Epidemic Trend and Molecular Evolution of HV Family in the Main Hantavirus Epidemic Areas From 2004 to 2016, in P.R. China

Hemorrhagic fever with renal syndrome (HFRS) is caused by hantavirus (HV) infection, and is prevalent across Europe and Asia (mainly China). The genetic variation and wide host range of the HV family may lead to vaccine failure. In this study, we analyzed the gene sequences of HV isolated from different regions of China in order to trace the molecular evolution of HV and the epidemiological trends of HFRS. A total of 16,6975 HFRS cases and 1,689 HFRS-related deaths were reported from 2004 to 2016, with the average annual incidence rate of 0.9674 per 100,000, 0.0098 per 100,000 mortality rate, and case fatality rate 0.99%. The highest number of cases were detected in 2004 (25,041), and after decreasing to the lowest numbers (8,745) in 2009, showed an incline from 2010. The incidence of HFRS is the highest in spring and winter, and three times as many men are affected as women. In addition, farmers account for the largest proportion of all cases. The main hosts of HV are Rattus norvegicus and Apodemus agrarius, and the SEOV strain is mainly found in R. norvegicus and Niviventer confucianus. Phylogenetic analysis showed that at least 10 HTNV subtypes and 6 SEOV subtypes are endemic to China. We found that the clustering pattern of M genome segments was different from that of the S segments, indicating the possibility of gene recombination across HV strains. The recent increase in the incidence of HFRS may be related to climatic factors, such as temperature, relative humidity and hours of sunshine, as well as biological factors like rodent density, virus load in rodents and genetic variation. The scope of vaccine application should be continuously expanded, and surveillance measures and prevention and control strategies should be improved to reduce HFRS infection in China.

Molecular Cytogenetic Identification of Wheat-Aegilops Biuncialis 5Mb Disomic Addition Line with Tenacious and Black Glumes

Production of wheat-alien disomic addition lines is of great value to the exploitation and utilization of elite genes originated from related species to wheat. In this study, a novel wheat-Aegilops biuncialis 5Mb disomic addition line WA317 was characterized by in situ hybridization (ISH) and specific-locus amplified fragment sequencing (SLAF-seq) markers. Compared to its parent Chinese Spring (CS), the glumes of WA317 had black color and were difficult to remove after harvesting, suggesting chromosome 5Mb carried gene(s) related to glume development and Triticeae domestication process. A total of 242 Ae. biuncialis SLAF-based markers (298 amplified patterns) were developed and further divided into four categories by Ae. biuncialis Y17, Ae. umbellulata Y139 and Ae. comosa Y258, including 172 markers amplifying the same bands of U and M genome, six and 102 markers amplifying U-specific and M-specific bands, respectively and eighteen markers amplifying specific bands in Y17. Among them, 45 markers had the specific amplifications in WA317 and were 5Mb specific markers. Taken together, line WA317 with tenacious and black glumes should serve as the foundation for understanding of the Triticeae domestication process and further exploitation of primitive alleles for wheat improvement. Ae. biuncialis SLAF-based markers can be used for studying syntenic relationships between U and M genomes as well as rapid tracking of U and M chromosomal segments in wheat background.

Evidence for a Recombinant Origin of HIV-1 group M from Genomic Variation

Reconstructing the early dynamics of the HIV-1 pandemic can provide crucial insights into the socioeconomic drivers of emerging infectious diseases in human populations, including the roles of urbanization and transportation networks. Current evidence indicates that the global pandemic comprising almost entirely of HIV-1/M originated around the 1920s in central Africa. However, these estimates are based on molecular clock estimates that are assumed to apply uniformly across the virus genome. There is growing evidence that recombination has played a significant role in the early history of the HIV-1 pandemic, such that different regions of the HIV-1 genome have different evolutionary histories. In this study, we have conducted a dated-tip analysis of all near full-length HIV-1/M genome sequences that were published in the GenBank database. We used a sliding window approach similar to the ‘bootscanning’ method for detecting breakpoints in intersubtype recombinant sequences. We found evidence of substantial variation in estimated root dates among windows, with an estimated mean time to the most recent common ancestor (tMRCA) of 1922. Estimates were significantly autocorrelated, which was more consistent with an early recombination event than with stochastic error variation in phylogenetic reconstruction and dating analyses. A piecewise regression analysis supported the existence of at least one recombination breakpoint in the HIV-1/M genome with interval-specific means around 1929 and 1913, respectively. This analysis demonstrates that a sliding window approach can accommodate early recombination events outside the established nomenclature of HIV-1/M subtypes, although it is difficult to incorporate the earliest available samples due to their limited genome coverage.

Esx Paralogs Are Functionally Equivalent to ESX-1 Proteins but Are Dispensable for Virulence inMycobacterium marinum

ABSTRACTMycobacterium marinumis a nontuberculous pathogen of poikilothermic fish and an opportunistic human pathogen. Like tuberculous mycobacteria, theM. marinumM strain requires the ESX-1 (ESAT-6 system 1) secretion system for virulence in host cells. EsxB and EsxA, two major virulence factors exported by the ESX-1 system, are encoded by theesxBAgenes within the ESX-1 locus. Deletion of theesxBAgenes abrogates ESX-1 export and attenuatesM. marinuminex vivoandin vivomodels of infection. Interestingly, there are several duplications of theesxBandesxAgenes (esxB_1,esxB_2,esxA_1,esxA_2, andesxA_3) in theM. marinumM genome located outside the ESX-1 locus. We sought to understand if this region, known as ESX-6, contributes to ESX-1-mediated virulence. We found that deletion of theesxB_1gene alone or the entire ESX-6 locus did not impact ESX-1 export or function, supporting the idea that theesxBAgenes present at the ESX-1 locus are the primary contributors to ESX-1-mediated virulence. Nevertheless, overexpression of theesxB_1locus complemented ESX-1 function in the ΔesxBAstrain, signifying that the two loci are functionally equivalent. Our findings raise questions about why duplicate versions of theesxBAgenes are maintained in theM. marinumM genome and how these proteins, which are functionally equivalent to virulence factors, contribute to mycobacterial biology.IMPORTANCEMycobacterium tuberculosisis the causative agent of the human disease tuberculosis (TB). There are 10.4 million cases and 1.7 million TB-associated deaths annually, making TB a leading cause of death globally. Nontuberculous mycobacteria (NTM) cause chronic human infections that are acquired from the environment. Despite differences in disease etiology, both tuberculous and NTM pathogens use the ESX-1 secretion system to cause disease. The nontubercular mycobacterial species,Mycobacterium marinum, has additional copies of specific ESX-1 genes. Our findings demonstrate that the duplicated genes do not contribute to virulence but can substitute for virulence factors inM. marinum. These findings suggest that the duplicated genes may play a specific role in NTM biology.

Molecular Cytogenetic Mapping of Satellite DNA Sequences in Aegilops geniculata and Wheat

Fluorescence in situ hybridization (FISH) provides an efficient system for cytogenetic analysis of wild relatives of wheat for individual chromosome identification, elucidation of homoeologous relationships, and for monitoring alien gene transfers into wheat. This study is aimed at developing cytogenetic markers for chromosome identification of wheat and Aegilops geniculata (2n = 4x = 28, UgUgMgMg) using satellite DNAs obtained from flow-sorted chromosome 5Mg. FISH was performed to localize the satellite DNAs on chromosomes of wheat and selected Aegilops species. The FISH signals for satellite DNAs on chromosome 5Mg were generally associated with constitutive heterochromatin regions corresponding to C-band-positive chromatin including telomeric, pericentromeric, centromeric, and interstitial regions of all the 14 chromosome pairs of Ae. geniculata. Most satellite DNAs also generated FISH signals on wheat chromosomes and provided diagnostic chromosome arm-specific cytogenetic markers that significantly improved chromosome identification in wheat. The newly identified satellite DNA CL36 produced localized Mg genome chromosome-specific FISH signals in Ae. geniculata and in the M genome of the putative diploid donor species Ae. comosa subsp. subventricosa but not in Ae. comosa subsp. comosa, suggesting that the Mg genome of Ae. geniculata was probably derived from subsp. subventricosa.

Visualization of U and M genome chromosomes by multicolour genomic in situ hybridization in Aegilops biuncialis and Triticum aestivum-Ae. biuncialis amphiploids

The multicolour genomic in situ hybridization (mcGISH) method was improved in order to visualize the U b and M b genomes of Aegilops biuncialis Vis. (2n=4x=28, U b U b M b M b ). Hybridization probes prepared from the diploid U and M genome donors, Ae. umbellulata and Ae. comosa , resulted in clear hybridization signals on the U and M chromosomes in Ae. biuncialis . The random primed labelling method made it possible to decrease the blocking ratio to 1:30. McGISH allowed the simultaneous discrimination of individual Ae. biuncialis genomes and wheat chromosomes in γ-irradiated Triticum aestivum-Ae. biuncialis amphiploids (2n=70; AABBDDU b U b M b M b ). Dicentric chromosomes, terminal and interstitial translocations and centric fusions were detected in the irradiated generation. The irradiation-induced wheat- Ae. biuncialis intergenomic translocations will facilitate the successful introgression of useful agronomic traits into bread wheat.

Production and fish identification of wheat- Aegilops biuncialis addition lines and their use for the selection of U and M genome-specific molecular (SSR) markers

One way of incorporating useful traits from Aegilops biuncialis (2n=4x=28, U b U b M b M b ) into wheat ( Triticum aestivum L. 2n=6x=42, AABBDD) is to develop first addition then translocation lines. The 2M b , 3M b , 7M b , 3U b , 5U b and 5U b /6U b wheat- Ae. biuncialis addition lines were produced in Martonvásár. To facilitate the exact identification of the addition lines, it was necessary to analyse the fluorescence in situ hybridisation patterns of the parental wheat genotype, Ae. biuncialis and its diploid progenitors ( Ae. umbellulata 2n=2x=14, UU and Ae. comosa 2n=2x=14, MM). The great genetic variability of the Aegilops species causes polymorphism in the fluorescence in situ hybridisation (FISH) patterns of the individual chromosomes. Due to the high level of FISH polymorphism, it is advisable to confirm the identification of the Ae. biuncialis chromosomes with the help of molecular (microsatellite, SSR) markers, so 119 wheat SSR markers were tested on Aegilops biuncialis , on Ae. geniculata (2n=4x=28, U g U g M g M g ), on five wheat- Ae. biuncialis addition lines (2M b , 3M b , 7M b , 3U b , 5U b ) and on an addition series of wheat- Ae. geniculata in order to select SSR markers specific to the U and M genomes of Ae. biuncialis and Ae. geniculata .