A stochastic approach for co-evolution process of virus and human immune system

Infectious diseases have long been a shaping force in human history, necessitating a comprehensive understanding of their dynamics. This study introduces a co-evolution model that integrates both epidemiological and evolutionary dynamics. Utilizing a system of differential equations, the model represents the interactions among susceptible, infected, and recovered populations for both ancestral and evolved viral strains. Methodologically rigorous, the model's existence and uniqueness have been verified, and it accommodates both deterministic and stochastic cases. A myriad of graphical techniques have been employed to elucidate the model's dynamics. Beyond its theoretical contributions, this model serves as a critical instrument for public health strategy, particularly predicting future outbreaks in scenarios where viral mutations compromise existing interventions.

Towards Chinese text and DNA shift encoding scheme based on biomass plasmid storage

DNA, as the storage medium in organisms, can address the shortcomings of existing electromagnetic storage media, such as low information density, high maintenance power consumption, and short storage time. Current research on DNA storage mainly focuses on designing corresponding encoders to convert binary data into DNA base data that meets biological constraints. We have created a new Chinese character code table that enables exceptionally high information storage density for storing Chinese characters (compared to traditional UTF-8 encoding). To meet biological constraints, we have devised a DNA shift coding scheme with low algorithmic complexity, which can encode any strand of DNA even has excessively long homopolymer. The designed DNA sequence will be stored in a double-stranded plasmid of 744bp, ensuring high reliability during storage. Additionally, the plasmid's resistance to environmental interference ensuring long-term stable information storage. Moreover, it can be replicated at a lower cost.

Mesenchymal Stem Cells Pretreated with Collagen Promote Skin Wound-Healing

The existing treatment modalities for skin injuries mainly include dressings, negative-pressure wound treatment, autologous skin grafting, and high-pressure wound treatment. All of these therapies have limitations such as high time cost, the inability to remove inactivated tissue in a timely manner, surgical debridement, and oxygen toxicity. Mesenchymal stem cells have a unique self-renewal ability and wide differentiation potential, and they are one of the most promising stem cell types in cell therapy and have great application prospects in the field of regenerative medicine. Collagen exerts structural roles by promoting the molecular structure, shape, and mechanical properties of cells, and adding it to cell cultures can also promote cell proliferation and shorten the cell doubling time. The effects of collagen on MSCs were examined using Giemsa staining, EdU staining, and growth curves. Mice were subjected to allogeneic experiments and autologous experiments to reduce individual differences; all animals were separated into four groups. Neonatal skin sections were detected by HE staining, Masson staining, immunohistochemical staining, and immunofluorescence staining. We found that the MSCs pretreated with collagen accelerated the healing of skin wounds in mice and canines by promoting epidermal layer repair, collagen deposition, hair follicle angiogenesis, and an inflammatory response. Collagen promotes the secretion of the chemokines and growth factors associated with skin healing by MSCs, which positively influences skin healing. This study supports the treatment of skin injuries with MSCs cultured in medium with collagen added.

Using amino acid features to identify the pathogenicity of influenza B virus

BACKGROUND

Influenza B virus can cause epidemics with high pathogenicity, so it poses a serious threat to public health. A feature representation algorithm is proposed in this paper to identify the pathogenicity phenotype of influenza B virus.

METHODS

The dataset included all 11 influenza virus proteins encoded in eight genome segments of 1724 strains. Two types of features were hierarchically used to build the prediction model. Amino acid features were directly delivered from 67 feature descriptors and input into the random forest classifier to output informative features about the class label and probabilistic prediction. The sequential forward search strategy was used to optimize the informative features. The final features for each strain had low dimensions and included knowledge from different perspectives, which were used to build the machine learning model for pathogenicity identification.

RESULTS

The 40 signature positions were achieved by entropy screening. Mutations at position 135 of the hemagglutinin protein had the highest entropy value (1.06). After the informative features were directly generated from the 67 random forest models, the dimensions for class and probabilistic features were optimized as 4 and 3, respectively. The optimal class features had a maximum accuracy of 94.2% and a maximum Matthews correlation coefficient of 88.4%, while the optimal probabilistic features had a maximum accuracy of 94.1% and a maximum Matthews correlation coefficient of 88.2%. The optimized features outperformed the original informative features and amino acid features from individual descriptors. The sequential forward search strategy had better performance than the classical ensemble method.

CONCLUSIONS

The optimized informative features had the best performance and were used to build a predictive model so as to identify the phenotype of influenza B virus with high pathogenicity and provide early risk warning for disease control.

Melatonin treatment improves human umbilical cord mesenchymal stem cell therapy in a mouse model of type II diabetes mellitus via the PI3K/AKT signaling pathway

Background

Mesenchymal stem cells (MSCs) are promising candidates for tissue regeneration and disease treatment. However, long-term in vitro passaging leads to stemness loss of MSCs, resulting in failure of MSC therapy. This study investigated whether the combination of melatonin and human umbilical cord mesenchymal stem cells (hUC-MSCs) was superior to hUC-MSCs alone in ameliorating high-fat diet and streptozocin (STZ)-induced type II diabetes mellitus (T2DM) in a mouse model.

Methods

Mice were divided into four groups: normal control (NC) group; T2DM group; hUC-MSCs treatment alone (UCMSC) group and pretreatment of hUC-MSCs with melatonin (UCMSC/Mel) group.

Results

RNA sequence analysis showed that certain pathways, including the signaling pathway involved in the regulation of cell proliferation signaling pathway, were regulated by melatonin. The blood glucose levels of the mice in the UCMSC and UCMSC/Mel treatment groups were significantly reduced compared with the T2DM group without treatment (P < 0.05). Furthermore, hUC-MSCs enhance the key factor in the activation of the PI3K/Akt pathway in T2DM mouse hepatocytes.

Conclusion

The pretreatment of hUC-MSCs with melatonin partly boosted cell efficiency and thereby alleviated impaired glycemic control and insulin resistance. This study provides a practical strategy to improve the application of hUC-MSCs in diabetes mellitus and cytotherapy.

Graphical abstract

Overview of the PI3K/AKT signaling pathway. (A) Underlying mechanism of UCMSC/Mel inhibition of hyperglycemia and insulin resistance T2DM mice via regulation of PI3K/AKT pathway. hUC-MSCs stimulates glucose uptake and improves insulin action thus should inhibition the clinical signs of T2DM, through activation of the p-PI3K/Akt signaling pathway and then regulates glucose transport through activating AS160. UCMSC/Mel increases p53-dependent expression of BCL2, and inhibit BAX and Capase3 protein activation. Leading to the decrease in apoptosis. (B) Melatonin modulated PI3K/AKT signaling pathway. Melatonin activated PI3K/AKT response pathway through binding to MT1and MT2 receptor. Leading to the increase in hUC-MSCs proliferation, migration and differentiation. → (Direct stimulatory modification); ┴ ( Direct Inhibitory modification); → ┤ (Multistep inhibitory modification); ↑ (Up regulate); ↓ (Down regulate); PI3K (Phosphoinositide 3-Kinase); AKT ( protein kinase B); PDK1 (Phosphoinositide-dependent protein kinase 1); IR, insulin receptor; GLUT4 ( glucose transporter type 4); ROS (reactive oxygen species); BCL-2 (B-cell lymphoma-2); PDK1 (phosphoinositide-dependent kinase 1) BAX (B-cell lymphoma-2-associated X protein); PCNA (Proliferating cell nuclear antigen); Cell cycle-associated proteins (KI67, cyclin A, cyclin E)

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-022-02832-0.

Melatonin Promotes the Therapeutic Effect of Mesenchymal Stem Cells on Type 2 Diabetes Mellitus by Regulating TGF-β Pathway

Abundant evidence proves the therapeutic effect of adipose-derived mesenchymal stem cells (ADMSCs) in the treatment of diabetes mellitus. However, the problems have not been solved that viability of ADMSCs were inconsistent and the cells quickly undergo senescence after in vitro cell culture. In addition, the therapeutic effect of ADMSCs is still not satisfactory. In this study, melatonin (MLT) was added to canine ADMSC culture medium, and the treated cells were used to treat type 2 diabetes mellitus (T2DM). Our research reveals that adding MLT to ADMSC culture medium can promote the viability of ADMSCs. This effect depends on the binding of MLT and MLT receptors, which activates the transforming growth factor β (TGF-β) pathway and then changes the cell cycle of ADMSCs and improves the viability of ADMSCs. Since ADMSCs were found to be used to treat T2DM by anti-inflammatory and anti-endoplasmic reticulum (ER) stress capabilities, our data demonstrate that MLT augment several effects of ADMSCs in remission hyperglycemia, insulin resistance, and liver glycogen metabolism in T2DM patients. This suggest that ADMSCs and MLT-ADMSCs is safe and vabulable for pet clinic.

Prediction of pandemic risk for animal-origin coronavirus using a deep learning method

Background

Coronaviruses can be isolated from bats, civets, pangolins, birds and other wild animals. As an animal-origin pathogen, coronavirus can cross species barrier and cause pandemic in humans. In this study, a deep learning model for early prediction of pandemic risk was proposed based on the sequences of viral genomes.

Methods

A total of 3257 genomes were downloaded from the Coronavirus Genome Resource Library. We present a deep learning model of cross-species coronavirus infection that combines a bidirectional gated recurrent unit network with a one-dimensional convolution. The genome sequence of animal-origin coronavirus was directly input to extract features and predict pandemic risk. The best performances were explored with the use of pre-trained DNA vector and attention mechanism. The area under the receiver operating characteristic curve (AUROC) and the area under precision-recall curve (AUPR) were used to evaluate the predictive models.

Results

The six specific models achieved good performances for the corresponding virus groups (1 for AUROC and 1 for AUPR). The general model with pre-training vector and attention mechanism provided excellent predictions for all virus groups (1 for AUROC and 1 for AUPR) while those without pre-training vector or attention mechanism had obviously reduction of performance (about 5–25%). Re-training experiments showed that the general model has good capabilities of transfer learning (average for six groups: 0.968 for AUROC and 0.942 for AUPR) and should give reasonable prediction for potential pathogen of next pandemic. The artificial negative data with the replacement of the coding region of the spike protein were also predicted correctly (100% accuracy). With the application of the Python programming language, an easy-to-use tool was created to implements our predictor.

Conclusions

Robust deep learning model with pre-training vector and attention mechanism mastered the features from the whole genomes of animal-origin coronaviruses and could predict the risk of cross-species infection for early warning of next pandemic.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s40249-021-00912-6.

A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path

BACKGROUND

MicroRNAs are a class of important small noncoding RNAs, which have been reported to be involved in the processes of tumorigenesis and development by targeting a few genes. Existing studies show that the imbalance between cell proliferation and apoptosis is closely related to the initiation and development of cancers. However, the impact of miRNAs on this imbalance has not been studied systematically.

RESULTS

In this study, we first construct a cell fate miRNA-gene regulatory network. Then, we propose a systematical method for calculating the global impact of miRNAs on cell fate genes based on the shortest path. Results on breast cancer and liver cancer datasets show that most of the cell fate genes are perturbed by the differentially expressed miRNAs. Most of the top-identified miRNAs are verified in the Human MicroRNA Disease Database (HMDD) and are related to breast and liver cancers. Function analysis shows that the top 20 miRNAs regulate multiple cell fate related function modules and interact tightly based on their functional similarity. Furthermore, more than half of them can promote sensitivity or induce resistance to some anti-cancer drugs. Besides, survival analysis demonstrates that the top-ranked miRNAs are significantly related to the overall survival time in the breast and liver cancers group.

CONCLUSION

In sum, this study can help to systematically study the important role of miRNAs on proliferation and apoptosis and thereby uncover the key miRNAs during the process of tumorigenesis. Furthermore, the results of this study will contribute to the development of clinical therapy based miRNAs for cancers.

Highly sensitive and specific detection of hepatitis B virus DNA and drug resistance mutations utilizing the PCR-based CRISPR-Cas13a system

OBJECTIVES

Undetectable or low-level hepatitis B virus (HBV) DNA and drug resistance mutations in patients may increase the risk of HBV transmission or cause active viral replication and other clinical problems. Here, we established a highly sensitive and practical method for HBV and drug resistance detection using a polymerase chain reaction (PCR) -based CRISPR-Cas13a detection system (referred to as PCR-CRISPR) and evaluated its detection capability using clinical samples.

METHODS

Specific CRISPR RNAs (crRNAs) are designed for HBV DNA detection and YMDD (tyrosine-methionine-aspartate-aspartate) variant identification. The HBV DNA was detected in 312 serum samples for HBV diagnosis using quantification PCR (qPCR) and PCR-CRISPR. Additionally, 424 serum samples for YMDD testing were detected by qPCR, direct sequencing, and our assay.

RESULTS

Using PCR-CRISPR, one copy per test of HBV DNA was detected with HBV-1 crRNA in 15 min after PCR amplification. Consistent results with qPCR were observed for 302 samples, while the remaining 10 samples with low-level HBV DNA were detectable by PCR-CRISPR and droplet digital PCR but not by qPCR. PCR-CRISPR diagnosed all 412 drug-resistant samples detected by the YMDD detection qPCR kit and direct sequencing, as well as the other 12 drug-resistant samples with low-level HBV DNA undetectable by qPCR and direct sequencing.

CONCLUSIONS

We developed a novel PCR-CRISPR method for highly sensitive and specific detection of HBV DNA and drug resistance mutations. One copy per test for HBV DNA and YMDD drug resistance mutations could be detected. This method has wide application prospects for the early detection of HBV infection, drug resistance monitoring and treatment guidance.

A Systematic Way to Infer the Regulation Relations of miRNAs on Target Genes and Critical miRNAs in Cancers

MicroRNAs (miRNAs) are a class of important non-coding RNAs, which play important roles in tumorigenesis and development by targeting oncogenes or tumor suppressor genes. One miRNA can regulate multiple genes, and one gene can be regulated by multiple miRNAs. To promote the clinical application of miRNAs, two fundamental questions should be answered: what's the regulatory mechanism of a miRNA to a gene, and which miRNAs are important for a specific type of cancer. In this study, we propose a miRNA influence capturing (miRNAInf) to decipher regulation relations of miRNAs on target genes and identify critical miRNAs in cancers in a systematic approach. With the pair-wise miRNA/gene expression profiles data, we consider the assigning problem of a miRNA on target genes and determine the regulatory mechanisms by computing the Pearson correlation coefficient between the expression changes of a miRNA and that of its target gene. Furthermore, we compute the relative local influence strength of a miRNA on its target gene. Finally, integrate the local influence strength and target gene's importance to determine the critical miRNAs involved in specific cancer. Results on breast, liver and prostate cancers show that positive regulations are as common as negative regulations. The top-ranked miRNAs show great potential as therapeutic targets driving cancer to a normal state, and they are demonstrated to be closely related to cancers based on biological functional analysis, drug sensitivity/resistance analysis and survival analysis. This study will be helpful for the discovery of critical miRNAs and development of miRNAs-based clinical therapeutics.

Using the spike protein feature to predict infection risk and monitor the evolutionary dynamic of coronavirus

BACKGROUND

Coronavirus can cross the species barrier and infect humans with a severe respiratory syndrome. SARS-CoV-2 with potential origin of bat is still circulating in China. In this study, a prediction model is proposed to evaluate the infection risk of non-human-origin coronavirus for early warning.

METHODS

The spike protein sequences of 2666 coronaviruses were collected from 2019 Novel Coronavirus Resource (2019nCoVR) Database of China National Genomics Data Center on Jan 29, 2020. A total of 507 human-origin viruses were regarded as positive samples, whereas 2159 non-human-origin viruses were regarded as negative. To capture the key information of the spike protein, three feature encoding algorithms (amino acid composition, AAC; parallel correlation-based pseudo-amino-acid composition, PC-PseAAC and G-gap dipeptide composition, GGAP) were used to train 41 random forest models. The optimal feature with the best performance was identified by the multidimensional scaling method, which was used to explore the pattern of human coronavirus.

RESULTS

The 10-fold cross-validation results showed that well performance was achieved with the use of the GGAP (g = 3) feature. The predictive model achieved the maximum ACC of 98.18% coupled with the Matthews correlation coefficient (MCC) of 0.9638. Seven clusters for human coronaviruses (229E, NL63, OC43, HKU1, MERS-CoV, SARS-CoV, and SARS-CoV-2) were found. The cluster for SARS-CoV-2 was very close to that for SARS-CoV, which suggests that both of viruses have the same human receptor (angiotensin converting enzyme II). The big gap in the distance curve suggests that the origin of SARS-CoV-2 is not clear and further surveillance in the field should be made continuously. The smooth distance curve for SARS-CoV suggests that its close relatives still exist in nature and public health is challenged as usual.

CONCLUSIONS

The optimal feature (GGAP, g = 3) performed well in terms of predicting infection risk and could be used to explore the evolutionary dynamic in a simple, fast and large-scale manner. The study may be beneficial for the surveillance of the genome mutation of coronavirus in the field.

Efficient Gaussian sample specific network marker discovery and drug enrichment analysis validation

Identifying stable gene markers at an individual level can help to understand the genetic mechanisms of each individual patient and accomplish personalized medicine. In this paper, we propose an efficient framework to identify sample-specific markers. Gene expression data first is transformed to a corresponding likelihood matrix to alleviate inherent noise besides adding population information to each sample. Then those significantly differential genes or gene pairs are further mapped to a STRING network for analysis by assuming that the likelihood of each gene or gene pairs in the control group follows a Gaussian distribution. The proposed method is applied to three benchmark datasets including lung adenocarcinoma, kidney renal clear cell carcinoma, and uterine corpus endometrial carcinoma. It is found that disease gene markers identified by the proposed methods outperform the previous sample-specific network (SSN) method in both subtyping and survival analysis. Furthermore, we exploit the application of the subtype markers in following drug selection. The difference of the enriched drug set may reflect some underlying mechanisms of the subtypes and shed light on selecting appropriate drugs for each cancer subtype.

Scoring amino acid mutation to predict pandemic risk of avian influenza virus

BACKGROUND

Avian influenza virus can directly cross species barriers and infect humans with high fatality. As antigen novelty for human host, the public health is being challenged seriously. The pandemic risk of avian influenza viruses should be analyzed and a prediction model should be constructed for virology applications.

RESULTS

The 178 signature positions in 11 viral proteins were firstly screened as features by the scores of five amino acid factors and their random forest rankings. The Supporting Vector Machine algorithm achieved well performance. The most important amino acid factor (Factor 5) and the minimal range of signature positions (63 amino acid residues) were also explored. Moreover, human-origin avian influenza viruses with three or four genome segments from human virus had pandemic risk with high probability.

CONCLUSION

Using machine learning methods, the present paper scores the amino acid mutations and predicts pandemic risk with well performance. Although long evolution distances between avian and human viruses suggest that avian influenza virus in nature still need time to fix among human host, it should be notable that there are high pandemic risks for H7N9 and H9N2 avian viruses.

Predicting interspecies transmission of avian influenza virus based on wavelet packet decomposition

Using wavelet packet decomposition, the energy coefficients in the fifth level of viral protein sequences were achieved to predict interspecies transmission. Since avian-origin influenza viruses could have high sequence similarities with human-origin avian influenza virus and could have the phenotype of interspecies transmission, viral data should be filtered to prevent the misconduct of feature selection and false performance of predicting models. Considering the balance of data size, the empirical cut-off value 97% was used to screen avian-origin influenza virus with high sequence similarity. The excellent performances of cross validation show that the SVM model has the best capability of predicting transmission and evaluating the contribution of five amino acid factors. The robust model was finally used to evaluate the filtered data of avian-origin virus and the results confirmed that double check for ambiguous phenotype of avian-origin virus with high sequence similarity was necessary and part of them have the ability to across species barriers.

The Complete Genome of a New Betabaculovirus from Clostera anastomosis

Clostera anastomosis (Lepidoptera: Notodontidae) is a defoliating forest insect pest. Clostera anastomosis granulovirus-B (ClasGV-B) belonging to the genus Betabaculovirus of family Baculoviridae has been used for biological control of the pest. Here we reported the full genome sequence of ClasGV-B and compared it to other previously sequenced baculoviruses. The circular double-stranded DNA genome is 107,439 bp in length, with a G+C content of 37.8% and contains 123 open reading frames (ORFs) representing 93% of the genome. ClasGV-B contains 37 baculovirus core genes, 25 lepidopteran baculovirus specific genes, 19 betabaculovirus specific genes, 39 other genes with homologues to baculoviruses and 3 ORFs unique to ClasGV-B. Hrs appear to be absent from the ClasGV-B genome, however, two non-hr repeats were found. Phylogenetic tree based on 37 core genes from 73 baculovirus genomes placed ClasGV-B in the clade b of betabaculoviruses and was most closely related to Erinnyis ello GV (ErelGV). The gene arrangement of ClasGV-B also shared the strongest collinearity with ErelGV but differed from Clostera anachoreta GV (ClanGV), Clostera anastomosis GV-A (ClasGV-A, previously also called CaLGV) and Epinotia aporema GV (EpapGV) with a 20 kb inversion. ClasGV-B genome contains three copies of polyhedron envelope protein gene (pep) and phylogenetic tree divides the PEPs of betabaculoviruses into three major clades: PEP-1, PEP-2 and PEP/P10. ClasGV-B also contains three homologues of P10 which all harbor an N-terminal coiled-coil domain and a C-terminal basic sequence. ClasGV-B encodes three fibroblast growth factor (FGF) homologues which are conserved in all sequenced betabaculoviruses. Phylogenetic analysis placed these three FGFs into different groups and suggested that the FGFs were evolved at the early stage of the betabaculovirus expansion. ClasGV-B is different from previously reported ClasGV-A and ClanGV isolated from Notodontidae in sequence and gene arrangement, indicating the virus is a new notodontid betabaculovirus.

[Recent Advances in Vaccines and Drugs Against the Ebola Virus]

The Ebola virus belongs to the Filovirus family, which causes Ebola hemorrhagic fever (mortality, 25%-90%). An outbreak of infection by the Ebola virus is sweeping across West Africa, leading to high mortality and worldwide panic. The Ebola virus has caused a serious threat to public health, so intensive scientific studies have been carried out. Several vaccines (e.g., rVSV-ZEBOV, ChAd3-ZEBOV) have been put into clinical trials and antiviral drugs (e.g., TKM-Ebola, ZMAPP) have been administered in the emergency setting to patients infected by the Ebola virus. Here, recent advances in vaccines and drugs against the Ebola virus are reviewed.

Metagenomic profile of the viral communities in Rhipicephalus spp. ticks from Yunnan, China

Besides mosquitoes, ticks are regarded as the primary source of vector-borne infectious diseases. Indeed, a wide variety of severe infectious human diseases, including those involving viruses, are transmitted by ticks in many parts of the world. To date, there are no published reports on the use of next-generation sequencing for studying viral diversity in ticks or discovering new viruses in these arthropods from China. Here, Ion-torrent sequencing was used to investigate the presence of viruses in three Rhipicephalus spp. tick pools (NY-11, NY-13, and MM-13) collected from the Menglian district of Yunnan, China. The sequencing run resulted in 3,641,088, 3,106,733, and 3,871,851 reads in each tick pool after trimming. Reads and assembled contiguous sequences (contigs) were subject to basic local alignment search tool analysis against the GenBank database. Large numbers of reads and contigs related to known viral sequences corresponding to a broad range of viral families were identified. Some of the sequences originated from viruses that have not been described previously in ticks. Our findings will facilitate better understanding of the tick virome, and add to our current knowledge of disease-causing viruses in ticks living under natural conditions.

Effects of actin-like proteins encoded by two Bacillus pumilus phages on unstable lysogeny, revealed by genomic analysis

We characterized two newly isolated myoviruses, Bp8p-C and Bp8p-T, infecting the ginger rhizome rot disease pathogen Bacillus pumilus GR8. The plaque of Bp8p-T exhibited a clear center with a turbid rim, suggesting that Bp8p-T could transform into latent phage. Lysogeny assays showed that both the two phages could form latent states, while Bp8p-T could form latent phage at a higher frequency and stability than Bp8p-C. The genomes of Bp8p-C and Bp8p-T were 151,417 and 151,419 bp, respectively; both encoded 212 putative proteins, and only differed by three nucleotides. Moreover, owing to this difference, Bp8p-C encoded a truncated, putative actin-like plasmid segregation protein Gp27-C. Functional analysis of protein Gp27 showed that Gp27-T encoded by Bp8p-T exhibited higher ATPase activity and assembly ability than Gp27-C. The results indicate that the difference in Gp27 affected the phage lysogenic ability. Structural proteome analysis of Bp8p-C virion resulted in the identification of 14 structural proteins, among which a pectin lyase-like protein, a putative poly-gamma-glutamate hydrolase, and three proteins with unknown function, were firstly identified as components of the phage virion. Both phages exhibited specific lytic ability to the host strain GR8. Bp8p-C showed better control effect on the pathogen in ginger rhizome slices than Bp8p-T, suggesting that Bp8p-C has a potential application in bio-control of ginger rhizome rot disease.

Predicting transmission of avian influenza A viruses from avian to human by using informative physicochemical properties

Some strains of avian influenza A virus (AIV) can directly transmit from their natural hosts to humans. These avian-to-human transmissions have continuously been reported to cause human deaths worldwide since 1997. Predicting whether AIV strains can transmit from avian to human is valuable for early warning of AIV strains with human pandemic potential. In this study, we constructed a computational model to predict avian-to-human transmission of AIV based on physicochemical properties. Initially, ninety signature positions in the inner protein sequences were extracted with the entropy method. These positions were then encoded with 531 physicochemical features. Subsequently, the optimal subset of these physicochemical features was mined with several feature selection methods. Finally, a support vector machine (SVM) model named A2H was established to integrate the selected optimal features. The experimental results of cross-validation and an independent test show that A2H has the capability of predicting transmission of AIV from avian to human.

Using amino acid factor scores to predict avian-to-human transmission of avian influenza viruses: a machine learning study

In this study, the problem of predicting interspecies transmission of avian influenza viruses (AIVs) was investigated with machine learning methods. We identified 87 signature positions in AIV protein sequences with information entropy method and encoded these positions with five amino acid factor scores (AAFactors) concentrated from 491 physicochemical and biochemical properties of amino acids. We constructed four prediction models by integrating these five features with commonly used machine learning technologies including Decision Tree, Naive Bayes, Random Forest and Support Vector Machine. The cross validation experiment results demonstrated the power of AAFactors in predicting avian-to-human transmission of AIVs. Comparative analysis revealed the strengths and weaknesses of different machine learning methods, and the importance of different AAFactors to the prediction.

An improved system for the evaluation of antiviral compounds against herpes simplex virus type 2

Infection with herpes simplex virus type 2 (HSV-2) can result in lesions in reproductive organs, along with long-term latency. In this work, a non-lethal strain of HSV-2 which was isolated clinically was used to infect female mice intravaginally. Body weight, vulval lesions, histological examination of vaginal tissue, and viral load were monitored and used as indices for evaluating antiviral drugs against HSV-2 infection. The results indicated that mice infected with HSV-2 exhibited significant reduction in body weight, serious vulval lesions, massive lymphocyte invasion of vaginal tissue, and approximately 10⁴ copies/μl of HSV-2 were found in vaginal and uterine tissues. Aciclovir (ACV) treatment inhibited loss in body weight, genital pathology and virus replication (reduced to 10⁰·³ copies/μl) effectively. The study provides a simple, reproducible and feasible animal model for anti-HSV-2 drugs evaluation and HSV-2 vaccine research.

Infection and propagation of Crimean-Congo hemorrhagic fever virus in embryonated chicken eggs

The embryonated chicken egg (ECE) provides a convenient, space-saving incubator for the cultivation of many kinds of animal viruses where the egg can be easily observed for viral replication throughout the development of the chicken embryo. Within the family Bunyaviridae, the embryonated egg has been used as a host system for many viruses such as Rift Valley fever virus and Akabane virus. The current study was conducted to determine the cultivation of Crimean-Congo hemorrhagic fever virus (CCHFV) in ECE. Four-day-old eggs were infected with CCHFV via the yolk sac route and harvested embryonic tissues and amino-allantoic fluid (AAF) that were used for virus passage and viral RNA (vRNA) detection. Quantification of vRNA copies was performed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Our study indicated that CCHFV caused the death of the embryonated egg in a dose-dependent manner and the 50% egg infectious dose (EID50) was determined to be 6.47×10(5) copies/egg. CCHFV replicated and passaged well in the egg and high viral loads were detected both in embryonic tissue (10(9-10) copies/g) and AAF (10(7-9) copies/ml) of the embryonated egg. Thus, ECE could be used for viral cultivation and preservation, and as a potential host infection model for the study of the pathogenesis of CCHFV.

Molecular characterization of influenza B viruses isolated in east-central China in 2009-2010

The current circulating influenza B viruses can be divided into two major phylogenetic lineages: the Victoria and Yamagata lineages. We conducted a survey of influenza B viruses in Hubei and Zhejiang provinces during 2009-2010. Out of 341 throat swabs, 18 influenza B viruses were isolated. Five isolates were selected for genetic and phylogenetic analysis. The molecular analyses revealed that all the isolates had similar antigenic characteristics to B/Brisbane/60/2008. However, in the three viruses isolated from Zhejiang, a single asparagine to aspartic acid substitution in position 197 was observed, thereby eliminating the glycosylation at that site and possibly causing an antigenic change. None of the viruses had amino acid mutations at positions 116, 149, 152, 198, 222, 250, 291, and 402 of the neuraminidase (NA) gene, predicting that the viruses would still be sensitive to NA inhibitors. Phylogenetic analyses revealed that all five isolates were closely related to B/Brisbane/60/2008-the 2010 vaccine strain-and contained Victoria-like hemagglutinin and Yamagata-like NA genes, suggesting that reassortment may had occurred. In addition, similar phylogenetic patterns among the acidic polymerase, nucleoprotein and matrix protein genes, as well as between the basic polymerase 1 and basic polymerase 2 genes, were observed, suggesting possible functional interactions among these proteins. All the results highlighted the importance of molecular monitoring of influenza B viruses for reassortment and antigenic drift.

Genetic characteristics of 2009 pandemic H1N1 influenza a viruses isolated from Mainland China

A total of 100 H1N1 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/California/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/75/2009 PKVRDQEG → 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.

Clinical correlates of white matter blood flow perfusion changes in Sturge-Weber syndrome: a dynamic MR perfusion-weighted imaging study

BACKGROUND AND PURPOSE

Low brain tissue perfusion due to abnormal venous drainage is thought to be a central mechanism of brain damage in SWS. Here, HR-PWI was used to quantify WM perfusion abnormalities and to correlate these with brain atrophy and clinical variables.

MATERIALS AND METHODS

Fourteen children (age range, 0.8-10.0 years) with unilateral SWS underwent MR imaging examinations, including HR-PWI. rCBV, rCBF, and MTT in the affected WM and in contralateral homotopic WM were measured. AI for each perfusion parameter was correlated with age, brain atrophy, and motor and seizure variables as well as IQ.

RESULTS

Increased perfusion was seen in the affected hemisphere in 5 children and decreased perfusion in 9 children. Brain atrophy was more severe in the low-perfusion group (P = .01) and was related to both CBF-AI and CBV-AI (r = -0.69, P = .007; r = -0.64, P = .014, respectively). Older children had lower CBV values on the affected side (r = -0.62, P = .02). Longer duration of epilepsy was related to lower CBF (more negative CBF-AI, r = -0.58, P = .03) and low CBV (r = -0.55, P = .04) on the affected side. Lower perfusion was associated with more frequent seizures (rCBF-AI: r = -0.56, P = .04; rCBV-AI: r = -0.63, P = .02).

CONCLUSIONS

Increased perfusion in the affected cerebral WM may indicate an early stage of SWS without severe brain atrophy. Decreased perfusion is associated with frequent seizures, long duration of epilepsy, and brain atrophy.

Epidemiological survey of Crimean-Congo hemorrhagic fever virus in Yunnan, China, 2008

OBJECTIVES

We aimed to determine the seroprevalence of Crimean-Congo hemorrhagic fever virus (CCHFV) infection in Yunnan Province, China.

MATERIALS AND METHODS

One thousand six hundred and fifty-seven human serum samples and 1280 ticks (Hyalomma asiaticum) were collected from five counties (Menglian, Menghai, Lancang, Mengla, and Ximeng). Serum samples were analyzed independently by indirect immunofluorescence assay and Western blotting to detected CCHFV antibody. The ticks were examined by reverse transcriptase-polymerase chain reaction (RT-PCR) to detect virus RNA.

RESULTS

The CCHFV IgG positivity was 3.4% (57/1657). A multivariate analysis was performed, and variables that increased the chance of infection were found to include history of tick bite or contact (odds ratio (OR) 16.6, 95% confidence interval (CI) 7.5-37.0) and age>30 years (OR 6.8, 95% CI 1.6-28.2). The RT-PCR positive rate for ticks was 14.3% (6/42).

CONCLUSIONS

The five counties (Menglian, Menghai, Lancang, Mengla, and Ximeng) in Yunnan are areas with the potential for CCHF outbreaks. Residents should protect themselves against tick bites and the surveillance of CCHFV in this region should be improved.

Persistent circulation of highly pathogenic influenza H5N1 virus in Lake Qinghai area of China

To trace the endemic situation of highly pathogenic influenza H5N1 virus in wildlife in the Lake Qinghai area of northwest China, a continuous surveillance program was implemented from September 2005 to September 2007. A total of 2699 field samples were collected, and 95 of the samples were positive by a reverse transcription-polymerase chain reaction (RT-PCR) test of subtype H5 influenza virus. To some extent, the detection rate correlated with the species, the location, and the seasons of collection. In 2007, two H5N1 isolates were identified from two species of migratory birds. The two 2007 isolates showed high similarities of the hemagglutinin and neuraminidase genes with those of the 2005 and 2006 Qinghai isolates (98.6-99.8% for HA and 98.7-98.9% for NA at the nucleotide level). Both isolates fell into clade 2.2.2 and were experimentally highly pathogenic to chickens and mice. According to our surveillance results, HPAI H5N1 viruses still exist in this region.

Characterization of a highly pathogenic avian influenza H5N1 clade 2.3.4 virus isolated from a tree sparrow

The spread of H5N1 virus into a wide range of avian and mammalian species may facilitate the adaptation of the virus to human populations. In the present study, a survey of avian influenza virus in tree sparrows was performed and a HPAI H5N1 virus (A/tree sparrow/Jiangsu/1/08) was isolated. The H5N1 virus was found to be a genotype V variant belonging to clade 2.3.4, which had newly emerged in southern China in 2005. Genetic analysis showed that it had a close relation with A/Jiangsu/1/07 (H5N1), which was thought to be responsible for a probable limited person-to-person transmission in a family cluster in China in 2007. Pathogencity studies showed that the virus was highly virulent when experimentally inoculated into the chickens, tree sparrow, and mouse. As clade 2.3.4, genotype V variant of H5N1 virus has been accounted for the most of human fatal cases in China during 2005-2008, the existence of such H5N1 variants in the tree sparrows highlights the potential threat of this type of wild bird infection to veterinary and public health.

The survey of H5N1 flu virus in wild birds in 14 Provinces of China from 2004 to 2007

Background

The highly pathogenic H5N1 avian influenza emerged in the year 1996 in Asia, and has spread to Europe and Africa recently. At present, effective monitoring and data analysis of H5N1 are not sufficient in Chinese mainland.

Methodology/Principal Findings

During the period from April of 2004 to August of 2007, we collected 14,472 wild bird samples covering 56 species of 10 orders in 14 provinces of China and monitored the prevalence of flu virus based on RT-PCR specific for H5N1 subtype. The 149 positive samples involved six orders. Anseriformes had the highest prevalence while Passeriformes had the lowest prevalence (2.70% versus 0.36%). Among the 24 positive species, mallard (Anas platyrhynchos) had the highest prevalence (4.37%). A difference of prevalence was found among 14 provinces. Qinghai had a higher prevalence than the other 13 provinces combined (3.88% versus 0.43%). The prevalence in three species in Qinghai province (Pintail (Anas acuta), Mallard (Anas platyrhynchos) and Tufted Duck (Aythya fuligula)) were obviously higher than those in other 13 provinces. The results of sequence analysis indicated that the 17 strains isolated from wild birds were distributed in five clades (2.3.1, 2.2, 2.5, 6, and 7), which suggested that genetic diversity existed among H5N1 viruses isolated from wild birds. The five isolates from Qinghai came from one clade (2.2) and had a short evolutionary distance with the isolates obtained from Qinghai in the year 2005.

Conclusions/Significance

We have measured the prevalence of H5N1 virus in 56 species of wild birds in 14 provinces of China. Continuous monitoring in the field should be carried out to know whether H5N1 virus can be maintained by wild birds.

Difference between the abilities of human Fcgamma receptor-expressing CV-1 cells to neutralize American and Asian genotypes of dengue virus 2

Sera from patients involved in a Peruvian outbreak of dengue virus serotype 1 infection cross-neutralized the American genotype of dengue virus serotype 2 up to 100-fold more efficiently than they did the virulent Asian genotype of dengue virus serotype 2, as determined by a plaque reduction neutralization test (PRNT) with CV-1 fibroblasts modified to express human Fcgamma receptor CD32. The concordant preferential immune enhancement of the Asian genotype of dengue virus serotype 2 in human monocytes suggests that such a modification might strengthen the correlation between the PRNT titer and protection.

Molecular characterizations of avian polyomavirus isolated from budgerigar in China

Budgerigar fledgling disease is an acute viral infectious disease caused by avian polyomavirus (APV). In this study, 34 liver tissue samples of young, dead budgerigar with typical symptoms were collected in 2004. All the samples had positive polymerase chain reaction (PCR) test based on the VP1 specific primers. VP1 genes of these samples were sequenced and had high similarities to each other (99%-100%). A strain (HBYM02) was isolated and sequenced. As shown in the phylogenetic tree, there are two branches. One branch was composed by strains isolated from Passeriformes, and the other was composed only by one strain isolated from Falconiformes. The genome similarities between our isolate and other reported isolates were very high (> 99%), and the evolution distances in the phylogenetic tree were very short (< 0.005), which suggests that APV in China has the same genotype as those in other regions. The results will be useful for the diagnoses of, and vaccine development for, APV.

Characterization of H5N1 Influenza Viruses Isolated from Migratory Birds in Qinghai Province of China in 2006

Avian influenza H5N1 viruses pose a significant threat to human health because of their ability to infect humans directly. In the paper, three highly pathogenic H5N1 influenza viruses were isolated from three species of migratory birds in Qinghai Province of China in 2006. The analysis of the genome sequences indicated that the three isolates shared high homology with each other (94% to 99%). Three isolates shared a common ancestor and were closest to strains isolated from Qinghai and Siberia in 2005, but distinct from poultry viruses found in Southeast Asia. In experimental infection, all three viruses were highly pathogenic to chickens and mice. The results suggest that highly pathogenic avian influenza H5N1 viruses still exist in the migratory birds and could spread to other regions with wild bird migration.

New genotype of avian influenza H5N1 viruses isolated from tree sparrows in China

The 2004 outbreaks of highly pathogenic avian influenza H5N1 disease in China led to a great poultry loss and society attention. A survey of avian influenza viruses was conducted on tree sparrows (Passer montanus) collected in China in 2004. Four viruses were isolated from free-living tree sparrows. The results of the whole-genome analysis indicated that an H5N1 virus with a new genotype is circulating among tree sparrows. The hemagglutinin and neuraminidase genes of the new genotype were derived from Gs/Gd/96-like viruses and the nuclear protein gene descended from the 2001 genotype A H5N1 viruses, while the other inner genes originated from an unknown influenza virus. In experimental infection, all four viruses were highly pathogenic to chickens but not pathogenic to ducks or mice. The four tree sparrow viruses were different from the 2003 tree sparrow strain (genotype Z) in Hong Kong. The results suggested that H5N1 viruses might be distributed widely in tree sparrows.

In vivo T-lymphocyte activation and transient reduction of viral replication in macaques infected with simian immunodeficiency virus

While it is well established that cellular activation can increase human immunodeficiency virus (HIV) replication in T lymphocytes, it is also clear that both activated CD8+ and CD4+ T lymphocytes mediate anti-HIV activity. To assess the relative importance of these contrary effects on HIV replication in vivo, we evaluated the consequences of Mycobacterium bovis BCG and staphylococcal enterotoxin B (SEB) inoculation in vivo in rhesus monkeys chronically infected with simian immunodeficiency virus of macaques (SIVmac). BCG inoculation induced as much as a 2.5-log reduction of plasma and intracellular SIV RNA in SIVmac-infected monkeys. This down-regulation of virus replication persisted as long as 4 weeks after BCG inoculation. Similarly, SEB injection resulted in up to a 3-log decrease in plasma and intracellular SIV RNA in SIVmac-infected macaques. Interestingly, the short-term reduction of viremia in these monkeys correlated with the peak in vivo production of SEB- and BCG-induced cytokine responses. However, no long-term clinical benefit was observed in the SIVmac-infected macaques. These studies provide in vivo evidence that potent T-cell stimulation driven by antigens other than the virus itself can, under some circumstances, mediate short-term reduction of viremia in AIDS virus-infected individuals.

Prolonged dominance of clonally restricted CD4(+) T cells in macaques infected with simian immunodeficiency viruses

The repertoire of functional CD4(+) T lymphocytes in human immunodeficiency virus type 1-infected individuals remains poorly understood. To explore this issue, we have examined the clonality of CD4(+) T cells in simian immunodeficiency virus (SIV)-infected macaques by assessing T-cell receptor complementarity-determining region 3 (CDR3) profiles and sequences. A dominance of CD4(+) T cells expressing particular CDR3 sequences was identified within certain Vbeta-expressing peripheral blood lymphocyte subpopulations in the infected monkeys. Studies were then done to explore whether these dominant CD4(+) T cells represented expanded antigen-specific cell subpopulations or residual cells remaining in the course of virus-induced CD4(+) T-cell depletion. Sequence analysis revealed that these selected CDR3-bearing CD4(+) T-cell clones emerged soon after infection and dominated the CD4(+) T-cell repertoire for up to 14 months. Moreover, inoculation of chronically infected macaques with autologous SIV-infected cell lines to transiently increase plasma viral loads in the monkeys resulted in the dominance of these selected CDR3-bearing CD4(+) T cells. Both the temporal association of the detection of these clonal cell populations with infection and the dominance of these cell populations following superinfection with SIV suggest that these cells may be SIV specific. Finally, the inoculation of staphylococcal enterotoxin B superantigen into SIV-infected macaques uncovered a polyclonal background underlying the few dominant CDR3-bearing CD4(+) T cells, demonstrating that expandable polyclonal CD4(+) T-cell subpopulations persist in these animals. These results support the notions that a chronic AIDS virus infection can induce clonal expansion, in addition to depletion of CD4(+) T cells, and that some of these clones may be SIV specific.

[Ecological process of vegetation restoration in Caragana mirophylla sand-fixing area]

The occurrence and development of artificial vegetation after mobile sandy dunes being fixed by adopting straw check combining with seeding Caragana microphylla were studied. Especially the process of species invasion and the changes of community structure in 35 years were analyzed in detail. The results showed that the species richness of artificial community of C. microphylla increased, from 5 species (in 2 years) to 23 species in 35 years. In the structure concerning plant lifeform, therophytes were in dominant position, while the ratio of therophytes to all plant species had a tendency of decrease. The rates of species number and the quantity of hemicryptophytes and geocryptophytes increased gradually. Species diversity and community evenness indexes increased and ecological dominance index decreased gradually. The similarity index of the artificial plant community to natural one increased with age. The changes of physical and chemical property of soil were also discussed.

The disruption of macaque CD4+ T-cell repertoires during the early simian immunodeficiency virus infection

T-cell receptor (TCR) complementarily determining region 3 (CDR3) spetratyping analysis was employed to assess the ability of an AIDS virus to disrupt CD4 + T-cell repertoires during the primary infection. Rhesus and pig-tailed macaques infected with simian immunodeficiency virus (SIV)mac 251 and SIVsmmFGb, respectively, were evaluated. Following SIV infection, the macaques exhibited an apparent decline of CD4 + peripheral blood lymphocyte (PBL) counts, which was associated with a change in CDR3 profiles from multiple-length distribution to one- or two-length dominance in the selected TCR Vbeta-expressing CD4 + PBL subpopulations. Molecular analysis of the perturbed cell subpopulations suggested that the CD4 + T cells bearing the dominant CDR3 length were clonally expanded. These results indicate that SIV infection can induce a disruption of macaque CD4 + T-cell repertoires during the primary infection. The finding in this study, therefore, suggests that the virus-induced clonal dominance can contribute to the disruption of CD4 + T-cell repertoires.

The T cell receptor gene usage by simian immunodeficiency virus gag-specific cytotoxic T lymphocytes in rhesus monkeys

MHC class I-restricted CTL play an important role in limiting the spread of HIV-1 in the infected individual. Elucidating the molecular interactions of CTL with the virus is, therefore, of central importance for characterizing the immune control of this infection. In exploring this CTL response, we have defined the TCR usage by SIVmac Gag-specific CTL in rhesus monkeys. Thirty-nine CTL clones were generated from PBL of three SIVmac-infected monkeys expressing the MHC class I Mamu-A*01 gene product, all of which were shown to recognize a single SIVmac Gag peptide in association with Mamu-A*01. Sixty-six percent of CTL clones derived from two monkeys early after infection expressed TCR genes of the V beta 13 family; 70% of these V beta 13+ CTL clones expressed a TCR heterodimer composed of V alpha 1 and V beta 13 gene products. In addition, there appeared to be a selection of a single conserved amino acid and restricted CDR3 lengths in junctional regions of TCR beta-chains expressed by the V beta 13+ CTL clones. These findings indicate significant structural constraints on the CTL-TCR interaction with the AIDS virus. Interestingly, 55% of the CTL clones derived from the third animal at a later time following infection employed genes of the V beta 6 family in their TCR. Despite the preferential use of TCR V family genes by the CTL clones, the SIVmac Gag-specific CTL response was clearly polyclonal; TCR expressed by these CTL clones displayed varied sequences in their CDR3 regions. Other V gene families, including V beta 23, V alpha 8, and V alpha 20, were used in TCR expressed by SIVmac Gag-specific CTL clones. These studies, therefore, indicate that the TCR repertoire of SIVmac Gag-specific CTL that share a peptide and MHC class I recognition specificity can be diverse. Such a broad CTL-TCR repertoire may be advantageous for the host in containing an AIDS virus infection.

The T cell receptor gene usage by simian immunodeficiency virus gag-specific cytotoxic T lymphocytes in rhesus monkeys

MHC class I-restricted CTL play an important role in limiting the spread of HIV-1 in the infected individual. Elucidating the molecular interactions of CTL with the virus is, therefore, of central importance for characterizing the immune control of this infection. In exploring this CTL response, we have defined the TCR usage by SIVmac Gag-specific CTL in rhesus monkeys. Thirty-nine CTL clones were generated from PBL of three SIVmac-infected monkeys expressing the MHC class I Mamu-A*01 gene product, all of which were shown to recognize a single SIVmac Gag peptide in association with Mamu-A*01. Sixty-six percent of CTL clones derived from two monkeys early after infection expressed TCR genes of the V beta 13 family; 70% of these V beta 13+ CTL clones expressed a TCR heterodimer composed of V alpha 1 and V beta 13 gene products. In addition, there appeared to be a selection of a single conserved amino acid and restricted CDR3 lengths in junctional regions of TCR beta-chains expressed by the V beta 13+ CTL clones. These findings indicate significant structural constraints on the CTL-TCR interaction with the AIDS virus. Interestingly, 55% of the CTL clones derived from the third animal at a later time following infection employed genes of the V beta 6 family in their TCR. Despite the preferential use of TCR V family genes by the CTL clones, the SIVmac Gag-specific CTL response was clearly polyclonal; TCR expressed by these CTL clones displayed varied sequences in their CDR3 regions. Other V gene families, including V beta 23, V alpha 8, and V alpha 20, were used in TCR expressed by SIVmac Gag-specific CTL clones. These studies, therefore, indicate that the TCR repertoire of SIVmac Gag-specific CTL that share a peptide and MHC class I recognition specificity can be diverse. Such a broad CTL-TCR repertoire may be advantageous for the host in containing an AIDS virus infection.