A novel pre-CTX prophage in the Vibrio cholerae serogroup O139 strain.
In this study, by combining the short-read and long-read sequencing approaches of next generation sequencing, we obtained the complete genome sequence of the studied V. cholerae toxigenic serogroup O139 strain and identified the CTXΦ and a pre-CTXΦ genome type encoding a novel rstR allele, pre-CTXZHJΦ. This pre-CTX prophage integrates into the small chromosome of the V. cholerae host strain and coexists with a typical CTXETΦ prophage present in the large chromosome, which is commonly present in the seventh pandemic serogroup O1 and toxigenic serogroup O139 strains. RstRZHJ could bind to the ig-2 region in t...
Source: Infection, Genetics and Evolution - February 8, 2020 Category: Genetics & Stem Cells Authors: Li X, Zhao L, Gao H, Chen L, Fan F, Li Z, Fan Y, Li J, Liang W, Pang B, Kan B Tags: Infect Genet Evol Source Type: research

Microsatellite typing of Aedes albopictus (Diptera: Culicidae) populations from Germany suggests regular introductions.
, Tannich E Abstract The global spread of the Asian tiger mosquito Aedes albopictus is of concern, as this mosquito species constitutes an important vector of a number of emerging pathogens including dengue virus, chikungunya virus and Zika virus. Since its first appearance in Albania (1979) and Italy (1990), the species has been reported from more than twenty-five European countries. However, the dispersion process in Europe is largely unknown, as information on population genetic structure is lacking, which is relevant to understand the observed spread. In order to determine whether the ten Ae. albopictus popula...
Source: Infection, Genetics and Evolution - February 8, 2020 Category: Genetics & Stem Cells Authors: Lühken R, Heitmann A, Jansen S, Schmidt-Chanasit J, Börstler J, Werner D, Kampen H, Kuhn C, Pluskota B, Ferstl I, Jöst A, Becker N, Tannich E Tags: Infect Genet Evol Source Type: research

Detection and complete genome characterization of a novel RNA virus related to members of the Hepe-Virga clade in bird species, hoopoe (Upupa epops).
Pankovics P Abstract Using viral metagenomics, next-generation sequencing and RT-PCR techniques a genetically divergent hepevirus-like RNA virus was identified and characterized from a faecal sample of wild bird species, Hoopoe (Upupa epops) in Hungary. The complete viral genome sequence of hoopoe/BBanka01/2015/HUN (GenBank accession number MN852439) is 7052 nt long including a 54-nt 5' and an 18-nt 3' non-coding region without poly(A)-tail. Sequence analysis indicated that the hoopoe/BBanka01/2015/HUN genome has potentially three overlapping open reading frames (ORFs). The ORF1 (6558 nt/2185aa) encodes a long...
Source: Infection, Genetics and Evolution - February 6, 2020 Category: Genetics & Stem Cells Authors: Reuter G, Boros Á, Mátics R, Kapusinszky B, Delwart E, Pankovics P Tags: Infect Genet Evol Source Type: research

Genotyping Mycobacterium tuberculosis isolates with few copies of IS6110: Value of additional genetic markers.
CONCLUSION: Combination of FAFLP and Spoligotyping may prove to be valuable in studying the epidemiology of M. tuberculosis strains harboring few copies of IS6110 element. PMID: 32035976 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 6, 2020 Category: Genetics & Stem Cells Authors: Arora J, Suresh N, Porwal C, Pandey P, Pande JN, Singh UB Tags: Infect Genet Evol Source Type: research

Liver virome of healthy pigs reveals diverse small ssDNA viral genomes.
This report addresses the diversity of the liver virome of healthy pigs and expands the number of viruses detected, further characterizing their genomes to assist future studies. PMID: 32035977 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 6, 2020 Category: Genetics & Stem Cells Authors: Da Silva MS, Budaszewski RF, Weber MN, Cibulski SP, Paim WP, Mósena ACS, Canova R, Varela APM, Mayer FQ, Pereira WC, Canal CW Tags: Infect Genet Evol Source Type: research

Genomic epizoology of a Brucella abortus outbreak in Northern Ireland (1997-2012).
CONCLUSIONS: Genome sequence data suggested that MLVA hyper-variability in some MLVA loci contributed to an overestimate of pathogen diversity in the most recent outbreak. The low diversity observed in our genomic dataset made it inappropriate to apply phylodynamic methods to these data. We conclude that maintaining data repositories of genome sequence data will be invaluable for source attribution/epizoological inference should recrudescence ever re-occur. However genomic epizoological methods may have limited utility in some settings, such as when applied to recrudescent/re-emergent infections of slowly evolving bacteria...
Source: Infection, Genetics and Evolution - February 5, 2020 Category: Genetics & Stem Cells Authors: Allen AR, Milne G, Drees K, Presho E, Graham J, McAdam P, Jones K, Wright L, Skuce R, Whatmore AM, Graham J, Foster JT Tags: Infect Genet Evol Source Type: research

Phylogeographical diversity of Anaplasma phagocytophilum in the Asian part of Russia based on multilocus sequence typing and analysis of the ankA gene.
Abstract Anaplasma phagocytophilum is a tick-transmitted bacterium that replicates in neutrophil granulocytes and elicits febrile disease in humans and animals; it is widely distributed in the Americas, Europe, Africa, and Asia. A. phagocytophilum is commonly regarded as a single species, but several genetic variants with distinct host distribution and geographical origin have been described. In a previous study, we used multilocus sequence typing (MLST) to characterize 25 A. phagocytophilum strains from Ixodes spp. ticks collected in the Asian part of Russia. The obtained concatenated sequences formed two separat...
Source: Infection, Genetics and Evolution - February 3, 2020 Category: Genetics & Stem Cells Authors: Mukhacheva TA, Shaikhova DR, Kovalev SY, von Loewenich FD Tags: Infect Genet Evol Source Type: research

Phylogenetic diversity of Mycobacterium tuberculosis in two geographically distinct locations in Botswana - The Kopanyo Study.
This study demonstrates localized differences in strain diversity by two districts in Botswana, and contributes to a growing characterization of MTBC diversity globally. PMID: 32028055 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 3, 2020 Category: Genetics & Stem Cells Authors: Click ES, Finlay A, Oeltmann JE, Basotli J, Modongo C, Boyd R, Wen XJ, Shepard J, Moonan PK, Zetola N Tags: Infect Genet Evol Source Type: research

First molecular identification of the tapeworm Mesocestoides litteratus from an Italian wall lizard (Podarcis siculus).
This study represents the first evidence of parasitic infection by tetrathyridia of M. litteratus in P. siculus in Italy. PMID: 32028056 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 3, 2020 Category: Genetics & Stem Cells Authors: Berrilli E, Simbula G Tags: Infect Genet Evol Source Type: research

Novel coronavirus: From discovery to clinical diagnostics.
Abstract A novel coronavirus designated as 2019-nCoV first appeared in Wuhan, China in late December 2019. Dozens of people died in China, and thousands of people infected as 2019-nCoV continues to spread around the world. We have described the discovery, emergence, genomic characteristics, and clinical diagnostics of 2019-nCoV. PMID: 32007627 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 30, 2020 Category: Genetics & Stem Cells Authors: Phan T Tags: Infect Genet Evol Source Type: research

Identification of Enterocytozoon bieneusi and Cryptosporidium spp. in farmed wild boars (Sus scrofa) in Beijing, China.
In this study, a total of 257 fecal specimens of wild boars were collected. The overall prevalence of E. bieneusi and Cryptosporidium spp. was 42.0% (108/257) and 5.8%, respectively. Higher infection rate of E. bieneusi was discovered in the wild boar ≤2 months old (58.3%). The differences between the feeding pattern and gender were not significant. Furthermore, eight genotypes of E. bieneusi were determined by analyzing the internal transcribed spacer (ITS) of the rRNA gene, including seven known genotypes and one novel genotype. Phylogenetic analysis revealed that all the eight genotypes belonged to the zoonotic pot...
Source: Infection, Genetics and Evolution - January 30, 2020 Category: Genetics & Stem Cells Authors: Feng S, Jia T, Huang J, Fan Y, Chang H, Han S, Luo J, He H Tags: Infect Genet Evol Source Type: research

Pathogenic viruses: Molecular detection and characterization.
This article reviews the molecular biology of pathogenic viruses and the basic principles of molecular techniques commonly used for their detection and characterization. The principles of good laboratory practices for handling pathogenic viruses are also discussed. This review aims at providing researchers and laboratory personnel with an overview of the molecular biology of pathogenic viruses and the principles of molecular techniques and good laboratory practices commonly implemented for their detection and characterization. PMID: 32006706 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 29, 2020 Category: Genetics & Stem Cells Authors: Artika IM, Wiyatno A, Ma'roef CN Tags: Infect Genet Evol Source Type: research

The impact of bone marrow stromal antigen-2 (BST2) gene variants on HIV-1 control in black South African individuals.
This study investigated the frequency of four HIV-1-associated BST2 variants rs3217318, rs12609479, rs10415893 and rs113189798 in uninfected and HIV-1 infected black South Africans. Homozygosity for the rs12609479-A minor allele, previously associated with decreased HIV-1 acquisition risk, was underrepresented in HIV-1 uninfected black South Africans (2%) compared to reference African (9%) and in particular European populations (61%) (p = .047 and p 
Source: Infection, Genetics and Evolution - January 29, 2020 Category: Genetics & Stem Cells Authors: Dias BDC, Paximadis M, Martinson N, Chaisson RE, Ebrahim O, Tiemessen CT Tags: Infect Genet Evol Source Type: research

Complete genome sequences of the first parechoviruses A associated with sporadic pediatric acute gastroenteritis in Russia.
Abstract Parechovirus (the Picornaviridae family), recently classified as Parechovirus A and formerly known as Human parechovirus (HPeV), can cause a wide range of human diseases. Over the past decade, several studies have reported HPeV epidemiology in different regions; however, information from Russia is limited. A total of 632 stool samples collected in Novosibirsk, Russia during January-March 2012 were screened for HPeV by RT-PCR. The study cohort comprised 572 patients with acute gastroenteritis and 60 healthy children. Seven of 572 (1.2%) gastroenteritis cases were HPeV-positive, including one co-infection w...
Source: Infection, Genetics and Evolution - January 29, 2020 Category: Genetics & Stem Cells Authors: Zhirakovskaia E, Tikunov A, Babkin I, Tikunova N Tags: Infect Genet Evol Source Type: research

Virulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen.
Abstract Arcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome wit...
Source: Infection, Genetics and Evolution - January 29, 2020 Category: Genetics & Stem Cells Authors: Isidro J, Ferreira S, Pinto M, Domingues F, Oleastro M, Gomes JP, Borges V Tags: Infect Genet Evol Source Type: research

Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).
lueza-Fox C Abstract The French revolutionary Jean-Paul Marat (1743-1793) was assassinated in 1793 in his bathtub, where he was trying to find relief from the debilitating skin disease he was suffering from. At the time of his death, Marat was annotating newspapers, which got stained with his blood and were subsequently preserved by his sister. We extracted and sequenced DNA from the blood stain and also from another section of the newspaper, which we used for comparison. Results from the human DNA sequence analyses were compatible with a heterogeneous ancestry of Marat, with his mother being of French origin and ...
Source: Infection, Genetics and Evolution - January 28, 2020 Category: Genetics & Stem Cells Authors: De-Dios T, van Dorp L, Charlier P, Morfopoulou S, Lizano E, Bon C, Le Bitouzé C, Alvarez-Estape M, Marquès-Bonet T, Balloux F, Lalueza-Fox C Tags: Infect Genet Evol Source Type: research

Acarbose, as a potential drug, effectively blocked the dynamic metastasis of EV71 from the intestine to the whole body.
Abstract Enterovirus 71 (EV71) is one of the main pathogens causing hand-foot-and-mouth disease (HFMD). The nose and mouth are usually the main infection entries of EV71 virus. However, its dynamic transport pathway from mouth to the whole body remains unknown. The reveal of this physiological mechanism in vivo will help to understand its transport direction, find its key proliferation nodes, and develop new preventive strategies. We trained a new strain of GFP-EV71 virus to be susceptible to mice brain by intracranial injection of mice. The adapted virus was oral-administrated to suckling mice. Then, the dynamic ...
Source: Infection, Genetics and Evolution - January 28, 2020 Category: Genetics & Stem Cells Authors: Feng Q, Zhou H, Zhang X, Liu X, Wang J, Zhang C, Ma X, Quan C, Zheng Z Tags: Infect Genet Evol Source Type: research

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event.
CONCLUSIONS: The levels of genetic similarity between the 2019-nCoV and RaTG13 suggest that the latter does not provide the exact variant that caused the outbreak in humans, but the hypothesis that 2019-nCoV has originated from bats is very likely. We show evidence that the novel coronavirus (2019-nCov) is not-mosaic consisting in almost half of its genome of a distinct lineage within the betacoronavirus. These genomic features and their potential association with virus characteristics and virulence in humans need further attention. PMID: 32004758 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 28, 2020 Category: Genetics & Stem Cells Authors: Paraskevis D, Kostaki EG, Magiorkinis G, Panayiotakopoulos G, Sourvinos G, Tsiodras S Tags: Infect Genet Evol Source Type: research

High-throughput sequencing (HTS) for the analysis of viral populations.
N, González-Candelas F Abstract The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step ...
Source: Infection, Genetics and Evolution - January 27, 2020 Category: Genetics & Stem Cells Authors: Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F Tags: Infect Genet Evol Source Type: research

Bioinformatic analysis of post-transmission viral readaptation in Argentine patients with acute HIV-1 infection.
In this study, a total of 17 patients were enrolled during acute/early primary HIV infection and 8 subjects that were the HIV positive partner resulting in 8 transmission pairs. Genotyping of the genetic polymorphisms of HLA class I A and B was performed using PCR-SSOP. Viral RNA extraction was from plasma. 570 single Gag-gene amplifications were obtained by limiting-dilution RT-PCR. Epitope prediction was performed with NetMHC CBS prediction server for the 19 HLA-A and B alleles. Cytotoxic response prediction was performed by using the IEDB Analysis Resource. From our results, we deduce that the transmitted CTL / gag esca...
Source: Infection, Genetics and Evolution - January 25, 2020 Category: Genetics & Stem Cells Authors: Damilano G, Sued O, Satorres S, Ruiz MJ, Ghiglione Y, Guzman F, Turk G, Quiroga F, Cahn P, Salomón H, Dilernia D Tags: Infect Genet Evol Source Type: research

RNA sequencing analyses of gene expressions in a canine macrophages cell line DH82 infected with canine distemper virus.
Abstract Virulent morbillivirus infections, including Meals Virus (MeV) and Canine Distemper Virus (CDV), caused severe immune suppression and leukopenia, while attenuated vaccine strains developed protective host immune responses. However, the detailed molecular foundations of host antiviral responses were poorly characterized. In order to better understand the interactions between attenuated vaccine and host antiviral responses, the global gene expression changes in CDV-11-infected DH82 cells, a macrophage-derived cell line from canine, were investigated by transcriptomic analysis, and portions of results were c...
Source: Infection, Genetics and Evolution - January 23, 2020 Category: Genetics & Stem Cells Authors: Zheng X, Zhu Y, Zhao Z, Yan L, Xu T, Wang X, He H, Xia X, Zheng W, Xue X Tags: Infect Genet Evol Source Type: research

Genetics and evolution of tuberculosis pathogenesis: New perspectives and approaches.
Abstract Tuberculosis is the most lethal infectious disease globally, but the vast majority of people who are exposed to the primary causative pathogen, Mycobacterium tuberculosis (MTB), do not develop active disease. Most people do, however, show signs of infection that remain throughout their lifetimes. In this review, we develop of framework that describes several possible transitions from pathogen exposure to TB disease and reflect on the genetics studies to address many of these. The evidence strongly supports a human genetic component for both infection and active disease, but many of the existing studies, i...
Source: Infection, Genetics and Evolution - January 22, 2020 Category: Genetics & Stem Cells Authors: McHenry ML, Williams SM, Stein CM Tags: Infect Genet Evol Source Type: research

Molecular epidemiology and evolution of Haemophilus influenzae.
Abstract Haemophilus influenzae remains a common cause of illness in children worldwide. H. influenzae type b is the leading cause of bacterial meningitis in children before introduction of vaccination and is a common cause of pneumonia, epiglottis and septic arthritis. Since the implementation of the Hib conjugate vaccine, the non-typeable H. influenzae has rapidly decreased in respiratory and invasive infections in children and adults. However, the rate of antibiotic resistance of H. influenzae varies with region and period and is usually on the rise. In this review, typing of H. influenzae, virulence factors an...
Source: Infection, Genetics and Evolution - January 22, 2020 Category: Genetics & Stem Cells Authors: Wen S, Feng D, Chen D, Yang L, Xu Z Tags: Infect Genet Evol Source Type: research

Multigene typing and phylogenetic analysis of Fasciola from endemic foci in Iran.
Abstract Fasciolosis is a public health problem originally transmitted from livestock. Although molecular analysis of nuclear and mitochondrial genes allow discrimination between the two known species of Fasciola, F. hepatica and F. gigantica, these markers do not permit the detection of hybrid forms. On the other hand, molecular analysis of the pepck and pold genes from Fasciola do permit the detection of hybrid isolates and this study has not yet been performed on specimens from human and domesticated animals in Iran. Therefore, the aim of this study was to molecularly analyze Fasciola isolates using both conven...
Source: Infection, Genetics and Evolution - January 21, 2020 Category: Genetics & Stem Cells Authors: Javanmard E, Ohari Y, Sadeghi A, Cheraghipour K, Aghdaei HA, Mirjalali H, Zali MR, Itagaki T Tags: Infect Genet Evol Source Type: research

An improved and low-cost protocol for high-quality DNA isolation for the Chagas disease vectors.
ano E Abstract An improved protocol for DNA extraction for the Chagas disease vectors is proposed based on modification to a low cost method described twenty years ago. Quality DNA and high molecular weight were obtained from all samples. NADH-4 gene was successfully amplified by PCR using the isolated DNA. The extraction protocol presented in this technical note is a fast, low-cost, and non-aggressive method to human health for obtaining genetic data from this group of epidemiological importance and potentially other insects. PMID: 31972328 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 20, 2020 Category: Genetics & Stem Cells Authors: Flores DDC, Nava-García E, Arellano E Tags: Infect Genet Evol Source Type: research

Immunoinformatics guided rational design of a next generation multi epitope based peptide (MEBP) vaccine by exploring Zika virus proteome.
In this study combination of immuno-informatics and molecular docking approach was used to constitute a MEBP vaccine. The ZIKV proteome was used for prediction of B-cell, T-cell (HTL & CTL) and IFN-γ epitopes. After prediction, highly antigenic and overlapping epitopes have been shortlisted which includes 14 CTL and 11 HTL epitopes that have been linked to the final peptide through AAY and GPGPG linkers respectively. An adjuvant at the N-end of the vaccine was added to improve the immunogenicity of the vaccine through the EAAAK linker. The final construct constitutes 435 amino acids after the addition of linkers ...
Source: Infection, Genetics and Evolution - January 18, 2020 Category: Genetics & Stem Cells Authors: Shahid F, Ashfaq UA, Javaid A, Khalid H Tags: Infect Genet Evol Source Type: research

Hepatic TLR4, MBL and CRP gene expression levels are associated with chronic hepatitis C.
o ACR Abstract Contact with HCV triggers the activation of innate mechanisms responsible for initial infection control. Host cells expressed extra- or intracellularly molecules that promote recognition of pathogen-associated molecular patterns (PAMPs). Toll-like receptor 4 (TLR4), mannose-binding lectin (MBL) and C-reactive protein (CRP) are molecules available for HCV PAMP recognition. The present study evaluated TLR4, MBL and CRP gene expression in the hepatic tissue of chronic HCV carriers (n = 22) and the association of that expression with the pathogenesis of HCV as well as the progression of liver fibros...
Source: Infection, Genetics and Evolution - January 18, 2020 Category: Genetics & Stem Cells Authors: de Souza Pires-Neto O, da Silva Graça Amoras E, Queiroz MAF, Demachki S, da Silva Conde SR, Ishak R, Cayres-Vallinoto IMV, Vallinoto ACR Tags: Infect Genet Evol Source Type: research

Progress and applications of single-cell sequencing techniques.
In this study, we mainly summarized the methods and application fields of SCS, which may provide potential references for its future clinical applications, including the analysis of embryonic and organ development, the immune system, cancer progression, and parasitic and infectious diseases as well as stem cell research, antibody screening, and therapeutic research and development. PMID: 31958516 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 17, 2020 Category: Genetics & Stem Cells Authors: Yasen A, Aini A, Li W, Wang H, Ran B, Tuxun T, Maimaitinijiati Y, Shao Y, Aji T, Wen H Tags: Infect Genet Evol Source Type: research

Population genetic structure analysis of thrombospondin-related adhesive protein (TRAP) as a vaccine candidate antigen in worldwide Plasmodium falciparum isolates.
Abstract Antigenic diversity is a major concern in malaria vaccine development that requires to be considered in developing a malaria vaccine. Plasmodium falciparum thrombospondin-related adhesive protein (PfTRAP) is a leading malaria vaccine candidate antigen. In the current study, we investigated the level of genetic diversity and natural selection of pftrap sequences in P. falciparum isolates from Iran (n = 47). The gene diversity of Iranian pftrap sequences was also compared to available global pftrap sequences deposited in the GenBank or PlasmoDB databases (n = 220). Comparison of Iranian PfTRAP seque...
Source: Infection, Genetics and Evolution - January 16, 2020 Category: Genetics & Stem Cells Authors: Mehrizi AA, Zadeh AJ, Zakeri S, Djadid ND Tags: Infect Genet Evol Source Type: research

Genome-wide screening and in silico gene knockout to predict potential candidates for drug designing against Candida albicans.
Abstract C. albicans infections are increasingly becoming a threat to public health with emergence of drug resistant strains. It emphasizes the need to look for alternate drug targets through genome-wide screening. In the present study, whole proteome of C. albicans SC5314 was analyzed in single click target mining workflow of TiDv2. A protein-protein interaction network (PPI) for the resulting putative targets was generated based on String database. Ninety four proteins with higher connectivity (degree ≥10) in the network are noted as hub genes. Among them, 24 are observed to be known targets while 70 are nove...
Source: Infection, Genetics and Evolution - January 16, 2020 Category: Genetics & Stem Cells Authors: Verma R, Pradhan D, Maseet M, Singh H, Jain AK, Khan LA Tags: Infect Genet Evol Source Type: research

Comparative genomic analysis and identification of pathogenicity islands of hypervirulent ST-17 Streptococcus agalactiae Brazilian strain.
In this study, we sequenced the first genome of a S. agalactiae ST-17 strain isolated in Brazil using the Illumina HiSeq 2500 technology. S. agalactiae GBS90356 ST-17 belongs to the capsular type III and was isolated from a neonatal with a fatal case of meningitis. The genome presented a size of 2.03 Mbp and a G + C content of 35.2%. S. agalactiae has 706 genes in its core genome and an open pan-genome with a size of 5.020 genes, suggesting a high genomic plasticity. GIPSy software was used to identify 10 Pathogenicity islands (PAIs) which corresponded to 15% of the genome size. IslandViewer4 corroborated the predictio...
Source: Infection, Genetics and Evolution - January 15, 2020 Category: Genetics & Stem Cells Authors: Lannes-Costa PS, Baraúna RA, Ramos JN, Veras JFC, Conceição MVR, Vieira VV, de Mattos-Guaraldi AL, Ramos RTJ, Doran KS, Silva A, Nagao PE Tags: Infect Genet Evol Source Type: research

Pre-vaccine rotavirus surveillance in Buenos Aires, Argentina. Characterization of an emergent G1P[8] strain associated to fatal cases in 2014.
In conclusion, this work gives us a whole panorama of the pre-vaccine era of the RVA molecular epidemiology in the most populated region of Argentina. In this way, this work inspires us to continue with this type of studies in the post-vaccination era. PMID: 31931256 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 10, 2020 Category: Genetics & Stem Cells Authors: Mandile MG, Argüelles MH, Temprana CF, Peri Ibáñez ES, Silvestre D, Musto A, Pérez AR, Mistchenko A, Glikmann G, Castello AA Tags: Infect Genet Evol Source Type: research

Insect-specific flaviviruses and densoviruses, suggested to have been transmitted vertically, found in mosquitoes collected in Angola: Genome detection and phylogenetic characterization of viral sequences.
This report describes a survey of RNA and DNA viruses carried out in adult mosquitoes from Angola, raised under laboratory conditions from field-collected immature forms. This viral genomic survey was performed using different sets of primers targeting groups of arboviruses with a considerable impact on human health, including flaviviruses, alphaviruses, and phleboviruses. Furthermore, the viral survey that was performed also included detection of densoviruses. The obtained results did not reveal the presence of recognizable pathogenic arboviruses but allowed the identification of insect-specific flaviviruses from two gene...
Source: Infection, Genetics and Evolution - January 10, 2020 Category: Genetics & Stem Cells Authors: Morais P, Pinto J, Jorge CP, Troco AD, Fortes F, Sousa CA, Parreira R Tags: Infect Genet Evol Source Type: research

Frequency and expression of st313-td gene and virulence of Salmonella Dublin strains isolated from humans and animals in Brazil.
In conclusion, the presence of st313-td in all the S. Dublin strains studied besides its expression among strains from invasive cases suggest that this gene might be related to the invasive characteristic of this serovar. The low expression of sopE2 in strains from human invasive cases suggests that the expression of this gene may not be a limiting factor to the invasion of S. Dublin strains. Moreover, the absence fliC expression and the low motility rates observed suggest that the flagella absence may favor the host immune system evasion by S. Dublin and the establishment of invasive infection. The high invasion to human ...
Source: Infection, Genetics and Evolution - January 10, 2020 Category: Genetics & Stem Cells Authors: Vilela FP, Gomes CN, Paziani MH, Braz VS, Dos Prazeres Rodrigues D, Costa RG, Casas MRT, von Zeska Kress MR, Falcão JP, Campioni F Tags: Infect Genet Evol Source Type: research

Bioinformatics analyses of immunogenic T-cell epitopes of LeIF and PpSP15 proteins from Leishmania major and sand fly saliva used as model antigens for the design of a multi-epitope vaccine to control leishmaniasis.
In this study, diverse computational methods were integrated to calculate evolutionary divergence, immunogenicity, IFN-γ production, epitope conservancy, and population coverage of protein fusion models of LeIF-SP15 namely SaLeish. Immunogenicity of LeIF of Leishmania species and SP15 of sandfly saliva has not been investigated in-silico in fusion form. A complete set of 9-mer MHC class I and 15-mer MHC class II peptides were identified with a high affinity for the antigenic epitopes of SaLeish inducing specific responses of CD8+ and CD4+ T cells from BALB/c and human. Our preferred approach was determining truncated...
Source: Infection, Genetics and Evolution - January 10, 2020 Category: Genetics & Stem Cells Authors: Bordbar A, Bagheri KP, Ebrahimi S, Parvizi P Tags: Infect Genet Evol Source Type: research

Thorough analysis of a rapid spread tuberculosis outbreak by epidemiological and whole-genome sequencing.
per S Abstract The genotyping is applied to analyse tuberculosis detected in Aragon, Spain, since 2004. The new sequencing technologies were applied to analyse an outbreak which, the first time the responsible Myocbacterium tuberculosis strain of the outbreak appeared was in 2014, spreading to 14 patients in the next three years. We perform whole-genome sequencing (WGS) to characterise the strain and try to elucidate the transmission chain. The WGS results showed that this strain belonged to the Linage 4.3.3 and was genetically susceptible to anti-tuberculosis drugs. We found scarce variability between the isolate...
Source: Infection, Genetics and Evolution - January 10, 2020 Category: Genetics & Stem Cells Authors: Comin J, Chaure A, Cebollada A, Ibarz D, Viñuelas J, Vitoria MA, Iglesias MJ, Samper S Tags: Infect Genet Evol Source Type: research

Detection of three independently-generated DS-1-like G9P[8] reassortant rotavirus A strains during the G9P[8] dominance in Vietnam, 2016-2018.
Abstract A rapid increase and dominance of G9P[8] Rotavirus A strains occurred in northern Vietnam between 2016 and 2018, during which period there appeared three G9P[8] strains possessing short RNA patterns. To understand how the first-ever G9P[8] strains possessing short RNA patterns were formed, next generation sequencing technology was used to examine the whole genomes of the three strains, i.e., RVA/Human-wt/VNM/RVN16.1024/2016/G9P[8], RVA/Human-wt/VNM/RVN17.0879/2017/G9P[8], and RVA/Human-wt/VNM/RVN18.0197/2018/G9P[8], and those of seven representative G9P[8] strains possessing long RNA patterns. The VP7 gen...
Source: Infection, Genetics and Evolution - January 10, 2020 Category: Genetics & Stem Cells Authors: Hoa-Tran TN, Nakagomi T, Vu HM, Nguyen TTT, Takemura T, Hasebe F, Dao ATH, Anh PHQ, Nguyen AT, Dang AD, Nakagomi O Tags: Infect Genet Evol Source Type: research

Acute enterovirus infections significantly alter host cellular DNA methylation status.
In this study, we analyzed the genome-wide DNA methylation patterns of host cells in response to EV71 and CVA16 infections using the Illumina Infinium HumanMethylation450 BeadChip. Of over 480,000 loci studied, significant differential methylation was observed between EV71 infected-cells and control cells at 3957 CpG sites, out of which 2478 were hypermethylated and 1479 were hypomethylated, whereas CVA16 infection resulted in methylation level changes of 5194 CpG sites with 4288 hypermethylated and 906 hypomethylated. These differential methylated loci displayed a wide range of genomic distributions in chromosomes, inside...
Source: Infection, Genetics and Evolution - January 9, 2020 Category: Genetics & Stem Cells Authors: Zhu Z, Li Y, Zhou J, Zhang Y, Cao RY Tags: Infect Genet Evol Source Type: research

Innate and adaptive immunity in wild rodents spontaneously and experimentally infected with the tick-borne encephalitis virus.
Abstract Two dominant species of wild small rodents trapped in Novosibirsk region, South-Western Siberia, Russia differed in their susceptibility to the tick-borne encephalitis virus (TBEV) infection. TBEV RNA average detection rate for Northern red-backed vole Myodes rutilus (Pallas, 1779) (82.2 ± 5.8% blood samples and 63.1 ± 2.7% organ samples) significantly exceeded the corresponding values for the striped field mouse Apodemus agrarius (Pallas, 1771) (47.0 ± 8.7% blood and 24.5 ± 2.8% organ samples) (p 
Source: Infection, Genetics and Evolution - January 9, 2020 Category: Genetics & Stem Cells Authors: Morozova OV, Panov VV, Bakhvalova VN Tags: Infect Genet Evol Source Type: research

Joint selection for two malaria resistance mutations in a south-west Colombian population.
The objective of this study was to evaluate the individual and joint selection actions of these two genes in an Afro-descendant Colombian population. A total of 819 individuals were analysed using stratified random sampling. PCR-RFLP and Hardy-Weinberg equilibrium deviation analysis (H-W eq.), linkage disequilibrium (LD), D'IS2 and D'ST2 indexes, neutrality tests, correlations and fitness were performed using Arlequin 3.5.2.2 and R 3.4.1 software. In general, the population showed neutrality and H-W eq. for the HbS gene but not for the Duffy gene (FYA/FYB, FYA/FYBES and FYB/FYBES genotypes were responsible for this dev...
Source: Infection, Genetics and Evolution - January 9, 2020 Category: Genetics & Stem Cells Authors: Ortega DC, Cárdenas H, Barreto G Tags: Infect Genet Evol Source Type: research

Designing and evaluation of an antibody-targeted chimeric recombinant vaccine encoding Shigella flexneri outer membrane antigens.
In this study, emphasis was made on designing a candidate that could elicit both B-cell and T-cell immune response. Hence B- and T-cell epitopes of outer membrane channel protein (OM) and putative lipoprotein (PL) from S. flexneri 2a were computationally predicted using immunoinformatics approach and a chimeric construct (chimeric-OP) containing the immunogenic epitopes selected from OM and PL was designed, cloned and expressed in E. coli system. The immunogenicity of the recombinant chimeric-OP was assessed using Shigella antigen infected rabbit antibody. The result showed that the chimeric-OP was a synthetic peptide cand...
Source: Infection, Genetics and Evolution - January 7, 2020 Category: Genetics & Stem Cells Authors: Kazi A, Ismail CMKH, Amilda AA, Chuah C, Leow CH, Lim BH, Singh KKB, Leow CY Tags: Infect Genet Evol Source Type: research

Mechanism of eravacycline resistance in Acinetobacter baumannii mediated by a deletion mutation in the sensor kinase adeS, leading to elevated expression of the efflux pump AdeABC.
Abstract Acinetobacter baumannii is an important pathogen and presents a major burden in healthcare as strains frequently cause hospital associated opportunistic infections with high mortality rates. Due to increasing numbers of drug resistant A. baumannii strains, newly developed antibiotics are being used to treat infections caused by such strains. One novel synthetic antibiotic of the tetracycline class with activity against A. baumannii is eravacycline. To investigate possible mechanisms of eravacycline resistance, we performed an in vitro evolution experiment to select for an eravacycline resistant strain, wi...
Source: Infection, Genetics and Evolution - January 7, 2020 Category: Genetics & Stem Cells Authors: Shi Y, Hua X, Xu Q, Yang Y, Zhang L, He J, Mu X, Hu L, Leptihn S, Yu Y Tags: Infect Genet Evol Source Type: research

Epitope promiscuity and population coverage of Mycobacterium tuberculosis protein antigens in current subunit vaccines under development.
In this study, using computational approaches, we predicted the capacity of the epitopes to be presented by the HLA molecules for ten MTB protein antigens (Mtb39a, Mtb32a, Ag85B, ESAT-6, TB10.4, Rv2660, Rv3619, Rv2608, Rv3620, and Rv1813) constituting five MTB subunit vaccines (M72, H1, H4, H56, and ID93) that are currently in clinical trials. We also assessed the promiscuity of the predicted epitopes based on a reference set of alleles and supertype alleles, and estimated the population coverage of the ten antigens in three high TB burden countries (China, India, and South Africa). Among the ten antigens evaluated, Rv2608...
Source: Infection, Genetics and Evolution - January 7, 2020 Category: Genetics & Stem Cells Authors: Ong E, He Y, Yang Z Tags: Infect Genet Evol Source Type: research

CRISPR elements and their association with antimicrobial resistance and virulence genes among vancomycin-resistant and vancomycin-susceptible enterococci recovered from human and food sources.
In conclusion, we found evident associations between the lack of CRISPR elements with species, multidrug resistance, and major resistance- and virulence-associated genes. PMID: 31923727 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 7, 2020 Category: Genetics & Stem Cells Authors: Dos Santos BA, da Silva de Oliveira J, Parmanhani-da-Silva BM, Ribeiro RL, Teixeira LM, Neves FPG Tags: Infect Genet Evol Source Type: research

Molecular epidemiological study of multidrug-resistant tuberculosis isolated from sputum samples in Eastern Cape, South Africa.
This study gives a general overview of drug resistant strains and the circulating strains in the Eastern Cape, South Africa and it shows that the common Mycobacteria in the province is the Beijing strain. PMID: 31923728 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 7, 2020 Category: Genetics & Stem Cells Authors: Bhembe NL, Green E Tags: Infect Genet Evol Source Type: research

Characterization of the complete mitochondrial genome of Cavisoma magnum () (Acanthocephala: Palaeacanthocephala), first representative of the family Cavisomidae, and its phylogenetic implications.
Abstract The phylum Acanthocephala is a small group of endoparasites occurring in the alimentary canal of all major lineages of vertebrates worldwide. In the present study, the complete mitochondrial (mt) genome of Cavisoma magnum (Southwell, 1927) (Palaeacanthocephala: Ehinorhynchida) was determined and annotated, the representative of the family Cavisomidae with the characterization of the complete mt genome firstly decoded. The mt genome of this acanthocephalan is 13,594 bp in length, containing 36 genes plus two non-coding regions. The positions of trnV and SNCR (short non-coding region) in the mt genome of ...
Source: Infection, Genetics and Evolution - January 6, 2020 Category: Genetics & Stem Cells Authors: Muhammad N, Li L, Suleman, Zhao Q, Bannai MA, Mohammad ET, Khan MS, Zhu XQ, Ma J Tags: Infect Genet Evol Source Type: research

Genomic features, whole-genome phylogenetic and comparative genomic analysis of extreme-drug-resistant ventilator-associated-pneumonia Acinetobacter baumannii strain in a Vietnam hospital.
CONCLUSION: Our findings provide insight into the virulence-associated genes and then compared with the genomes of other A. baumannii strains by calculation of ANI values and pan-genome analysis. Functional studies of these pathogens are required to validate these findings. PMID: 31917358 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 6, 2020 Category: Genetics & Stem Cells Authors: Nguyen ST, Ngoc HM, Nhat LD, Cuong N, Pham HQ, Huong NT Tags: Infect Genet Evol Source Type: research

Molecular characteristics of Mycobacterium tuberculosis in the "closed" Russian town with limited population migration.
Molecular characteristics of Mycobacterium tuberculosis in the "closed" Russian town with limited population migration. Infect Genet Evol. 2020 Jan 06;:104174 Authors: Umpeleva T, Belousova K, Golubeva L, Boteva T, Morozova I, Vyazovaya A, Mokrousov I, Eremeeva N, Vakhrusheva D Abstract The aim of this study was to perform a molecular characterization of Mycobacterium tuberculosis strains circulating in one of the "closed" Russian cities under conditions of the limited population migration and high HIV coinfection rate. We analyzed 109 M. tuberculosis isolates recovered from TB pat...
Source: Infection, Genetics and Evolution - January 6, 2020 Category: Genetics & Stem Cells Authors: Umpeleva T, Belousova K, Golubeva L, Boteva T, Morozova I, Vyazovaya A, Mokrousov I, Eremeeva N, Vakhrusheva D Tags: Infect Genet Evol Source Type: research

Cutavirus: A newly discovered parvovirus on the rise.
Abstract Cutavirus is a new member of the Parvoviridae family. It was first discovered in 2016 through unbiased metagenomics performed on fecal samples collected from patients with diarrhea, and also in skin biopsies collected from patients with cutaneous T-cell lymphoma (CTCL, also known as mycosis fungoides). We have systematically reviewed the literature to describe the discovery, genomic organization, prevalence, and geographic distribution of cutavirus. PMID: 31917360 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 6, 2020 Category: Genetics & Stem Cells Authors: Phan T, Nagaro K Tags: Infect Genet Evol Source Type: research

Phylogenetic analysis of near full-length sequences of the Desmodus rotundus genetic lineage of rabies virus.
In this study, we sequenced and analyzed the genome of a RABV variant detected in D. rotundus. The sample, collected from an endemic area in São Paulo State, was phylogenetically compared with the genome of the standard sample for species Rabies virus as well as other samples belonging to terrestrial and bat-associated cycles of rabies transmission, available in GenBank. Distinct patterns linked to the genetic lineage were identified. These data can aid in the understanding of the molecular epidemiology of this virus and the epidemiological importance of this species in the transmission of the RABV. PMID: 31917...
Source: Infection, Genetics and Evolution - January 6, 2020 Category: Genetics & Stem Cells Authors: de Almeida Campos AC, Romano CM, Melo FL, Araújo DB, Cunha EMS, Sacramento DRV, Durigon EL, Lazarini SRF Tags: Infect Genet Evol Source Type: research