Juncai Ma

Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses

BACKGROUND On March 30, 2013, a novel avian influenza A H7N9 virus that infects human beings was identified. This virus had been detected in six provinces and municipal cities in China as of April 18, 2013. We correlated genomic sequences from avian influenza viruses with ecological information and did phylogenetic and coalescent analyses to extrapolate the potential origins of the virus and possible routes of reassortment events. METHODS We downloaded H7N9 virus genome sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database and public sequences used from the Influenza Virus Resource. We constructed phylogenetic trees and did 1000 bootstrap replicates for each tree. Two rounds of phylogenetic analyses were done. We used at least 100 closely related sequences for each gene to infer the overall topology, removed suspicious sequences from the trees, and focused on the closest clades to the novel H7N9 viruses. We compared our tree topologies with those from a bayesian evolutionary analysis by sampling trees (BEAST) analysis. We used the bayesian Markov chain Monte Carlo method to jointly estimate phylogenies, divergence times, and other evolutionary parameters for all eight gene fragments. We used sequence alignment and homology-modelling methods to study specific mutations regarding phenotypes, specifically addressing the human receptor binding properties. FINDINGS The novel avian influenza A H7N9 virus originated from multiple reassortment events. The HA gene might have originated from avian influenza viruses of duck origin, and the NA gene might have transferred from migratory birds infected with avian influenza viruses along the east Asian flyway. The six internal genes of this virus probably originated from two different groups of H9N2 avian influenza viruses, which were isolated from chickens. Detailed analyses also showed that ducks and chickens probably acted as the intermediate hosts leading to the emergence of this virulent H7N9 virus. Genotypic and potential phenotypic differences imply that the isolates causing this outbreak form two separate subclades. INTERPRETATION The novel avian influenza A H7N9 virus might have evolved from at least four origins. Diversity among isolates implies that the H7N9 virus has evolved into at least two different lineages. Unknown intermediate hosts involved might be implicated, extensive global surveillance is needed, and domestic-poultry-to-person transmission should be closely watched in the future. FUNDING China Ministry of Science and Technology Project 973, National Natural Science Foundation of China, China Health and Family Planning Commission, Chinese Academy of Sciences.

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

The human gut microbiota is a reservoir of antibiotic resistance genes, but little is known about their diversity and richness within the gut. Here we analyse the antibiotic resistance genes of gut microbiota from 162 individuals. We identify a total of 1,093 antibiotic resistance genes and find that Chinese individuals harbour the highest number and abundance of antibiotic resistance genes, followed by Danish and Spanish individuals. Single-nucleotide polymorphism-based analysis indicates that antibiotic resistance genes from the two European populations are more closely related while the Chinese ones are clustered separately. We also confirm high abundance of tetracycline resistance genes with this large cohort study. Our study provides a broad view of antibiotic resistance genes in the human gut microbiota.

An atlas of DNA methylomes in porcine adipose and muscle tissues

It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DNA immunoprecipitation libraries, and provide a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth.

Dynamic reassortments and genetic heterogeneity of the human-infecting influenza A (H7N9) virus

Influenza A (H7N9) virus has been causing human infections in China since February 2013, raising serious concerns of potential pandemics. Previous studies demonstrate that human infection is directly linked to live animal markets, and that the internal genes of the virus are derived from H9N2 viruses circulating in the Yangtze River Delta area in Eastern China. Here following analysis of 109 viruses, we show a much higher genetic heterogeneity of the H7N9 viruses than previously reported, with a total of 27 newly designated genotypes. Phylogenetic and genealogical inferences reveal that genotypes G0 and G2.6 dominantly co-circulate within poultry, with most human isolates belonging to the genotype G0. G0 viruses are also responsible for the inter- and intra-province transmissions, leading to the genesis of novel genotypes. These observations suggest the province-specific H9N2 virus gene pools increase the genetic diversity of H7N9 via dynamic reassortments and also imply that G0 has not gained overwhelming fitness and the virus continues to undergo reassortment.

Full 180° Magnetization Reversal with Electric Fields

Achieving 180° magnetization reversal with an electric field rather than a current or magnetic field is a fundamental challenge and represents a technological breakthrough towards new memory cell designs. Here we propose a mesoscale morphological engineering approach to accomplishing full 180° magnetization reversals with electric fields by utilizing both the in-plane piezostrains and magnetic shape anisotropy of a multiferroic heterostructure. Using phase-field simulations, we examined a patterned single-domain nanomagnet with four-fold magnetic axis on a ferroelectric layer with electric-field-induced uniaxial strains. We demonstrated that the uniaxial piezostrains, if non-collinear to the magnetic easy axis of the nanomagnet at certain angles, induce two successive, deterministic 90° magnetization rotations, thereby leading to full 180° magnetization reversals.

Phylogenetics of varied subtypes of avian influenza viruses in China: potential threat to humans

Since February 2013, infections with several novel avianorigin influenza viruses have occurred in Taiwan and the Mainland of China. The H7N9 influenza virus has caused 136 human infections with 44 deaths in the first influenza season, and has continued to cause infections during the current influenza season (Li et al., 2014). As of February 11th, 2014, a total of 331 human infections with 101 deaths in China have been reported (http://www.nhfpc.gov.cn). During the outbreak of H7N9 in the Mainland of China, Taiwan reported the first human infection of avian H6N1 influenza virus, which again hit the public (Shi et al., 2013a; Wei et al., 2013). In November 2013, the first infection of H10N8 influenza virus was reported by Nanchang Center for Disease Control and Prevention (Chen et al., 2014). Questions have since been raised as to how many novel avian influenza viruses could emerge and infect humans, and which have the potential to cause a pandemic? The three novel avian-origin influenza viruses causing human infections were most likely transmitted from poultry to human (Chen et al., 2014; Chen et al., 2013; Shi et al., 2013a; Wu andGao, 2013). Studies of the origin of these novel avianorigin influenza viruses have revealed that H7N9 and H10N8 have retained those surface protein-encoding genes that originated in wild birds during the transmission to domestic poultry (Chenet al., 2014;Cui et al., 2014; Liu et al., 2013). The internal genes of H7N9 and H10N8 were all derived from the H9N2 influenza viruses circulating within poultry (Cui et al., 2014). Multiple reassortment events within wild birds and poultry have resulted in theestablishment ofH7N9andH10N8 viruses, respectively, and finally resulted in human infections. In contrast to H7N9 and H10N8, the H6N1 virus in Taiwan is probably the result of the reassortment of different lineages of poultry H6N1 viruses, though poultry H5N2 virusesmight also been involved (Shi et al., 2013a). The H7N9 virus in particular has diversified and experienced many dynamic reassortments within poultry (Cui et al., 2014; Li et al., 2013; Liu et al., 2013). The higher diversity of the internal genes makes the H7N9 virus rather different to the H5N1 and the pandemic H1N1 (09-pH1N1), whose surface protein-encoding genes exhibited more divergence during the first influenza season (Cui et al., 2014). There were at least 27 genotypes of the H7N9 virus discovered in the first influenza season, and novel genotypes continued to emerge in the 2013–2014 influenza season (Cui et al., 2014). The lack of an overwhelmingly dominant genotype of the H7N9 virus suggests that the virus has been continuing to evolve by means of rapid genetic reassortments, after they were transported to new regions, in order to adapt to local hosts. The genetic diversity has also endowed the H7N9 virus with functional diversity, in that some of the important amino acid sites: the receptor-binding site; the oseltamivir-resistance site; and mammalian host adaptation sites, have showed varied degrees of polymorphism (Li et al., 2013; Shi et al., 2013b; Wu et al., 2013). The uncertainty of the combination of both the avian influenza virus subtypes and genotypes in poultry has made the preparedness for pandemic difficult. Therefore, tracing the potential evolutionary route of these avian influenza viruses in poultry is one of the pivotal steps for the control and prevention of novel human-infecting avian-origin influenza viruses. For this purpose, we performed the phylogenetic analyses of some of the prevalent avian influenza viruses in poultry in China. The results uncovered that H9N2 virus continued to act as genetic donor for the establishment of novel lineages of other subtypes of influenza virus, which could probably infect humans. The study also suggest that those hidden subtypes of influenza viruses, such as H1, H3, H4, and H11, which have not yet been found to infect humans, should not be neglected as hidden threats. To provide insight into the avian influenza virus pool existing in poultry in China, we first searched the Influenza Virus Resources database maintained by NCBI for the avian influenza viruses (http://www.ncbi.nih.gov/genomes/FLU/). From 2006, there are a total of 2,146 HA gene sequences and 35 subtypes of avian influenza viruses (Supplementary Table 1). As shown in Fig. 1, the H9N2 virus in poultry has spread to nearly all provinces in China in recent years. As it is of a low pathogenicity to poultry, the transmission of this virus is likely to have been neglected through poultry transportations. The second most prevalent influenza virus in

TCRklass: A New K-String–Based Algorithm for Human and Mouse TCR Repertoire Characterization

The next-generation sequencing technology has promoted the study on human TCR repertoire, which is essential for the adaptive immunity. To decipher the complexity of TCR repertoire, we developed an integrated pipeline, TCRklass, using K-string–based algorithm that has significantly improved the accuracy and performance over existing tools. We tested TCRklass using manually curated short read datasets in comparison with in silico datasets; it showed higher precision and recall rates on CDR3 identification. We applied TCRklass on large datasets of two human and three mouse TCR repertoires; it demonstrated higher reliability on CDR3 identification and much less biased V/J profiling, which are the two components contributing the diversity of the repertoire. Because of the sequencing cost, short paired-end reads generated by next-generation sequencing technology are and will remain the main source of data, and we believe that the TCRklass is a useful and reliable toolkit for TCR repertoire analysis.

Optical monitoring of PKS 1510¿089: a binary black hole system?

Three deep flux minima with nearly the same time-scales and intervals have been observed for the blazar PKS 1510−089 in the past few years. It has been proposed that there is a binary black hole system at the nucleus of this object, and a new minimum was predicted to occur in 2002 March. We monitored this source with a 60/90 cm Schmidt telescope from 2002 February to April. In combination with the data obtained by Xie et al. in the same period, for the 2002 minimum we present a nearly symmetric light curve, which would be required by an eclipsing model of a binary black hole system. We also constrain the time-scale of the minimum to be 35 min, which is more consistent with the time-scales (∼42 min) of the three previous minima than is the 89 min time-scale given by Xie et al. The wiggling milliarcsecond radio jet observed in this object is taken as further evidence for the binary black hole system. The ‘coupling’ of the periodicity in the light curve and the helicity in the radio jet is discussed for blazars in the framework of a binary black hole system.

Intra-host dynamics of Ebola virus during 2014

Since 2013, West Africa has encountered the largest Ebola virus (EBOV) disease outbreak on record, and Sierra Leone is the worst-affected country, with nearly half of the infections. By means of next-generation sequencing and phylogeographic analysis, the epidemiology and transmission of EBOV have been well elucidated. However, the intra-host dynamics that mainly reflect viral–host interactions still need to be studied. Here, we show a total of 710 intra-host single nucleotide variations (iSNVs) from deep-sequenced samples from EBOV-infected patients, through a well-tailored bioinformatics pipeline. We present a comprehensive distribution of iSNVs during this outbreak and along the EBOV genome. Analyses of iSNV and its allele frequency reveal that VP40 is the most conserved gene during this outbreak, and thus it would be an ideal therapeutic target. In the co-occurring iSNV network, varied iSNV sites present different selection features. Intriguingly, the T-to-C substitutions at the 3′-UTR of the nucleoprotein (NP; positions 3008 and 3011), observed in many patients, result in the upregulation of the transcription of NP through an Ebola mini-genome reporting system. Additionally, no iSNV enrichment within B-cell epitopes of GP has been observed.

Characterization of human αβTCR repertoire and discovery of D-D fusion in TCRβ chains

ABSTRACTThe characterization of the human T-cell receptor (TCR) repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we analyzed the diversity and complexity of both the TCRα and TCRβ repertoires of three healthy donors. We found that the diversity of the TCRα repertoire is higher than that of the TCRβ repertoire, whereas the usages of the V and J genes tended to be preferential with similar TRAV and TRAJ patterns in all three donors. The V-J pairings, like the V and J gene usages, were slightly preferential. We also found that the TRDV1 gene rearranges with the majority of TRAJ genes, suggesting that TRDV1 is a shared TRAV/DV gene (TRAV42/DV1). Moreover, we uncovered the presence of tandem TRBD (TRB D gene) usage in ~2% of the productive human TCRβ CDR3 sequences.