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Viral genotyping

Noboru Hirashima, Hiroaki Iwase, Masaaki Shimada, Nobumitsu Ryuge, Junji Imamura, Hiroki Ikeda, Yasuhito Tanaka, Nobuyuki Matsumoto, Chiaki Okuse, Fumio Itoh, Yoshiyuki Yokomaku, Tsunamasa Watanabe
Co-infection with human immunodeficiency virus (HIV) and hepatitis C virus (HCV) often accelerates the course of HCV-associated liver disease. Daclatasvir (DCV) plus asunaprevir (ASV) have been shown to be highly effective for HCV-infected patients with genotype 1b. Three patients co-infected with HIV/HCV genotype 1b were enrolled in this study. Prior to initiation of HCV treatment, the variants associated with L31 and Y93 in the non-structural protein 5A (NS5A) region of the HCV genome were confirmed to be absent using a direct sequencing method...
October 20, 2016: Clinical Journal of Gastroenterology
J Y Zhao, X J Shen, B F Zhang, Z Q Wang, S L Xia, X Y Huang, B L Xu
Objective: To investigate the infection status of human rotavirus, calicivirus, astrovirus and enteric adenovirus in children aged <5 years in disease surveillance areas in Henan province from 2013 to 2015. Methods: A total of 880 stool samples were collected from four sentinel hospitals and group A rotavirus was detected by ELISA and group A rotavirus G/P genotyping was performed with nested multiplex RT-PCR, while rotavirus (group B, C), calicivirus and astrovirus were detected by two-step multiplex RT-PCR and adenovirus were detected by PCR...
October 10, 2016: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
M M Chen, Y Tan, Z Z Tang, M Lin, K J Zhou, W T He, Y P Yang, J Wang
Objective: To understand the epidemiological characteristics and viral sources of dengue fever outbreak in Guangxi Zhuang Autonomous Region (Guangxi) in 2014. Methods: A combined analysis of epidemiological characteristics and genetic characteristics were performed in this study. The time, population and area distributions of the cases were analyzed. Serum samples were collected from dengue fever cases to detect NS1 antigen by using commercial ELISA kits according to the guideline of the manufacture. RT-PCR assay was conducted to detect dengue virus in NS1 positive samples...
October 10, 2016: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Lisai Zhu, Haibing Lu, Yufeng Cao, Xiaochun Gai, Changming Guo, Yajing Liu, Jiaxu Liu, Xinping Wang
As one of the major pathogens, bovine viral diarrhea virus caused a significant economic loss to the livestock industry worldwide. Although BVDV infections have increasingly been reported in China in recent years, the molecular aspects of those BVDV strains were barely characterized. In this study, we reported the identification and characterization of a novel BVDV isolate designated as SD-15 from cattle, which is associated with an outbreak characterized by severe hemorrhagic and mucous diarrhea with high morbidity and mortality in Shandong, China...
2016: PloS One
Christian Quinet, Guy Czaplicki, Elise Dion, Fabiana Dal Pozzo, Anke Kurz, Claude Saegerman
BACKGROUND: Infection due to bovine viral diarrhoea virus (BVDV) is endemic in most cattle-producing countries throughout the world. The key elements of a BVDV control programme are biosecurity, elimination of persistently infected animals and surveillance. Bovine viral diarrhoea (BVD) is a notifiable disease in Belgium and an official eradication programme started from January 2015, based on testing ear notches sampled during the official identification and registration of calves at birth...
2016: PloS One
Jeong Eun Song, Do Young Kim
Hepatitis B virus (HBV) infection is a major global health problems leading to severe liver disease such as cirrhosis and hepatocellular carcinoma (HCC). HBV is a circular, partly double-stranded DNA virus with various serological markers: hepatitis B surface antigen (HBsAg) and anti-HBs, anti-HBc IgM and IgG, and hepatitis B e antigen (HBeAg) and anti-HBe. It is transmitted by sexual, parenteral and vertical route. One significant method to diminish the burden of this disease is timely diagnosis of acute, chronic and occult cases of HBV...
September 2016: Annals of Translational Medicine
Seung Man Cho, Byung-Ho Choe
This review article was requested by editor-in-chief of this journal as 'pediatric CHB treatment' for the upcoming special issue. The main objective of chronic hepatitis B (CHB) treatment is diminishing the risk of complications related to chronic liver disease. In Asia, there are already some reports about hepatocellular carcinoma (HCC) in hepatitis B virus (HBV) infected children. The key points of treatment in children with CHB infections are selection of which patients to treat and conformation of the optimal therapy time that would reduce viral resistance...
September 2016: Annals of Translational Medicine
Jeni Staykova, Tanja Belovska, Ayla Murad, Sevinch Kakid, Aneta Nacheva, Evelina Shikova
AIM: Although sexually transmitted viral infections are significant and increasing public health concern, little is known about their prevalence among Bulgarian women. The aim of this study was to investigate cervical viral infections in asymptomatic women. METHODS: The study group included 52 randomly selected asymptomatic female volunteers from Bulgarian border town Kardzhali. Cervical specimens were tested by real-time PCR for human papillomaviruses (HPV), herpes simplex virus (HSV) types 1 and 2, cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV)...
September 2016: Central European Journal of Public Health
Ying Liu, Chaoting Zhang, Weijiao Gao, Limin Wang, Yaqi Pan, Yunong Gao, Zheming Lu, Yang Ke
HPV integration plays an important role in cervical carcinogenesis. HPV genotypes and the exact integration sites were investigated using HPV capture technology combined with next generation sequencing in 166 women. Three, one and six integration sites were verified in 7 HPV-positive 'normal cervical epithelium', 6 HPV-positive CIN2 and 15 HPV-positive CIN 3 samples, respectively. Of the 10 integrations, one and nine were involved with HPV33 and HPV16, respectively. Our study accurately evaluated HPV integration level in CINs and normal cervical tissues using high-throughput viral integration detection method providing basic evidence for HPV integration-driven cervical carcinogenesis...
October 19, 2016: Scientific Reports
Qianqian Xu, Yuqiu Chen, Wenjun Zhao, Tingting Zhang, Chenggang Liu, Tianming Qi, Zongxi Han, Yuhao Shao, Deying Ma, Shengwang Liu
Newcastle disease (ND), caused by virulent strains of Newcastle disease virus (NDV), is a highly contagious disease of birds that is responsible for heavy economic losses for the poultry industry worldwide. However, little is known about host-virus interactions in waterfowl, goose. In this study, we aim to characterize the host immune response in goose, based on the previous reports on the host response to NDV in chickens. Here, we evaluated viral replication and mRNA expression of 27 immune-related genes in 10 tissues of geese challenged with a genotype VIId NDV strain of goose origin (go/CH/LHLJ/1/06)...
2016: Frontiers in Microbiology
Zhonglan Wu, Lijia Cui, Weiming Zhao, Dongzhi Yang, Hui Chen, Ruiqing Wang, Xuemin Wang, Linqi Zhang, Tianhua He
BACKGROUND: Current prevalence and genotype distribution of hepatitis C virus (HCV) infection remain unknown in Ningxia, northwest China. METHODS: From June to December 2013, 13,022 individuals were screened in Ningxia HIV/AIDS Sentinel Surveillance System, with their demographic features collected and serum samples tested for HCV antibody. Sero-positive drug users were further subjected to sequencing of NS5B and Core regions of HCV. RESULTS: The anti-HCV prevalence was 0...
October 18, 2016: Virology Journal
Eric M Nordstrom, Angela Keniston, Fafa Baouchi, Alvaro Martinez-Camacho
AIMS: This study assesses the efficacy, accessibility, and safety of hepatitis C virus (HCV) treatment in a safety net hospital population. METHODS: Patients at Denver Health receiving pegylated interferon for HCV infection between 2008 and 2012 were included in this retrospective study. Sociodemographic, biochemical, and virologic data were collected on each patient. The primary outcomes were the rate of sustained virologic response and early treatment discontinuation, with reason for discontinuation documented...
October 13, 2016: European Journal of Gastroenterology & Hepatology
Gerrit Ahrenstorf, Hui-Zhi Low, Katja Kniesch, David Ordonez, Dirk Meyer-Olson, Fareed Ahmad, Claudia Kücherer, Barbara Gunsenheimer-Bartmeyer, Matthias Stoll, Torsten Matthias, Reinhold E Schmidt, Torsten Witte
OBJECTIVE: To analyze the influence of LILRA3 and the genetic LILRA3 deletion on transmission and clinical course of HIV infection. DESIGN: Case and control study. METHODS: LILRA3 genotypes were determined by polymerase chain reaction. HIV patients were categorized into short-term progressors, normal progressors and long-term non-progressors according to the clinical course. Functional studies were performed using real-time PCR, intracellular flow cytometry and ELISA...
October 14, 2016: AIDS
Catherine Forconi, Philippe Gatault, Elodie Miquelestorena-Standley, Johan Noble, Sally Al-Hajj, Romain Guillemain, Marc Stern, Thomas Hoffmann, Louis Prat, Caroline Suberbielle, Emeline Masson, Anne Cesbron-Gautier, Catherine Gaudy-Graffin, Alain Goudeau, Gilles Thibault, Fabrice Ivanes, Roseline Guibon, Ihab Kazma, Yvon Lebranchu, Matthias Büchler, Antoine Magnan, Jean-Michel Halimi, Christophe Baron
BACKGROUND: Cytomegalovirus (CMV) has a role in chronic rejection and graft loss in kidney transplant (KTx) and lung transplant (LTx) recipients. In addition, donor CMV seropositivity is an independent risk factor for renal graft loss. The anti-CMV response might modulate this risk. Expression of programmed cell death 1 (PD-1), a receptor involved in viral-specific T-cell exhaustion, is influenced by a single nucleotide polymorphism called PD-1.3 (wild-type allele G, variant allele A)...
August 26, 2016: Journal of Heart and Lung Transplantation
Kayo Sugimoto, Soo Ki Kim, Soo Ryang Kim, Mana Kobayashi, Airi Kato, Eri Morimoto, Susumu Imoto, Chi Wan Kim, Yasuhito Tanaka, Masatoshi Kudo, Yoshihiko Yano, Yoshitake Hayashi
OBJECTIVES: The efficacy of sofosbuvir plus ribavirin (RBV) treatment for hepatitis C virus (HCV) genotype 2 focusing on virological response was compared with that of pegylated interferon (peg-IFN) plus RBV treatment. Safety of the former focusing on the decline in hemoglobin levels was compared with that of the latter and assessed in terms of age and inosine triphosphatase (ITPA). METHODS: Patients (n = 17) receiving sofosbuvir plus RBV and those (n = 24) receiving peg-IFN plus RBV diagnosed with chronic HCV genotype 2 were enrolled in this study, and the efficacy and safety of both treatments were assessed...
2016: Digestive Diseases
Robert Flisiak, Mitchell Shiffman, Juan Arenas, Hugo Cheinquer, Igor Nikitin, Yuping Dong, Khurram Rana, Subasree Srinivasan
BACKGROUND: A randomized, double-blind, multinational, phase 3 study was conducted comparing the efficacy and safety of peginterferon lambda-1a (Lambda)/ribavirin (RBV)/telaprevir (TVR) vs. peginterferon alfa-2a (Alfa)/RBV/TVR in patients with chronic hepatitis C virus (HCV) genotype-1 (GT-1) infection. METHODS: Patients (treatment-naïve or relapsers on prior Alfa/RBV treatment) were randomly assigned in a 2:1 ratio to receive Lambda/RBV/TVR or Alfa/RBV/TVR. Total duration of treatment was either 24 or 48 weeks (response-guided treatment), with TVR administered for the first 12 weeks...
2016: PloS One
María Bergua, Sung-Hwan Kang, Svetlana Y Folimonova
Superinfection exclusion (SIE) is a phenomenon in which a primary viral infection restricts a secondary infection with the same or closely related virus. Previously we showed that SIE by Citrus tristeza virus (CTV) occurs only between isolates of the same virus genotype. This work, however, was done using single genotype-containing isolates, while most field citrus trees harbor complex populations composed of different virus genotypes. Here we examined SIE in plants simultaneously infected with several CTV genotypes...
October 12, 2016: Virology
Kendall R Beck, Nicole Kim, Mandana Khalili
BACKGROUND: Vulnerable populations are disproportionately affected by hepatitis C virus (HCV) infection and experience high rates of health disparity. There are no data on real-world experience with highly efficacious direct-acting anti-HCV treatment in this population. AIMS: We aimed to evaluate the real-world experience with sofosbuvir-based regimens among a vulnerable HCV-infected population. METHODS: HCV treatment response was assessed among 204 patients who completed 12-24 weeks of sofosbuvir-based regimens (in combination with pegylated interferon and ribavirin, simeprevir, ledipasvir, or daclatasvir) at the San Francisco safety-net healthcare system liver specialty clinic between January 2014 and December 2015...
October 14, 2016: Digestive Diseases and Sciences
Ana Georgina Cobián Güemes, Merry Youle, Vito Adrian Cantú, Ben Felts, James Nulton, Forest Rohwer
Viruses are the most abundant and the most diverse life form. In this meta-analysis we estimate that there are 4.80×10(31) phages on Earth. Further, 97% of viruses are in soil and sediment-two underinvestigated biomes that combined account for only ∼2.5% of publicly available viral metagenomes. The majority of the most abundant viral sequences from all biomes are novel. Our analysis drawing on all publicly available viral metagenomes observed a mere 257,698 viral genotypes on Earth-an unrealistically low number-which attests to the current paucity of viral metagenomic data...
September 29, 2016: Annual Review of Virology
Phunchai Charatcharoenwitthaya, Ananya Pongpaibul, Uayporn Kaosombatwattana, Patommatat Bhanthumkomol, Wimolrak Bandidniyamanon, Nonthalee Pausawasdi, Tawesak Tanwandee
BACKGROUND & AIMS: The clinical significance of steatohepatitis in chronic hepatitis B (CHB) remains unclear. This study aimed to determine the prevalence and risk factors for steatohepatitis in CHB, and to determine its correlation with liver fibrosis and response to antiviral therapy. METHODS: Liver histopathology of 256 consecutive CHB patients with serum HBV DNA >2,000 IU/ml were analyzed with clinical and laboratory characteristics. Virological and biochemical responses were prospectively assessed in the 112 patients treated with antiviral monotherapy...
October 14, 2016: Liver International: Official Journal of the International Association for the Study of the Liver
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