It is well established that different sites within a protein evolve at different rates according to their role within the protein; identification of these correlated mutations can aid in tasks such as ab initio protein structure,structure function analysis or sequence alignment.Mutual Information is a standard measure for coevolution between two sites but its application is limited by signal to noise ratio.In this work we report a preliminary study to investigate whether larger sequence sets could circumvent this problem by calculating mutual information arrays for two sets of drug naive sequences from the HIV gp120 protein for the B and C subtypes.Our results suggest that while the larger sequences sets can improve the signal to noise ratio,the gain is offset by the high mutation rate of the HIV virus which makes it more difficult to achieve consistent alignments.Nevertheless,we were able to predict a number of coevolving sites that were supported by previous experimental studies as well as a region close to the C terminal of the protein that was highly variable in the C subtype but highly conserved in the B subtype.

In recent years, the in silico epitopes prediction tools have facilitated the progress of vaccines development significantly and many have been applied to predict epitopes in viruses successfully. Herein, a general overview of different tools currently available, including T cell and B cell epitopes prediction tools, is presented. And the principles of different prediction algorithms are reviewed briefly. Finally, several examples are present to illustrate the application of the prediction tools.

To analyze features of the rabies epidemic in China between 2007 and 2011,identify factors influencing the epidemic and to provide a scientific basis for further control and prevention of rabies,Descriptive epidemiological methods and statistical analysis was used on data collected from the National Disease Reporting Information System between 2007 to 2011 and the National Active Surveillance System between 2007 and 2010.Our analysis shows that while the number of human rabies cases decreased year by year,the number of districts reporting cases did not show significant change.The situations in Guangdong,Guangxi,Guizhou and Hunan provinces clearly improved over the period but they remain provinces with high-incidence,and consequently influence the epidemic situation of surrounding provinces and possibly the whole country.Summer and autumn were high-incidence seasons.Farmers,students and pre-school children represent the high-risk populations,and rates of cases in farmers increased,those for students decreased,and pre-school children remained unchanged.Provinces with active surveillance programs reported a total of 2346 individual cases,of which 88.53％ were associated with canines.Postexposure prophylaxis (PEP) of rabies cases was not significantly improved,whereas PEP in post-exposure population was good.In rural regions of China,canine density was reduced somewhat,and the immunization rate increased slightly.Finally we show that while the epidemic decreased 2007 to 2011 in China,cases continued to be diffused in certain regions.Lack of standardization of PEP on rabies cases was the main reason of morbidity.The high density and low immunization of dog in rural areas and the defective situation of PEP are still continuous occurrences in China and remain a cause for concern.

The World Health Organization (WHO) standard assay for determining antibody level is the rapid fluorescent focus inhibition test (RFFIT) and is used to determine the degree of immunity after vaccination against rabies.To compare the difference in RFFIT results between the laboratories of The National Institute of Infectious Disease in Japan (NIID) and the Chinese Centre for Disease Control (CCDC) as well the influence of the choice of standard serum (STD) for the detection,the two laboratories detection methods were simultaneously manipulated by RFFIT.The reference serums used in NIID and the WHO standard serum used in CCDC were compared in the same RFFIT detection to determine the titer of four sera samples C1,S1,S2 and S4 in parallel,and the titers of the detected sera samples were calculated using the standard formula for neutralizing antibody titer.No significant difference was found in RFFIT methods from the two laboratories and the RFFIT testing procedures of the two laboratories have good consistency.However,different titers were obtained with the tentative internal standard serum (TI-STD) produced by adjusting to 2.0 IU of WHO standard serum in NIID and the WHO STD.The titer determined with the TI-STD was higher than that determined with WHO STD,This difference appears to be significant and requires further investigation.

Naturally occurring mutations in surface proteins of Hepatitis B virus(HBV)usually result in altered hepatitis B surface antigen(HBsAg)secretion efficiency.In the present study,we reported two conserved residues,M75 and M103 with respect to HBsAg,mutations of which not only attenuated HBsAg secretion(M75 only),but also suppressed HBV genome replication without compromising the overlapping p-gene product.We also found M75 and M103 can initiate truncated surface protein(TSPs)synthesis upon over-expression of full-length surface proteins,which may possibly contribute to HBV genome replication.However,attempts to rescue replicationdefective HBV mutant by co-expression of TSPs initiated from M75 or M103 were unsuccessful,which indicated surface proteins rather than the putative TSPs were involved in regulation of HBV genome replication.

Porcine reproductive and respiratory syndrome virus (PRRSV) has been recognized as one of the most important pathogens of pigs throughout the world. In 2006, more than 10 provinces of China have experienced an epizootic outbreak of pig diseases characterized by high fever, reddened skin and high morbidity and mortality. From June 2006 to April 2007, we have investigated some clinical samples in Hubei province by RT-PCR and cloned several major genes, N, GP5 and NSP2 gene, shown in this study. Phylogenetic analysis of these genes revealed that the highly pathogenic PRRSV variant, ZB, was responsible for 2006 emergent outbreak of pig disease in Hubei province similar with those variants isolated from other provinces in China in 2006, and belongs to the NA-type PRRSV. In the PRRSV variants, the N and GP5 shear about 90% identity with prototypic ATCC VR-2332 and some typical NA-type Chinese isolates, except the 2850bp NSP2 gene (only shares 65% identity with ATCC VR-2332). But they all shear more than and 97% identity with other highly pathogenetic Chinese PRRSV strains. Additionally, there are extensive amino acid (aa) mutations in the GP5 protein and 2 deletions in the Nsp2 protein when compared with the previous isolates. Most of the variants found in 2006 epizootic outbreak of pig diseases in China were the farthest variants from the typical NA-type PRRSV in phylogenetic distance, and these diversities may be responsible for the differences in the pathogenicity observed between these variants and original Chinese PRRSV strains.

A total of 100 HIN1 flu real-time-PCR positive throat swabs collected from fever patients in Zhejiang,Hubei and Guangdong between June and November 2009,were provided by local CDC laboratories.After MDCK cell culture,57 Influenza A Pandemic (H1N1) viruses were isolated and submitted for whole genome sequencing.A total of 39 HA sequences,52 NA sequences,36 PB2 sequences,31 PB1 sequences,40 PA sequences,48 NP sequences,51 MP sequences and 36 NS sequences were obtained,including 20 whole genome sequences.Sequence comparison revealed they shared a high degree of homology (96％～99％) with known epidemic strains (A/Califomia/04/2009(H1N1).Phylogenetic analysis showed that although the sequences were highly conserved,they clustered into a small number of groups with only a few distinct strains.Site analysis revealed three substitutions at loop 220 (221-228) of the HA receptor binding site in the 39 HA sequences:A/Hubei/86/2009 PKVRDQEG→PKVRDQEA,A/Zhejiang/08/2009 PKVRDQEG→PKVRDQER,A/Hubei/75/2009PKVRDQEG→PKVRDQGG,the A/Hubei/75/2009 was isolated from an acute case,while the other two were from patients with mild symptoms.Other key sites such as 119,274,292 and 294 amino acids of NA protein,627 of PB2 protein were conserved.Meanwhile,all the M2 protein sequences possessed the Ser32Asn mutation,suggesting that these viruses were resistant to adamantanes.Comparison of these sequences with other H1N1 viruses collected from the NCBI database provides insight into H1N1 transmission and circulation patterns.

OBJECTIVETo investigate the virulence characteristics of two fixed strains (CTN and aG) and a street strain (HN10) of rabies viruses isolated in China.

METHODSICR mice of different age groups were inoculated with CTN, aG and HN10 rabies virus strains via the intracracerebral (i.c.) or intramuscular (i.m.) routes, and observed for 20 days.

RESULTSThe CTN strain was pathogenic to 7-day-old suckling mice that received i.c. inoculations and 3-day-old suckling mice that received i.m. inoculations. The aG strain was pathogenic to 4-week-old mice that received i.c. inoculations and 7-day-old suckling mice that received i.m. inoculations. The HN10 strain was pathogenic to mice of all age groups via both inoculation routes. In moribund mice, the viruses had spread to most regions of the brain. The CTN and HN10 strains had similar dissemination patterns in the brain; both viral antigens could be found in the dentate gyrus (DG), whereas few viral antigens were present in the DG from specimens that had been infected with the aG strain.

CONCLUSIONA comprehensive sequence analysis of the G protein suggested that differences in gene sequences may be responsible for producing strain-specific differences in pathogenicity and distribution in the brain.

Animals ; Antigens, Viral ; immunology ; Brain ; immunology ; virology ; China ; Mice ; Mice, Inbred ICR ; Nucleocapsid Proteins ; immunology ; Rabies ; virology ; Rabies virus ; immunology ; isolation & purification ; pathogenicity

OBJECTIVETo sequence and analyze the whole genome of Japanese encephalitis virus (JEV) strain named 47 which was isolated from patient's cerebrospinal fluid sample in Heilongjiang province in 1950.

METHODSRNA was extracted from the recovery strain 47 and amplified with self-designed JEV genome sequencing primers. The differentiation analysis for nucleotides and coding amino acids and phylogenetic analysis were performed by the software of DNAStar, Modeltest, and Phylip.

RESULTSThe whole genome of strain 47 has 10,977 nucleotides. An open reading frame from 95 to 10,391 including 10,296 nucleotides is capable of coding a 3432 amino acid polyprotein. The nucleotide difference between strain 47 and 5 vaccine strains is 2.4%-4.4%, the amino acid difference between strain 47 and 5 vaccine strains is 0.3%-1.1%. The best evolution model for the whole genome is GTR + I + G. Based on the phylogenetic analysis, strain 47 belongs to the genotype III JEV.

CONCLUSIONStrain 47 is highly conserved on whole genome nucleotide and amino acid sequence. And it is belongs to the genotype III JEV.

China ; Encephalitis Virus, Japanese ; classification ; genetics ; isolation & purification ; Encephalitis, Japanese ; virology ; Genome, Viral ; Humans ; Molecular Sequence Data ; Open Reading Frames ; Phylogeny ; RNA, Viral ; cerebrospinal fluid ; genetics ; isolation & purification

To understand the epidemic situation and factors influencing rabies cases in children in China, we obtained an overview of the current epidemic based on individual data of rabies cases in children and a descriptive analysis was carried on the prevalence and related factors. The results showed that the rabies cases in children accounted for 21.3% of the total number of rabies cases in China, 97.0% of these cases occurred in rural areas, they were mainly caused by dogs (81.5%), and were primarily level III exposure (47.7%). More than half of the cases were not treated with wound care, vaccination rate was extremely low (15.7%), and only 5.9% of cases were injected with antibodies. Furthermore, 25.4% of cases adopted incorrect treatments such as extruding bleed and wound closure, cases vaccinated with 5 injections accounted for only 22.5%. In conclusion, the prevalence of rabies cases in children in China remains a serious concern, the number and immune status of dogs in rural areas, and knowledge of rabies by risk populations should be considered in future rabies prevention and control programs.
Adolescent ; Animals ; Child ; Child, Preschool ; China ; epidemiology ; Dog Diseases ; epidemiology ; prevention & control ; Dogs ; Female ; Humans ; Male ; Prevalence ; Rabies ; epidemiology ; prevention & control ; Rabies Vaccines ; therapeutic use