15.5% (97 of 99). Analysis of nucleotide and amino acid sequences revealed that NoVGII strains comprised GII/4 (89%), GII/3 (6.4%), GII/7 (2.3%), and GII/2 (2.3%) genotypes. Among NoVGII/4 strains, all of them belonged to genotype GII/4 2006b variants. Our results clearly indicated that NoV infections were most commonly observed in winter seasons in Japan.
In conclusion, this study shows the predominance of NoVGII/4 2006b variants and NoV is still burden of disease among Japanese pediatric population.
Clinical laboratory 01/2011; 57(3-4):193-9. · 0.90 Impact Factor
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Wisoot Chan-it,
Aksara Thongprachum, Shuvra Kanti Dey,
Tung Gia Phan,
Pattara Khamrin,
Shoko Okitsu,
Shuichi Nishimura,
Masaaki Kobayashi,
Hideaki Kikuta,
Tsuneyoshi Baba,
Atsuko Yamamoto,
Kumiko Sugita,
Shintaro Hashira,
Takeshi Tajima,
Shinichi Ishida,
Masashi Mizuguchi,
Hiroshi Ushijima
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ABSTRACT: The molecular epidemiology of rotavirus infections in non-hospitalized children in five different regions (Sapporo, Saga, Tokyo, Osaka, and Maizuru) of Japan during 2007-2009 was investigated. Overall, rotavirus was detected in 156 out of 1008 (15.5%) specimens. The rotavirus infection in 2007-2008 (19.3%) was higher than those in 2008-2009 (12.1%). G1P[8] was the most prevalent (62.8%), followed by G3P[8] (21.8%), G9P[8] (14.7%), and G2P[4] (0.7%). Interestingly, the number of G3P[8] strains increased threefold from the former season (2006-2007) from 7.3% to 21.8%, whereas G2P[4] and G9P[8] decreased from 11.4% to 0.7% and 20.3% to 14.7%, respectively. In the phylogenetic analysis, G3 rotaviruses were closely related to "the new variant G3" 5091 strain, which previously emerged in Japan and China. G9 viruses isolated in 2007-2008 were genetically close to the Thai strain, while those isolated in 2008-2009 had a close relationship with Chinese strains. G1 viruses appeared to be more similar to the recently reported G1 strain in China. Nucleotide sequence analysis of 33 P[8]-nontypeable strains revealed 5 nucleotide mismatches at the primer binding site. Based on previously reported (2003-2007) and current (2007-2009) data of rotavirus surveillance in the five areas of Japan, it was revealed that in Sapporo, Osaka, and Maizuru, G1P[8] and G3P[8] were detected at high frequencies, ranging from 47.2 to 57.7% and 31.7 to 47.4%, respectively. In Tokyo, G1P[8] (47.4%) was the predominant strain, followed by G9P[8] (20.6%), whereas in Saga, G3P[8] (38.9%) and G9P[8] (36.1%) were identified as the most dominant types. None of G9P[8] was detected in Sapporo. This study highlights the genetic diversity and the significance of rotavirus diarrhea in Japan.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 12/2010; 11(2):415-22. · 3.22 Impact Factor
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ABSTRACT: A total of 6231 fecal specimens collected from infants and children with gastroenteritis in 7 different regions of Japan during 1995 to 2007 were examined for norovirus. Norovirus was detected in 779 patients (12.5%) and norovirus activity peak in the winter season (November to January) during 1995 to 2007. During the last 11 years, NoVGII/4 was the predominant strain in Japan followed by GII/3, GII/6, GII/2, GII/12, and GI.
The Pediatric Infectious Disease Journal 03/2010; 29(5):e32-4. · 3.58 Impact Factor
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ABSTRACT: Based on the genetic analysis, novel, naturally occurring recombinant norovirus strains were identified in Japan. Breakpoint analysis of recombinant norovirus showed that the recombination site was at the open reading frame ORF1/ORF2 overlap.
Virus Genes 02/2010; 40(3):362-4. · 1.85 Impact Factor
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Journal of Tropical Pediatrics 09/2009; 56(3):205-7. · 1.39 Impact Factor
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Journal of Tropical Pediatrics 08/2009; 56(2):129-31. · 1.39 Impact Factor
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ABSTRACT: A total of 917 fecal specimens collected from infants and children with acute gastroenteritis in Dhaka City, Bangladesh during 2004-2005 were examined for the presence of adenoviruses by PCR. Adenoviruses were identified in 17 of 917 (1.9%) specimens. Detected adenoviruses were subjected to molecular genetic analysis by sequencing method. Adenoviruses detected in this study were classified into three serotypes, namely Ad9, Ad10 and Ad40. Of these, Ad40 was predominant, followed by Ad9 and accounted for 42% (7 of 17) and 36% (6 of 17), respectively. This is the first report of acute gastroenteritis attributed to Ad9 and Ad10 in Dhaka City, Bangladesh. Another interesting feature of the study was absence of Ad41 serotype. Our results clearly indicated that adenovirus infections were most commonly observed in winter season (October 2004 through January 2005) and in rainy season (May 2005 through July 2005) in Dhaka City. The most common clinical symptoms of adenovirus-infected patients were dehydration (94%), abdominal pain (59%) and vomiting (30%). To our knowledge, this is the first 1-year molecular epidemiological research of adenovirus infection in Bangladesh.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 08/2009; 9(4):518-22. · 3.22 Impact Factor
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ABSTRACT: This study investigated the prevalence of group A, B, and C rotavirus (RAV, RBV, RCV) and adenovirus (AdV) infections in infants and children with acute gastroenteritis in Japan from July 2006 to June 2007. A total of 628 fecal specimens collected from infants and children with acute gastroenteritis in five different places (Maizuru, Tokyo, Sapporo, Saga and Osaka) in Japan during the period of July 2006-June 2007 were examined for RAV, RBV, RCV and AdV by RT-multiplex PCR. RAV was further characterized to G-typing and P-typing by RT-multiplex PCR and sequencing method. It was found that 123 (19.6%) fecal specimens were positive for RAV followed by AdV of 4.5%. RBV and RCV could not be detected in this study. Serotype G1 (58.5%) was identified at high levels followed by G9 (20.3%), G2 (11.4%), and G3 (7.3%). P genotyping revealed P[8] as predominant (84.6%) followed by P[4] (13.8%) and P[6] (1.6%). During the 2006/2007 rotavirus season, G1P[8] strains were most common with G9P[8], G2P[4], G3P[8], G1P[4] and G9P[6] also detected. It is clear from this study that RAV is still the cause of diseases in Japan. To our knowledge, this is the first report of RV P[6] strain in humans in Japan.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 07/2009; 9(5):955-61. · 3.22 Impact Factor
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ABSTRACT: Between 2004 and 2005, 917 fecal specimens were collected from children below age 5 who presented to Child Health Institute for treatment of diarrhoea in Dhaka City, Bangladesh. The specimens were screened by RT-PCR for the presence of group A rotavirus and positive stools genotyped. Group A rotavirus was detected in 307 stools and serotype G3P[8] strains were detected in nine specimens. Sequence analysis clustered the G3 strains into one distinct lineage (lineage I) with other Asian G3 strains. In addition, one amino acid change at position 96 in antigenic region A, similar to lineage II G3 Chinese strains, was noted. To our knowledge this is the first report of serotype G3 strains in Bangladesh since 1993 and the first report of the molecular characterization of these strains.
Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases 07/2009; 9(5):983-6. · 3.22 Impact Factor
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ABSTRACT: To determine G and P genotypes, we performed nested PCR on 307 rotavirus specimens collected in Dhaka, Bangladesh, during 2004-2005. G2 (43.3%) was detected at the highest frequency, followed by G4 (19.5%), G9 (13.7%), G1 (12.7%), and G3 (2.6%). P[8] was the most predominant genotype (53.2%), followed by P[4] (42.9%).
Emerging Infectious Diseases 02/2009; 15(1):91-4. · 6.79 Impact Factor
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Ngan Thi Kim Pham,
Quang Duy Trinh,
Tuan Anh Nguyen, Shuvra Kanti Dey,
Tung Gia Phan,
Le Phuc Hoang,
Pattara Khamrin,
Niwat Maneekarn,
Shoko Okitsu,
Masashi Mizuguchi,
Hiroshi Ushijima
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ABSTRACT: A nested polymerase chain reaction method using genotype-specific primers based on the capsid gene was developed to differentiate between genotypes A and B of Aichi viruses. Results of the study showed that the PCR using newly designed genotype-specific primers could generate appropriate PCR products from all 17 samples tested, the newly developed primers could differentiate genotype A from genotype B, and all matched those obtained by nucleotide sequencing of the capsid regions. The nested PCR method using genotype-specific primers is useful and can be used for genotyping of Aichi viruses isolated from epidemiological studies.
Journal of Virological Methods 01/2009; 156(1-2):107-10. · 2.01 Impact Factor
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Journal of Tropical Pediatrics 08/2008; 54(6):423-5. · 1.39 Impact Factor
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Ngan Thi Kim Pham,
Quang Duy Trinh,
Pattara Khamrin,
Tuan Anh Nguyen, Shuvra Kanti Dey,
Tung Gia Phan,
Le Phuc Hoang,
Niwat Maneekarn,
Shoko Okitsu,
Masashi Mizuguchi,
Hiroshi Ushijima
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ABSTRACT: Sequence analysis of the capsid gene of Aichi viruses was performed on 12 strains detected in Japan, Bangladesh, Thailand, and Vietnam during 2002-2005. The phylogenetic tree constructed from 17 nucleotide sequences of the capsid gene of the strains studied and reference strains demonstrated that Aichi virus strains clustered into two branches. A classification of Aichi viruses based on the capsid gene was proposed, in which lineage I consists of the Aichi virus strains detected from Japan, Thailand, Vietnam, and Germany, and lineage II includes Bangladeshi strains and a Brazilian strain.
Journal of Medical Virology 08/2008; 80(7):1222-7. · 2.82 Impact Factor
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ABSTRACT: Diarrhea, over the years, has killed millions of people and continues to be a major threat in Bangladesh.
To determine the incidence of norovirus infection in infants and young children with acute gastroenteritis in Dhaka City, Bangladesh and to determine the genogroup and genotype in norovirus-positive stool specimens.
Fecal specimens were collected from infants and children with acute gastroenteritis in Dhaka City, Bangladesh from October 2004 to September 2005, and examined for norovirus by reverse transcription-polymerase chain reaction.
Noroviruses were detected in 41 of 917 fecal specimens. Molecular analysis of norovirus was carried out by sequencing methods. Only norovirus GII/4 strains were detected during this study. The dominant genotype throughout the study period was GII/4. Norovirus infections were most commonly observed in winter and rainy seasons in Dhaka City. The common clinical symptoms in norovirus-infected patients were diarrhea (90%), vomiting (75%) and abdominal pain (46%).
This is the first epidemiological research of norovirus in Bangladesh. Norovirus is an important enteropathogen responsible for viral gastroenteritis among infants and children in Bangladesh.
Journal of Clinical Virology 12/2007; 40(3):218-23. · 3.97 Impact Factor
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ABSTRACT: Sapovirus is an important causative agent of sporadic cases as well as of outbreaks of acute gastroenteritis in humans worldwide. A total of 603 fecal specimens collected from July 2005 to June 2006 from children with acute gastroenteritis in five localities in Japan (Maizuru, Tokyo, Sapporo, Saga, and Osaka) were screened for sapovirus by RT-PCR. It was found that 17 specimens were positive for sapovirus and it represented 2.8%. Interestingly, intragenotype recombinant sapovirus GI/1 emerged with 76.4% (13 of 17) and rapidly became the leading cause of acute gastroenteritis in Japan for the first time. The lower frequency of sapovirus GI/2 and GI/4 (each of 11.8%), which were the second prevailing genotypes, was also detected. A novel nomenclature of sapovirus was proposed, in which worldwide sapovirus strains were classified into seven genogroups. Of these, novel sapovirus genogroups VI and VII demonstrated the very low homologies, only 32.8-41.6% at the amino acid level and 43.6-49.9% at the nucleotide level, to those of sapovirus genogroups I-V. Of note, two distinct clusters of sapovirus were co-circulating in porcine. Interestingly, the worldwide sapovirus strains shared the 25 nucleotide-conserved region, covering the polymerase-capsid junction which differed according to each species due to multiple nucleotide substitutions. The finding suggests that the sapovirus recombination between human and animal hardly takes place in nature. This is also the first, to our best knowledge, demonstrating the emergence of the intragenotype recombinant sapovirus with its causing diarrheal illness in Japan.
Infection Genetics and Evolution 08/2007; 7(4):542-6. · 3.13 Impact Factor
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ABSTRACT: Sapovirus, a member of the family Caliciviridae is one of the major causative agents of viral gastroenteritis affecting all age group. Sapovirus was detected in 25 of 917 stool specimens from infants and children with acute gastroenteritis in a Children Hospital in Dhaka City, Bangladesh during 2004-2005. All fecal specimens were examined for sapovirus by reverse transcription-polymerase chain reaction. Molecular analysis of sapovirus was carried out by sequencing methods. Sapovirus detected in this study was clustered into only one distinct genogroup I. Sapovirus GI/1 was predominant, followed by GI/2 and accounted for 92% (23 of 25) and 8% (2 of 25), respectively. The results clearly indicated that sapovirus infections were observed most commonly in the autumn to winter seasons (September to January) in Dhaka City. The common clinical symptoms of sapovirus infected patients were dehydration (88%), vomiting (76%), and abdominal pain (60%). This is the first report of sapovirus in Bangladesh.
Journal of Medical Virology 06/2007; 79(5):633-8. · 2.82 Impact Factor
