Haizhou Liu

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

BackgroundMicroRNAs are a family of ~22 nt small RNAs that can regulate gene expression at the post-transcriptional level. Identification of these molecules and their targets can aid understanding of regulatory processes. Recently, HTS has become a common identification method but there are two major limitations associated with the technique. Firstly, the method has low efficiency, with typically less than 1 in 10,000 sequences representing miRNA reads and secondly the method preferentially targets highly expressed miRNAs. If sequences are available, computational methods can provide a screening step to investigate the value of an HTS study and aid interpretation of results. However, current methods can only predict miRNAs for short fragments and have usually been trained against small datasets which dont always reflect the diversity of these molecules.ResultsWe have developed a software tool, miRPara, that predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. We classified sequences from miRBase into animal, plant and overall categories and used a support vector machine to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering we found a subset of ~25 parameters produced higher prediction ability compared to the full set. Our software achieves an accuracy of up to 80% against experimentally verified mature miRNAs, making it one of the most accurate methods available.ConclusionsmiRPara is an effective tool for locating miRNAs coding regions in genome sequences and can be used as a screening step prior to HTS experiments. It is available at http://www.whiov.ac.cn/bioinformatics/mirpara

Emergence of Genotype I of Japanese Encephalitis Virus as the Dominant Genotype in Asia

ABSTRACT Japanese encephalitis virus (JEV), a mosquito-borne zoonotic pathogen, is one of the major causes of viral encephalitis worldwide. Previous phylogenetic studies based on the envelope protein indicated that there are four genotypes, and surveillance data suggest that genotype I is gradually replacing genotype III as the dominant strain. Here we report an evolutionary analysis based on 98 full-length genome sequences of JEV, including 67 new samples isolated from humans, pigs, mosquitoes, midges. and bats in affected areas. To investigate the relationships between the genotypes and the significance of genotype I in recent epidemics, we estimated evolutionary rates, ages of common ancestors, and population demographics. Our results indicate that the genotypes diverged in the order IV, III, II, and I and that the genetic diversity of genotype III has decreased rapidly while that of genotype I has increased gradually, consistent with its emergence as the dominant genotype.

The epidemic origin and molecular properties of B': a founder strain of the HIV-1 transmission in Asia.

Objective:To clarify the epidemic origin and molecular properties of the B′ subtype that is an important strain in the HIV-1 epidemic in Asia. Design:The genealogical relationship between the B′ and B subtype was investigated with two globally representative datasets covering the gag and env regions. B′ sequences were identified, from which the epidemic origin, population genetics and the signature mutation sites of the B′ subtype were inferred. Methods:Two globally representative datasets were compiled, using phylogenetic methods. Through coalescent-based analysis, the genealogical relationship between the B′ and B subtypes was investigated. The divergence times and population genetic parameters of B′ were estimated in a Bayesian framework using Markov Chains Monte Carlo sampling under a relaxed molecular clock method. Additionally, molecular properties of the B′ were identified by performing comparative sequence analysis with the HIV-1 M group. Results:About 15 years later after the B subtype began to spread, the B′ diverged from the B subtype. The demographic history of B′ was reconstructed, and the epidemic of B′ was estimated to originate around 1985. Eight and nine distinct signature mutation sites, unique to B′, were found around the p17 and V3 regions, respectively. Conclusion:Our research is the first large-scale investigation on HIV-1 B′ at a global level and provides a deep insight into one of the founder strains of HIV-1 epidemic in Asia. Our results provide an important reference for HIV scientists, public health officials and HIV vaccine designers.

The spatial and temporal dynamics of rabies in China

Background and Objectives Recent years have seen a rapid increase in the number of rabies cases in China and an expansion in the geographic distribution of the virus. In spite of the seriousness of the outbreak and increasing number of fatalities, little is known about the phylogeography of the disease in China. In this study, we report an analysis of a set of Nucleocapsid sequences consisting of samples collected through the trial Chinese National Surveillance System as well as publicly available sequences. This sequence set represents the most comprehensive dataset from China to date, comprising 210 sequences (including 57 new samples) from 15 provinces and covering all epidemic regions. Using this dataset we investigated genetic diversity, patterns of distribution, and evolutionary history. Results Our analysis indicates that the rabies virus in China is primarily defined by two clades that exhibit distinct population subdivision and translocation patterns and that contributed to the epidemic in different ways. The younger clade originated around 1992 and has properties that closely match the observed spread of the recent epidemic. The older clade originated around 1960 and has a dispersion pattern that suggests it represents a strain associated with a previous outbreak that remained at low levels throughout the country and reemerged in the current epidemic. Conclusions Our findings provide new insight into factors associated with the recent epidemic and are relevant to determining an effective policy for controlling the virus.

National Borders Effectively Halt the Spread of Rabies: The Current Rabies Epidemic in China Is Dislocated from Cases in Neighboring Countries

China has seen a massive resurgence of rabies cases in the last 15 years with more than 25,000 human fatalities. Initial cases were reported in the southwest but are now reported in almost every province. There have been several phylogenetic investigations into the origin and spread of the virus within China but few reports investigating the impact of the epidemic on neighboring countries. We therefore collected nucleoprotein sequences from China and South East Asia and investigated their phylogenetic and phylogeographic relationship. Our results indicate that within South East Asia, isolates mainly cluster according to their geographic origin. We found evidence of sporadic exchange of strains between neighboring countries, but it appears that the major strain responsible for the current Chinese epidemic has not been exported. This suggests that national geographical boundaries and border controls are effective at halting the spread of rabies from China into adjacent regions. We further investigated the geographic structure of Chinese sequences and found that the current epidemic is dominated by variant strains that were likely present at low levels in previous domestic epidemics. We also identified epidemiological linkages between high incidence provinces consistent with observations based on surveillance data from human rabies cases.

Characterization of catabolic meta-nitrophenol nitroreductase from Cupriavidus necator JMP134

Cupriavidus necator JMP134 utilizes meta-nitrophenol (MNP) as a sole source of carbon, nitrogen, and energy. The metabolic reconstruction of MNP degradation performed in silico suggested that the mnp cluster might have played important roles in MNP degradation. In order to experimentally confirm the prediction, we have now characterized mnpA-encoded meta-nitrophenol nitroreductase involved in the initial reaction of MNP degradation. Real-time PCR analysis indicated that mnpA played an essential role in MNP degradation. MnpA was purified to homogeneity as His-tagged proteins and was considered to be a dimer as determined by gel filtration. MnpA was an MNP nitroreductase with a tightly bound flavin mononucleotide (FMN), catalyzing the partial reduction of MNP to meta-hydroxylaminophenol via meta-nitrosophenol in the presence of NADPH and oxygen. The accumulation of meta-nitrosophenol was confirmed with the results of liquid chromatography–diode array detection and time-of-flight mass spectrometry for the first time. The low Km and high kcat of MnpA as well as MNP-inducible transcription of mnpA suggested that MNP was the physiological substrate for this nitroreductase. In addition, the phylogenetic analysis revealed that nitroreductases of known physiological function including MnpA constituted a new clade in the nitro-FMN-reductase superfamily.

Avian Influenza A (H7N9) Virus in a Wild Land Bird in Central China, Late 2015

To better understand the role of wild birds in the emergence and potential dissemination of subtype H7N9 viruses, in late 2015, we collected samples from wild land birds in Hubei province and performed virus isolation as well as full genome sequencing. A novel H7N9 virus was isolated from a Magpie-Robin. Genetic analysis showed that the virus was highly similar to the H7N9 viruses that circulated in poultry in other provinces in 2014, suggesting that virus transmission might have occurred between these two regions. The presence of influenza viruses among magpie-robins could increase opportunities for spread to domestic farms and even to humans. This clearly makes it challenging to control the influenza H7N9 subtype. Therefore, it is important to continue monitoring avian influenza virus in wild land birds.

Longitudinal Surveillance of Betacoronaviruses in Fruit Bats in Yunnan Province, China During 2009–2016

Previous studies indicated that fruit bats carry two betacoronaviruses, BatCoV HKU9 and BatCoV GCCDC1. To investigate the epidemiology and genetic diversity of these coronaviruses, we conducted a longitudinal surveillance in fruit bats in Yunnan province, China during 2009–2016. A total of 59 (10.63%) bat samples were positive for the two betacorona-viruses, 46 (8.29%) for HKU9 and 13 (2.34%) for GCCDC1, or closely related viruses. We identified a novel HKU9 strain, tentatively designated as BatCoV HKU9-2202, by sequencing the full-length genome. The BatCoV HKU9-2202 shared 83% nucleotide identity with other BatCoV HKU9 stains based on whole genome sequences. The most divergent region is in the spike protein, which only shares 68% amino acid identity with BatCoV HKU9. Quantitative PCR revealed that the intestine was the primary infection organ of BatCoV HKU9 and GCCDC1, but some HKU9 was also detected in the heart, kidney, and lung tissues of bats. This study highlights the importance of virus surveillance in natural reservoirs and emphasizes the need for preparedness against the potential spill-over of these viruses to local residents living near bat caves.

The limited number of available nucleotide and protein sequence data from the recent H7N9 cases in China impeded investigation and characterization of the outbreak.

Dear Editor,Nucleotide and protein sequences of isolates collectedfrom infected populations can be useful for determiningthe threats,such as host adaptation,which are associatedwith the emergence of new lineages.March 2013 saw thefirst reports of a new H7N9 lineage in Shanghai,Chinathat saw a gradual increase in the number of cases;but,by 17th May 2013,four Chinese provinces had ended

Use of mutual information arrays to predict coevolving sites in the full length HIV gp120 protein for subtypes B and C.

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 naïve 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.