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Detection of porcine circovirus genotypes 2a and 2b in aborted foetuses from infected swine herds in the State of S?o Paulo, Brazil
Alessnadra M.M.G. Castro, Taís F Cruz, Vanessa R Salgado, Tatiana M Kanashiro, Karen L Ferrari, Jo?o P Araujo, Paulo E Brand?o, Leonardo J Richtzenhain
Acta Veterinaria Scandinavica , 2012, DOI: 10.1186/1751-0147-54-29
Abstract: Samples of 168 aborted foetuses or mummified foetuses from five farrow-to-finish swine farms known to be infected with PCV2 and located in the State of S?o Paulo were tested for PCV2 by polymerase chain reaction (PCR). Positive samples were additionally tested for porcine parvovirus (PPV), Leptospira spp. and Brucella spp. by PCR. PCV2 was detected in 18 of the samples (10.7%). PPV, Brucella spp. and Leptospira spp were found in 2, 10 and 0 cases, respectively. Eleven PCV2 strains were sequenced and determined to be either genotype 2a (n?=?1) or 2b (n?=?10).The findings indicate that the frequency of PCV2 infections in aborted porcine foetuses from the State of S?o Paulo is rather low (10.7%) and that co-infection with other pathogens is common and may be involved in PCV2 associated reproductive failure. No repeatable, characteristic amino acid motifs for regions of the PCV2 capsid protein seemed to be associated with abortion in sows.
Development of PCR for the Identification of Porcine Circovirus Type 2 (PCV-2) Genotype PCV-2a and PCV-2b
Dongsheng He,Yanzong Zhao,Danping Su,Xiaoyun Niu
Journal of Animal and Veterinary Advances , 2012, DOI: 10.3923/javaa.2011.2398.2401
Abstract: PCR was developed to evaluate for its ability to simultaneously detect viral infections of swine. Specific primers were designed for each sub-type of porcine circovirus type 2 (PCV-2); porcine circovirus type 2a (PCV-2a) and porcine circovirus type 2b (PCV-2b). Each target produced specific amplicon with a size of 229 bp (PCV-2a) and 785 bp (PCV-2b). The assay was sensitive and specific in detecting the target agent in clinical specimens. In conclusion, the PCR has the potential to be useful for routine molecular diagnosis and epidemiology.
Filter Bank Common Spatial Pattern Algorithm on BCI Competition IV Datasets 2a and 2b  [PDF]
Kai Keng Ang,Zheng Yang Chin,Cuntai Guan,Haihong Zhang
Frontiers in Neuroscience , 2012, DOI: 10.3389/fnins.2012.00039
Abstract: The Common Spatial Pattern (CSP) algorithm is an effective and popular method for classifying 2-class motor imagery electroencephalogram (EEG) data, but its effectiveness depends on the subject-specific frequency band. This paper presents the Filter Bank Common Spatial Pattern (FBCSP) algorithm to optimize the subject-specific frequency band for CSP on Datasets 2a and 2b of the Brain-Computer Interface (BCI) Competition IV. Dataset 2a comprised 4 classes of 22 channels EEG data from 9 subjects, and Dataset 2b comprised 2 classes of 3 bipolar channels EEG data from 9 subjects. Multi-class extensions to FBCSP are also presented to handle the 4-class EEG data in Dataset 2a, namely, Divide-and-Conquer (DC), Pair-Wise (PW), and One-Versus-Rest (OVR) approaches. Two feature selection algorithms are also presented to select discriminative CSP features on Dataset 2b, namely, the Mutual Information-based Best Individual Feature (MIBIF) algorithm, and the Mutual Information-based Rough Set Reduction (MIRSR) algorithm. The single-trial classification accuracies were presented using 10 × 10-fold cross-validations on the training data and session-to-session transfer on the evaluation data from both datasets. Disclosure of the test data labels after the BCI Competition IV showed that the FBCSP algorithm performed relatively the best among the other submitted algorithms and yielded a mean kappa value of 0.569 and 0.600 across all subjects in Datasets 2a and 2b respectively.
A meta-analysis that compares the use of either peginterferon-α2a or peginterferon-α2b plus ribavirin for HCV infection
Nan Xiao, Shuang Shi, Hui Zhuang
Hepatic Medicine: Evidence and Research , 2010, DOI: http://dx.doi.org/10.2147/HMER.S11916
Abstract: meta-analysis that compares the use of either peginterferon-α2a or peginterferon-α2b plus ribavirin for HCV infection Original Research (3267) Total Article Views Authors: Nan Xiao, Shuang Shi, Hui Zhuang Published Date July 2010 Volume 2010:2 Pages 99 - 109 DOI: http://dx.doi.org/10.2147/HMER.S11916 Nan Xiao*, Shuang Shi*, Hui Zhuang Department of Microbiology, Peking University Health Science Center, Beijing, China, *These authors contributed equally to this work Background: Two kinds of peginterferons, peginterferon-α2a (PEG-IFN-α2a) and peginterferon-α2b (PEG-IFN-α2b), are used in the treatment of chronic hepatitis C virus (HCV) infection. However, it is unclear which is better in terms of virological responses and patient compliance. We conducted a meta-analysis to assess which peginterferon was better when used with ribavirin. Methods: Relevant clinical trials were identified through the PubMed and EMBASE databases. Primary outcomes included early virological response (EVR), end of treatment response (ETR) and sustained virological response (SVR). Secondary outcomes included biochemical and histological responses and the discontinuation of treatment after adverse events. Meta-analysis was performed using xed-effect or random-effect methods, depending on absence or presence of signi cant heterogeneity. Analyses were performed with Review Manager Version 4.2.2. Results: Seven clinical trials were included that involved 3,526 patients in total; six were randomized clinical trials (RCTs) and one was nonrandomized. PEG-IFN-α2a plus ribavirin was better than PEG-IFN-α2b plus ribavirin with regards to ETR (relative risk [RR] = 1.21, 95% confidence interval [CI]: 1.14–1.28). This advantage was less obvious for EVR (RR = 1.12, 95% CI: 1.06–1.19) and SVR (RR = 1.10, 95% CI: 1.02–1.18). Patients who received PEG-IFN-α2a were less likely to discontinue treatment for safety reasons (RR = 0.85, 95% CI: 0.52–1.38). Conclusion: We demonstrated that PEG-IFN-α2a was a better choice than PEG-IFN-α2b in terms of virological responses.
Efficacy of pegylated interferon α-2a and α-2b in patients with genotype 1 chronic hepatitis C: a meta-analysis  [cached]
Coppola Nicola,Pisaturo Mariantonietta,Tonziello Gilda,Sagnelli Caterina
BMC Infectious Diseases , 2012, DOI: 10.1186/1471-2334-12-357
Abstract: Background Two formulations of Pegylated interferon (Peg-IFN) are on the market for treatment of chronic hepatitis C virus (HCV) infection. The purpose of this meta-analysis was to assess the efficacy of Peg-IFN α-2a versus Peg-IFN α-2b in combination with ribavirin in anti-human immunodeficiency virus (HIV)-negative patients with genotype 1 chronic HCV infection. Methods The following criteria were to be met for inclusion in the meta-analysis: (a) original data from randomized and non-randomized clinical trials; (b) study on the efficacy of conventional doses of Peg-IFN α-2a (180 μg/week) versus Peg-IFN α-2b (1.5 μg/kg of body weight/week), both in combination with ribavirin, in antiviral therapy-na ve HCV-genotype 1 subjects; (c) at least one of these primary outcomes: Rapid Virological Response (RVR); Early Complete Virological Response (EVR); End of Treatment Response (ETR); Sustained Virological Response (SVR); (d) odds ratio estimates of relative risk (RR) and associated 95% confidence intervals (CIs) or at least data enabling them to be computed; (e) English language; and (f) published as a full paper up to December 2011. Results Seven published studies met the inclusion criteria, allowing a meta-analysis on 3,026 patients. Peg-IFN α-2a and Peg-IFN α-2b showed similar rate of RVR (RR = 1.05; 95% CI = 0.87-1.27, p = 0.62) and SVR (RR = 1.08; 95% CI = 0.99-1.18, p = 0.098). Peg-IFN α-2a more frequently than Peg-IFN α-2b achieved EVR (RR = 1.11; 95% CI = 1.02-1.21, p = 0.013) and ETR (RR = 1.22; 95% CI = 1.14-1.31, p < 0.0001). Conclusion The standard schedules of Peg-IFN α-2a and Peg-IFN α-2b, both in combination with ribavirin, can be used indifferently for patients with chronic HCV genotype 1 who are anti- to eliminate HIV-negative and antiviral treatment-na ve.
Profiling of Substrate Specificities of 3C-Like Proteases from Group 1, 2a, 2b, and 3 Coronaviruses  [PDF]
Chi-Pang Chuck, Hak-Fun Chow, David Chi-Cheong Wan, Kam-Bo Wong
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0027228
Abstract: Background Coronaviruses (CoVs) can be classified into alphacoronavirus (group 1), betacoronavirus (group 2), and gammacoronavirus (group 3) based on diversity of the protein sequences. Their 3C-like protease (3CLpro), which catalyzes the proteolytic processing of the polyproteins for viral replication, is a potential target for anti-coronaviral infection. Methodology/Principal Findings Here, we profiled the substrate specificities of 3CLpro from human CoV NL63 (group 1), human CoV OC43 (group 2a), severe acute respiratory syndrome coronavirus (SARS-CoV) (group 2b) and infectious bronchitis virus (IBV) (group 3), by measuring their activity against a substrate library of 19×8 of variants with single substitutions at P5 to P3' positions. The results were correlated with structural properties like side chain volume, hydrophobicity, and secondary structure propensities of substituting residues. All 3CLpro prefer Gln at P1 position, Leu at P2 position, basic residues at P3 position, small hydrophobic residues at P4 position, and small residues at P1' and P2' positions. Despite 3CLpro from different groups of CoVs share many similarities in substrate specificities, differences in substrate specificities were observed at P4 positions, with IBV 3CLpro prefers P4-Pro and SARS-CoV 3CLpro prefers P4-Val. By combining the most favorable residues at P3 to P5 positions, we identified super-active substrate sequences ‘VARLQ↓SGF’ that can be cleaved efficiently by all 3CLpro with relative activity of 1.7 to 3.2, and ‘VPRLQ↓SGF’ that can be cleaved specifically by IBV 3CLpro with relative activity of 4.3. Conclusions/Significance The comprehensive substrate specificities of 3CLpro from each of the group 1, 2a, 2b, and 3 CoVs have been profiled in this study, which may provide insights into a rational design of broad-spectrum peptidomimetic inhibitors targeting the proteases.
Development of a loop-mediated isothermal amplification method to rapidly detect porcine circovirus genotypes 2a and 2b  [cached]
Qiu Xiaohuo,Li Tian,Zhang Guorui,Cao Jingjing
Virology Journal , 2012, DOI: 10.1186/1743-422x-9-318
Abstract: Background Porcine circovirus type 2 (PCV2), is nowadays associated with a number of diseases known as porcine circovirus-associated diseases (PCVAD), especially postweaning multisystemic wasting syndrome (PMWS). The epidemiological investigation of PCV2 infection was usually conducted by PCR, nested PCR, PCR-RFLP, TaqMan-based assay and nucleotide sequencing. However, there is still no rapid, sensitive and practical method for detecting PCV2 genotypes. As a novel nucleic acid amplification method, the loop-mediated isothermal amplification method (LAMP) has been used to detect a variety of pathogenic microorganisms. Results Herein, a LAMP method is developed to detect the genotypes of PCV2. The diagnostic sensitivity of LAMP is 1 copy/reaction for differentiating genotypes PCV2a and PCV2b. The reaction process was completed at 65°C for 1 hour in a water bath. Cross-reactivity assay shows that this method is specific for PCV2a and PCV2b and no reactive for PCV2c and other swine-origin viruses (i.e. CSFV, PRRSV, BVDV, TGEV and PEDV, etc). Identity between LAMP and nested PCR was 92.3% on 52 field clinical samples. Conclusions LAMP method provides a rapid, sensitive, reliable way to detect PCV2a and PCV2b, and a better means for the large scale investigation of PCV2a and PCV2b infection.
Sequence Heterogeneity in NS5A of Hepatitis C Virus Genotypes 2a and 2b and Clinical Outcome of Pegylated-Interferon/Ribavirin Therapy  [PDF]
Ahmed El-Shamy, Ikuo Shoji, Soo-Ryang Kim, Yoshihiro Ide, Susumu Imoto, Lin Deng, Seitetsu Yoon, Takashi Fujisawa, Satoshi Tani, Yoshihiko Yano, Yasushi Seo, Takeshi Azuma, Hak Hotta
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0030513
Abstract: Pegylated-interferon plus ribavirin (PEG-IFN/RBV) therapy is a current standard treatment for chronic hepatitis C. We previously reported that the viral sequence heterogeneity of part of NS5A, referred to as the IFN/RBV resistance-determining region (IRRDR), and a mutation at position 70 of the core protein of hepatitis C virus genotype 1b (HCV-1b) are significantly correlated with the outcome of PEG-IFN/RBV treatment. Here, we aimed to investigate the impact of viral genetic variations within the NS5A and core regions of other genotypes, HCV-2a and HCV-2b, on PEG-IFN/RBV treatment outcome. Pretreatment sequences of NS5A and core regions were analyzed in 112 patients infected with HCV-2a or HCV-2b, who were treated with PEG-IFN/RBV for 24 weeks and followed up for another 24 weeks. The results demonstrated that HCV-2a isolates with 4 or more mutations in IRRDR (IRRDR[2a]≥4) was significantly associated with rapid virological response at week 4 (RVR) and sustained virological response (SVR). Also, another region of NS5A that corresponds to part of the IFN sensitivity-determining region (ISDR) plus its carboxy-flanking region, which we referred to as ISDR/+C[2a], was significantly associated with SVR in patients infected with HCV-2a. Multivariate analysis revealed that IRRDR[2a]≥4 was the only independent predictive factor for SVR. As for HCV-2b infection, an N-terminal half of IRRDR having two or more mutations (IRRDR[2b]/N≥2) was significantly associated with RVR, but not with SVR. No significant correlation was observed between core protein polymorphism and PEG-IFN/RBV treatment outcome in HCV-2a or HCV-2b infection. Conclusion: The present results suggest that sequence heterogeneity of NS5A of HCV-2a (IRRDR[2a]≥4 and ISDR/+C[2a]), and that of HCV-2b (IRRDR[2b]/N≥2) to a lesser extent, is involved in determining the viral sensitivity to PEG-IFN/RBV therapy.
左归降糖解郁方对糖尿病并发抑郁症大鼠海马谷氨酸及n-甲基-d-天冬氨酸受体2a、2b的影响  [PDF]
中国中医药信息杂志 , 2015, DOI: 10.3969/j.issn.1005-5304.2015.10.020
Abstract: 目的观察左归降糖解郁方对糖尿病并发抑郁症大鼠海马谷氨酸、n-甲基-d-天冬氨酸受体(nmdareceptor,nr)2a及nr2b表达的影响,探讨其对糖尿病并发抑郁症大鼠海马损伤的保护机制。方法建立糖尿病并发抑郁症大鼠模型,随机分为模型组、阳性药组及左归降糖解郁方高、中、低剂量组,以正常大鼠为正常组,每组16只,各给药组给予相应药物灌胃,连续28d。采用open-field实验评价大鼠行为变化,elisa检测海马谷氨酸含量,免疫荧光法检测海马nr2a、nr2b表达。结果与正常组比较,模型组大鼠自主活动次数明显减少(p<0.01),海马谷氨酸含量明显升高(p<0.01),nr2a、nr2b表达明显升高(p<0.01);与模型组比较,阳性药组和左归降糖解郁方高剂量组大鼠自主活动次数明显增加(p<0.01),海马谷氨酸含量明显下降(p<0.01),nr2a、nr2b表达降低(p<0.05)。结论左归降糖解郁方可明显改善糖尿病并发抑郁症大鼠的抑郁行为,其药效作用可能与调控大鼠海马谷氨酸含量及nr2a、nr2b表达有关。
Characteristics of Nucleotide and Codon Usage Bias of 2A Sequence of Foot and Mouth Disease Virus
Zong-Liang Gao,Yuan-Xing Gu,Jian-Hua Zhou,Yao-Zhong Ding,Jie Zhang,Hao-Tai Chen,Li-Na Ma,Yong-Sheng Liu
Journal of Animal and Veterinary Advances , 2012, DOI: 10.3923/javaa.2012.3627.3634
Abstract: The cleavage at 2A/2B junction of Foot and Mouth Disease Virus (FMDV) is mediated by the 2A sequence. Here researchers calculate some data of the 2A sequence including the nucleotide usage bias (R-value), the Authentic Codon Bias (ACB value) and accumulation of Codon Bias (CUB2A value) to estimate potential effects of nucleotide and codon bias on the auto-cleavage of this junction. Researchers find that a high nucleotide usage bias exists in the 2A sequence (R-value = 0.856±0.113), ten positions 3, 5, 8, 9, 11, 14-18 show a stable codon usage tendency in the 2A sequence across all serotype while the accumulation of Codon Bias (CUB2A = 0.293±0.043) is low. It is interesting that an obvious downward trend of accumulation of codon bias in C-termini is present in the 2A sequence. These phenomena suggest that the nucleotide and codon usage models play potential roles in impairing the formation of the peptide bond linking the 2A/2B junction during co-translation by affecting conformation changes of A and P sites in the ribosome.

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