Deshun Xu

Bioinformatics analysis of the epitope regions for norovirus capsid protein

BackgroundNorovirus is the major cause of nonbacterial epidemic gastroenteritis, being highly prevalent in both developing and developed countries. Despite of the available monoclonal antibodies (MAbs) for different sub-genogroups, a comprehensive epitope analysis based on various bioinformatics technology is highly desired for future potential antibody development in clinical diagonosis and treatment.MethodsA total of 18 full-length human norovirus capsid protein sequences were downloaded from GenBank. Protein modeling was performed with program Modeller 9.9. The modeled 3D structures of capsid protein of norovirus were submitted to the protein antigen spatial epitope prediction webserver (SEPPA) for predicting the possible spatial epitopes with the default threshold. The results were processed using the Biosoftware.ResultsCompared with GI, we found that the GII genogroup had four deletions and two special insertions in the VP1 region. The predicted conformational epitope regions mainly concentrated on N-terminal (1~96), Middle Part (298~305, 355~375) and C-terminal (560~570). We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup.ConclusionsThe predicted conformational epitope regions of norovirus VP1 mainly concentrated on N-terminal, Middle Part and C-terminal. We find two common epitope regions on sequences for GI and GII genogroup, and also found an exclusive epitope region for GII genogroup. The overlapping with experimental epitopes indicates the important role of latest computational technologies. With the fast development of computational immunology tools, the bioinformatics pipeline will be more and more critical to vaccine design.

Cocirculation of Three Hemagglutinin and Two Neuraminidase Subtypes of Avian Influenza Viruses in Huzhou, China, April 2013: Implication for the Origin of the Novel H7N9 Virus

ABSTRACT We detected three avian influenza hemagglutinin (HA) subtypes (H7, H9, and H5) and two neuraminidase (NA) subtypes (N9 and N2), as well as H7N9-related H9N9 reassortant intermediates, cocirculating among poultry in Huzhou, China, during April 2013. The results of our study reveal not only that Huzhou is one of the geographic origins of the novel H7N9 virus but also that cocirculation poses a potential threat to humans in the future.

Rapid Emergence of Novel GII.4 Sub-Lineages Noroviruses Associated with Outbreaks in Huzhou, China, 2008–2012

Infection caused by noroviruses (NoVs) is one of the most important causes of acute gastroenteritis in humans worldwide. To gain insight into the epidemiology of and genetic variation in NoV strains, stool samples collected from 18 outbreaks of acute gastroenteritis in Huzhou, China, between January 2008 and December 2012 were analyzed. Samples were tested for NoVs by real-time RT-PCR. Partial sequences of the RNA- dependent RNA polymerase (RdRp) and capsid gene of the positive samples were amplified by RT-PCR, and the PCR products were sequenced and used for phylogenetic analysis. NoVs were found to be responsible of 88.8% of all nonbacterial acute gastroenteritis outbreaks in Huzhou over the last 5 years. Genogroup II outbreaks largely predominated and represented 93% of all outbreaks. A variety of genotypes were found among genogroups I and II, including GI.4, GI.8, GII.4, and GII.b. Moreover, phylogenetic analyses identified two recombinant genotypes (polymerase/capsid): GI.2/GI.6 and GII.e/GII.4 2012 Sydney. GII.4 was predominant and involved in 8/10 typed outbreaks. During the study period, GII.4 NoV variants 2006b, New Orleans 2009, and Sydney 2012 were identified. This is the first report of the detection of GII.4 New Orleans 2009 variant, GII.e/GII.4 Sydney 2012 recombinant in outbreaks of acute gastroenteritis in China.

A cross-priming amplification assay coupled with vertical flow visualization for detection of Vibrio parahaemolyticus.

Vibrio parahaemolyticus is a marine seafood-borne pathogen that causes gastrointestinal disorders in humans. In this study, we developed a cross-priming amplification (CPA) assay coupled with vertical flow (VF) visualization for rapid and sensitive detection of V. parahaemolyticus. This assay correctly detected all target strains (n = 13) and none of the non-target strains (n = 27). Small concentrations of V. parahaemolyticus (1.8 CFU/mL for pure cultures and 18 CFU/g for reconstituted samples) were detected within 1 h. CPA-VF can be applied at a large scale and can be used to detect V. parahaemolyticus strains rapidly in seafood and environmental samples, being especially useful in the field.

Nearly complete genome sequence of one GII.17 Norovirus identified by direct sequencing from HuZhou, China

Human norovirus is the leading cause of acute gastroenteritis worldwide. However, in vitro culture system is complicated for human norovirus. Sequence analysis became more useful for norovirus research, particularly when using complete genomic sequences.

Detection and differentiation of Vibrio parahaemolyticus by multiplexed real-time PCR

Vibrio parahaemolyticus is a common and important pathogen that causes human gastroenteritis worldwide. A rapid, sensitive, and specific assay is urgently required for detection and differentiation of V. parahaemolyticus strains. We designed three sets of primers and probes using groEL and two virulence genes (tdh and trh) from V. parahaemolyticus, and developed a multiplex real-time PCR protocol. The sensitivity and specificity of the multiplex assay was evaluated by environmental and clinical specimens of V. parahaemolyticus. The multiplex PCR response system and annealing temperature were optimized. The detection limits of the multiplex real-time PCR were 104 and 105 CFU/mL (or CFU/g) in pure cultures and spiked oysters, respectively. The multiplex real-time PCR specifically detected and differentiated V. parahaemolyticus from 35 Vibrio strains and 11 other bacterial strains. Moreover, this method can detect and distinguish virulent from nonvirulent strains, with no cross-reactivity observed in the bacteria tested. This newly established multiplex real-time PCR assay offers rapid, specific, and reliable detection of the total and pathogenic V. parahaemolyticus strains, which is very useful during outbreaks and sporadic cases caused by V. parahaemolyticus infection.