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Phylogenetic analysis of dengue virus types 1 and 3 isolated in Jakarta, Indonesia in 1988

Sjatha F, Takizawa Y, Yamanaka A, Konishi E

Infect Genet Evol, 2012 Dec;12(8):1938-43.
PMID: 22959957 DOI: 10.1016/j.meegid.2012.08.006

Dengue viruses are mosquito-borne viruses that cause dengue fever and dengue hemorrhagic fever, both of which are globally important diseases. These viruses have evolved in a transmission cycle between human hosts and mosquito vectors in various tropical and subtropical environments. We previously isolated three strains of dengue type 1 virus (DENV1) and 14 strains of dengue type 3 virus (DENV3) during an outbreak of dengue fever and dengue hemorrhagic fever in Jakarta, Indonesia in 1988. Here, we compared the nucleotide sequences of the entire envelope protein-coding region among these strains. The isolates were 97.6-100% identical for DENV1 and 98.8-100% identical for DENV3. All DENV1 isolates were included in two different clades of genotype IV and all DENV3 isolates were included in a single clade of genotype I. For DENV1, three Yap Island strains isolated in 2004 were the only strains closely related to the present isolates; the recently circulated Indonesian strains were in different clades. Molecular clock analyses estimated that ancestors of the genotype IV strains of DENV1 have been indigenous in Indonesia since 1948. We predict that they diverged frequently around 1967 and that their offspring distributed to Southeast Asia, the Western Pacific, and Africa. For DENV3, the clade containing all the present isolates also contained strains isolated from other Indonesian regions and other countries including Malaysia, Singapore, China, and East Timor from 1985-2010. Molecular clock analyses estimated that the common ancestor of the genotype I strains of DENV3 emerged in Indonesia around 1967 and diverged frequently until 1980, and that their offspring distributed mainly in Southeast Asia. The first dengue outbreak in 1968 and subsequent outbreaks in Indonesia might have influenced the divergence and distribution of the DENV1 genotype IV strains and the DENV3 genotype I strains in many countries.
Divergence of the dengue virus type 2 Cosmopolitan genotype associated with two predominant serotype shifts between 1 and 2 in Surabaya, Indonesia, 2008-2014

Kotaki T, Yamanaka A, Mulyatno KC, Churrotin S, Sucipto TH, Labiqah A, et al.

Infect Genet Evol, 2016 Jan;37:88-93.
PMID: 26553170 DOI: 10.1016/j.meegid.2015.11.002

Indonesia is one of the biggest dengue endemic countries, and, thus, is an important place to investigate the evolution of dengue virus (DENV). We have continuously isolated DENV in Surabaya, the second biggest city in Indonesia, since 2008. We previously reported sequential changes in the predominant serotype from DENV type 2 (DENV-2) to DENV type 1 (DENV-1) in November 2008 and from DENV-1 to DENV-2 in July 2013. The predominance of DENV-2 continued in 2014, but not in 2015. We herein phylogenetically investigated DENV-2 transitions in Surabaya between 2008 and 2014 to analyze the divergence and evolution of DENV-2 concomitant with serotype shifts. All DENV-2 isolated in Surabaya were classified into the Cosmopolitan genotype, and further divided into 6 clusters. Clusters 1-3, dominated by Surabaya strains, were defined as the "Surabaya lineage". Clusters 4-6, dominated by strains from Singapore, Malaysia, and many parts of Indonesia, were the "South East Asian lineage". The most recent common ancestor of these strains existed in 1988, coinciding with the time that an Indonesian dengue outbreak took place. Cluster 1 appeared to be unique because no other DENV-2 isolate was included in this cluster. The predominance of DENV-2 in 2008 and 2013-14 were caused by cluster 1, whereas clusters 2 and 3 sporadically emerged in 2011 and 2012. The characteristic amino acids of cluster 1, E-170V and E-282Y, may be responsible for its prevalence in Surabaya. No amino acid difference was observed in the envelope region between strains in 2008 and 2013-14, suggesting that the re-emergence of DENV-2 in Surabaya was due to the loss or decrease of herd immunity in the 5-year period when DENV-2 subsided. The South East Asian lineage primarily emerged in Surabaya in 2014, probably imported from other parts of Indonesia or foreign countries.
Linked color imaging improves the visibility of various featured colorectal polyps in an endoscopist's visibility and color difference value

Yoshida N, Naito Y, Yasuda R, Murakami T, Hirose R, Ogiso K, et al.

Int J Colorectal Dis, 2017 Sep;32(9):1253-1260.
PMID: 28725959 DOI: 10.1007/s00384-017-2855-z

PURPOSE: Linked color imaging (LCI) by laser endoscopy is a novel narrow band light observation. In this study, we analyzed the efficacy of LCI for improving the various featured colorectal polyp's visibility utilizing a subjective endoscopist's visibility scoring and objective color difference (CD) value.
METHODS: We retrospectively reviewed two pictures both with white light (WL) and LCI for 54 consecutive neoplastic polyps 2-20 mm in size. All pictures were evaluated by four endoscopists according to a published polyp visibility score from four (excellent visibility) to one (poor visibility). Additionally, we calculated CD value between each polyp and surrounding mucosa in LCI and WL using an original software.
RESULTS: The mean polyp visibility scores of LCI (3.11 ± 1.05) were significantly higher than those of WL (2.50 ± 1.09, P
Fulltext The efficacy of the pocket-creation method for cases with severe fibrosis in colorectal endoscopic submucosal dissection

Yoshida N, Naito Y, Yasuda R, Murakami T, Hirose R, Ogiso K, et al.

Endosc Int Open, 2018 Aug;6(8):E975-E983.
PMID: 30083587 DOI: 10.1055/a-0593-5818

Background and study aims: Severe fibrosis poses a challenge in colorectal endoscopic submucosal dissection (ESD). Recently, the pocket-creation method (PCM) has been developed for overcoming various difficulties of ESD. A specific tapered hood is used for adequate traction in the PCM, and endoscopic operability becomes stable in the pocket. In this study, we investigated the efficacy of the PCM in ESD for cases with severe fibrosis.
Patients and methods : We retrospectively reviewed 1000 consecutive colorectal ESD cases (April 2006 to January 2017). Since 2016, the PCM was performed in 58 cases. The indications for ESD included (1) tumors ≥ 20 mm in size diagnosed as intramucosal cancer or high-grade dysplasia and part of T1a cancer using magnifying endoscopic examinations and (2) tumors that appeared impossible to resect with endoscopic mucosal resection because of suspected fibrosis. We identified 120 cases with severe fibrosis and compared them to cases without severe fibrosis. Additionally, the 120 severe fibrosis cases were divided into the PCM and non-PCM groups. En bloc resection, procedure time, discontinuation, and complications were analyzed between these 2 groups.
Results: Among all 1000 ESDs, severe fibrosis and discontinuation rates were 12.0 % (120 cases) and 1.8 % (18 cases), respectively. Regarding the comparison between cases with severe fibrosis and with no severe fibrosis, there were significant differences about en bloc resection rate (78.3 % vs. 95.7 %, P 0.6.
Conclusions: In cases with severe fibrosis, the PCM with ESD improved en bloc resection rates and shortened the procedure time compared to the conventional non-PCM method. Additionally, the PCM reduced the discontinuation rate.