The genetic divergences of codon usage shed new lights on transmission of hepatitis E virus from swine to human.
Abstract Hepatitis E virus (HEV) is an important pathogen causing public health burden. Swine has been recognized as a main reservoir. Interestingly, genotype 1 HEV only infects human; whereas genotype 3 and 4 are zoonotic. However, there is a lack of in-depth understanding in respect to the transmission from swine to human. Codon usage patterns generally participate in viral survival and fitness towards its hosts. We have analyzed codon usage patterns of the three open reading frames (ORFs) for 243 full-length genomes of HEV genotypes 1, 3 and 4. The divergence of synonymous codon usage patterns is different in e...
Source: Infection, Genetics and Evolution - December 2, 2018 Category: Genetics & Stem Cells Authors: Zhou JH, Li XR, Lan X, Han YS, Wang YN, Hu Y, Pan Q Tags: Infect Genet Evol Source Type: research

Antigenic relationship among zoonotic flaviviruses from Italy.
Abstract Here we report studies of the antigenic relationships of West Nile virus (WNV) and Usutu virus (USUV), two zoonotic flaviviruses from Italy, together with a Japanese encephalitis virus (JEV) strain and compared them with their genetic relationships using the immunodominant viral E protein. Thirty-nine isolates and reference strains were inactivated and used to immunize rabbits to produce hyper immune sera. Serum samples were tested by neutralization against all isolates and results visualized by generating antigenic map. Strains of WNV, USUV, and JEV grouped in separate clusters on the antigenic map. JEV ...
Source: Infection, Genetics and Evolution - December 2, 2018 Category: Genetics & Stem Cells Authors: Lorusso A, Marini V, Di Gennaro A, Ronchi GF, Casaccia C, Carelli G, Passantino G, D'Alterio N, D'Innocenzo V, Savini G, Monaco F, Horton DL Tags: Infect Genet Evol Source Type: research

Indel-informed bayesian analysis suggests cryptic divisions between Plasmodium knowlesi of humans and long-tailed macaques (Macaca fascicularis) in Malaysian Borneo.
We report distinct clades of P. knowlesi that predominantly contained sequences from either human or macaque hosts species for paralogous A-type and S-type 18S gene loci. We report significant partitioning of sequence distances between host species across both types of loci, and confirmed that sequences of the same locus type showed significantly biased assortment into different clades depending on their host species. Our results support the zoonotic potential of Plasmodium knowlesi, but also suggest that humans may be preferentially infected with certain strains of this parasite. Broadly, such patterns could arise through...
Source: Infection, Genetics and Evolution - November 24, 2018 Category: Genetics & Stem Cells Authors: Wilcox JJS, Kerschner A, Hollocher H Tags: Infect Genet Evol Source Type: research

A novel genetic lineage of Tula orthohantavirus in Altai voles (Microtus obscurus) from Turkey.
This report describes the initial documentation of TULV circulation and its potential reservoir in Anatolia. The extent of virus dispersion, alternate hosts or outcomes of human exposure require elucidation. PMID: 30465911 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - November 19, 2018 Category: Genetics & Stem Cells Authors: Polat C, Ergünay K, Irmak S, Erdin M, Brinkmann A, Çetintaş O, Çoğal M, Sözen M, Matur F, Nitsche A, Öktem İMA Tags: Infect Genet Evol Source Type: research

Aedes aegypti vector competence studies: A review.
Abstract Aedes aegypti is the primary transmitter of the four viruses that have had the greatest impact on human health, the viruses causing yellow fever (YFV), dengue fever (DENV), chikungunya (CHIKV), and Zika fever (ZIKV). Because this mosquito is easy to rear in the laboratory and these viruses grow in laboratory tissue culture cells, many studies have been performed testing the relative competence of different populations of the mosquito to transmit many different strains of viruses. We review here this large literature including studies on the effect of the mosquito microbiota on competence. Because of the h...
Source: Infection, Genetics and Evolution - November 19, 2018 Category: Genetics & Stem Cells Authors: Souza-Neto JA, Powell JR, Bonizzoni M Tags: Infect Genet Evol Source Type: research

Morphological and genetic characterization of Syphabulea tjanschani () (Nematoda: Oxyuridae), with phylogenetic position of Syphabulea in Oxyuridae.
Abstract Pinworms are important parasitic nematodes in animals and humans, and many species are of medical and veterinary importance. The genus Syphabulea is a poorly known group of pinworms. The systematic position of Syphabulea in Oxyuridae remains unclear. Moreover, there is still a paucity of detailed information on some morphological aspects of the type species S. tjanschani (Ablasov, 1962). In the present study, the detailed morphology of S. tjanschani was studied using light microscopy and, for the first time, scanning electron microscopy. The results revealed three traits useful for the characterization of...
Source: Infection, Genetics and Evolution - November 17, 2018 Category: Genetics & Stem Cells Authors: Li Y, Chen HX, Yang XL, Li L Tags: Infect Genet Evol Source Type: research

Phylogenetic analysis of Alphapapillomavirus based on L1, E6 and E7 regions suggests that carcinogenicity and tissue tropism have appeared multiple times during viral evolution.
dez A Abstract Members of the Alphapapillomavirus genus are causative agents for cervix cancer and benign lesions in humans. These viruses are classified according to sequence similarities in their L1 region. Yet, viral carcinogenicity has been associated with variations in the proteins encoded by the E6 and E7 genes. In order to relate evolutionary history with origin of carcinogenicity, we performed phylogenetic reconstructions using both nucleotide and predicted amino acid sequences of the L1, E6 and E7 genes. Whilst phylogenetic analysis of L1 reconstructed genus evolutionary history, phylogenies based on E6 a...
Source: Infection, Genetics and Evolution - November 17, 2018 Category: Genetics & Stem Cells Authors: Rojas-Cruz A, Reyes-Bermúdez A Tags: Infect Genet Evol Source Type: research

Prediction of HIV integrase resistance mutation using in silico approaches.
ura R Abstract The Antiretroviral Therapy (ART) has been providing better treatment for the Human Immunodeficiency Virus 1 (HIV) infection, by reducing its viral load to undetectable levels and recovering the immune system. However, new HIV mutations could induce drug resistance to ART, increasing the viral load and disruption of immune system. One of these drugs is Dolutegravir (DTG), which inhibits HIV integrase (INT) activity. Our objective was to predict novel HIV mutations related to DTG resistance using in silico approaches in order to stablish a framework of searching for new HIV drug-resistant mutations. T...
Source: Infection, Genetics and Evolution - November 16, 2018 Category: Genetics & Stem Cells Authors: da Silva HHSA, Pereira N, Brandão L, Crovella S, Moura R Tags: Infect Genet Evol Source Type: research

pncA gene mutations in reporting pyrazinamide resistance among the MDR-TB suspects.
Abstract Mutations in pncA gene contributing to PZA resistance was not clearly elucidated in China. To reveal the correlated mutations of pncA gene on pyrazinamide (PZA) resistance. 148 Mycobacterium tuberculosis clinical isolates were included from multi-drug resistant tuberculosis suspects. The MGIT 960 test and microscopic observation drug susceptibility (MODS) assay were adopted for PZA phenotype drug susceptibility test. 120 isolates with consistent MGIT 960 and MODS results were selected for pncA gene sequencing. 68 samples (56.7%) were resistant to PZA while leaving 52 PZA susceptible samples. Out of the 68...
Source: Infection, Genetics and Evolution - November 14, 2018 Category: Genetics & Stem Cells Authors: Wu X, Lu W, Shao Y, Song H, Li G, Li Y, Zhu L, Chen C Tags: Infect Genet Evol Source Type: research

Association of non-tuberculous mycobacteria with Mycobacterium leprae in environment of leprosy endemic regions in India.
Abstract Non-tuberculous mycobacteria (NTM) are environmental mycobacteria found ubiquitously in nature. The present study was conducted to find out the presence of various species of NTM in leprosy endemic region along with Mycobacterium (M) leprae. Water and wet soil samples from the periphery of ponds used by the community were collected from districts of Purulia of West Bengal and Champa of Chhattisgarh, India. Samples were processed and decontaminated followed by culturing on Lowenstein Jensen (LJ) media. Polymerase chain reaction (PCR) was performed using 16S rRNA gene target of mycobacteria and species was ...
Source: Infection, Genetics and Evolution - November 13, 2018 Category: Genetics & Stem Cells Authors: Turankar RP, Singh V, Gupta H, Pathak VK, Ahuja M, Singh I, Lavania M, Dinda A, Sengupta U Tags: Infect Genet Evol Source Type: research

Herpesvirus infection in marine mammals: A retrospective molecular survey of stranded cetaceans in the Portuguese coastline.
In this study we surveyed a total of 179 cetaceans belonging to 6 different species. Samples were obtained from cetaceans stranded along the Portuguese coastline, belonging to populations that roam the north-east region of the Atlantic Ocean. Detection of HVs was performed by conventional nested PCR. Amplicons were sequenced by Sanger's method and sequences used to construct phylogenetic trees by Maximum Likelihood method. Our results show that prevalence of positive samples, among fresh carcasses, reached 14.3% (10/70) and both alpha and gammaherpesvirus were detected. Histopathology showed that herpesvirus infection vari...
Source: Infection, Genetics and Evolution - November 13, 2018 Category: Genetics & Stem Cells Authors: Bento MC, Canha R, Eira C, Vingada J, Nicolau L, Ferreira M, Domingo M, Tavares L, Duarte A Tags: Infect Genet Evol Source Type: research

Multiple clones of metallo- β-lactamase-producing Acinetobacter ursingii in a children hospital from Argentina.
Multiple clones of metallo-β-lactamase-producing Acinetobacter ursingii in a children hospital from Argentina. Infect Genet Evol. 2018 Nov 12;: Authors: Faccone D, Martino F, Pasteran F, Albornoz E, Biondi E, Vazquez M, Rapoport M, Rodrigo V, De Belder D, Gomez S, Corso A Abstract Acinetobacter spp. are opportunistic pathogens being A. baumannii the most frequently identified in nosocomial settings. A. ursingii was mainly described as causing bacteremia and outbreaks in neonatal intensive care units. Ten A. ursingii isolates were recovered from rectal swab screening for carbapenemase-producing ba...
Source: Infection, Genetics and Evolution - November 12, 2018 Category: Genetics & Stem Cells Authors: Faccone D, Martino F, Pasteran F, Albornoz E, Biondi E, Vazquez M, Rapoport M, Rodrigo V, De Belder D, Gomez S, Corso A Tags: Infect Genet Evol Source Type: research

Changing pattern of prevalence and genetic diversity of rotavirus, norovirus, astrovirus, and bocavirus associated with childhood diarrhea in Asian Russia, 2009-2012.
Abstract This hospital-based surveillance study was carried out in Novosibirsk, Asian Russia from September 2009 to December 2012. Stool samples from 5486 children with diarrhea and from 339 healthy controls were screened for rotavirus, norovirus, astrovirus, and bocavirus by RT-PCR. At least one enteric virus was found in 2075 (37.8%) cases with diarrhea and 8 (2.4%) controls. In the diarrhea cases, rotavirus was the most commonly detected virus (24.9%), followed by norovirus (13.4%), astrovirus (2.8%) and bocavirus (1.1%). Mixed viral infections were identified in 4.3% cases. The prevalence of enteric viruses va...
Source: Infection, Genetics and Evolution - November 8, 2018 Category: Genetics & Stem Cells Authors: Zhirakovskaia E, Tikunov A, Tymentsev A, Sokolov S, Sedelnikova D, Tikunova N Tags: Infect Genet Evol Source Type: research

Chlorine dioxide inhibits the replication of porcine reproductive and respiratory syndrome virus by blocking viral attachment.
Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) causes a great economic loss to the swine industry globally. Current prevention and treatment measures are not effective to control the outbreak and spread of porcine reproductive and respiratory syndrome (PRRS). In other words, new antiviral strategies are urgently needed. Chlorine dioxide (ClO2) is regarded as a broad-spectrum disinfectant with strong inhibitory effects on microbes and parasites. The purpose of this study was to evaluate the inhibitory effects and underlying molecular mechanisms of ClO2 against PRRSV infection in vitro. Here, w...
Source: Infection, Genetics and Evolution - November 2, 2018 Category: Genetics & Stem Cells Authors: Zhu Z, Guo Y, Yu P, Wang X, Zhang X, Dong W, Liu X, Guo C Tags: Infect Genet Evol Source Type: research

Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar & Knab 1913, based on mitochondrial and nuclear ribosomal genes.
Intraspecific phylogeny of Anopheles (Kerteszia) neivai Howard, Dyar & Knab 1913, based on mitochondrial and nuclear ribosomal genes. Infect Genet Evol. 2018 Nov 02;: Authors: López-Rubio A, Vasco JDS, Solari S, Gutiérez L, Porter C, Uribe S Abstract Three mitochondrial regions and a fragment of a large nuclear ribosomal subunit was used to study the evolutionary patterns of An. neivai, a mosquito inhabiting the mangrove and tropical forest in the lowland and coastal areas of the Yucatan Peninsula, through the Pacific Ecuadorian coast. This species exhibits epidemiological importance...
Source: Infection, Genetics and Evolution - November 2, 2018 Category: Genetics & Stem Cells Authors: López-Rubio A, Vasco JDS, Solari S, Gutiérez L, Porter C, Uribe S Tags: Infect Genet Evol Source Type: research

Using high-throughput sequencing for investigating intra-host hepatitis C evolution over long retrospective periods.
ois O Abstract Collections of biological samples held by hospitals represent invaluable resources for conducting retrospective evolutionary studies of chronic infections. Using high-throughput sequencing, those collections permit analysis of within-host genetic diversity over long follow-up periods, and allow a better understanding of resistance to treatment regimes during disease evolution. Here, we studied the evolution of hepatitis C virus (HCV) populations in two patients with an absence of response to dual therapies. We implemented amplicon sequencing to survey genomic variation at the Core and NS5B regions o...
Source: Infection, Genetics and Evolution - November 2, 2018 Category: Genetics & Stem Cells Authors: Caporossi A, Kulkarni O, Mgb B, Leroy V, Morand P, Larrat S, François O Tags: Infect Genet Evol Source Type: research

Mutation in cyl operon alters hemolytic phenotypes of Streptococcus agalactiae.
This study compared the phenotypic differences among S. agalactiae hemolytic variant isolates and investigated the genetic composition of their hemolysin genes. Hemolysin is encoded by the cyl operon and mainly regulated by covS/R, which also regulates encapsulation. In total, 45 S. agalactiae clinical isolates were collected from cultured fishes in Taiwan. Three different hemolytic phenotypes-α, β, and γ-were identified. Of the 45 isolates, 39 were β hemolytic, 3 were α hemolytic, and 3 were γ hemolytic. The γ-hemolytic isolates demonstrated significantly thicker encapsulation and s...
Source: Infection, Genetics and Evolution - November 2, 2018 Category: Genetics & Stem Cells Authors: Chou CC, Lin MC, Su FJ, Chen MM Tags: Infect Genet Evol Source Type: research

Molecular dynamics simulation analysis of conessine against multi drug resistant Serratia marcescens.
Abstract Ornithine decarboxylase (ODC) is an immediate precursor of polyamine biosynthesis in Serratia marcescens and a potential target for inhibition of its growth. We predicted the 3D structural conformation of ODC enzyme and validated it using MDS in our previous study. In this current study, the potential inhibitors of ODC were obtained by virtual screening of potential inhibitors from ZINC database and studied in depth for their different binding pose. Among the ten virtually screened inhibitors, Conessine exhibited the best binding with ODC and its inhibition property was studied further by MDS studies. The...
Source: Infection, Genetics and Evolution - November 2, 2018 Category: Genetics & Stem Cells Authors: Dhusia K, Raja K, Thomas PPM, Yadav PK, Ramteke PW Tags: Infect Genet Evol Source Type: research

Molecular epidemiology and characterization of porcine adenoviruses in pigs with diarrhea in Thailand.
In this study, the presence of PAdV was investigated in fecal samples collected from piglets with and without diarrhea from 31 commercial pig farms in northern Thailand. A total of 781 fecal specimens (516 from diarrheic piglets and 265 from non-diarrheic piglets) were screened for adenovirus using nested-PCR. Initial screening both in diarrheic and non-diarrheic piglets showed the overall prevalence of PAdV infection in piglets at 16.9% (132/781). Co-infection with PRVA was found in 24 out of 132 (18.2%) PAdV positive cases whereas PAdV mono-infection was observed at 81.8% (108/132). The prevalence of PAdV infection in di...
Source: Infection, Genetics and Evolution - November 1, 2018 Category: Genetics & Stem Cells Authors: Kumthip K, Khamrin P, Kongkaew A, Vachirachewin R, Malasao R, Ushijima H, Maneekarn N Tags: Infect Genet Evol Source Type: research

Anticipating time-dependent antigenic variants of influenza A (H3N2) viruses.
Abstract Frequent variations in influenza vaccines are necessary to match antigenic variants which appear in influenza epidemics. Antigenic variants of influenza viruses result from frequent mutations in amino acid residues located on their hemagglutinin (HA) proteins. Knowledge of specific changes in these amino acids helps to characterize distinct antigenic variants. In this paper, statistical models are developed and used to investigate changes in amino acids which accompany antigenic variants of epidemiological importance. Amino acid sequences of the HA proteins of influenza A (H3N2) strains isolated from 1968...
Source: Infection, Genetics and Evolution - November 1, 2018 Category: Genetics & Stem Cells Authors: Adabor ES Tags: Infect Genet Evol Source Type: research

Microarray analysis of lncRNA expression in rabies virus infected human neuroblastoma cells.
This study is the first global analysis of lncRNA and mRNA co-expression during RABV infection, provides deeper insight into the mechanism of RABV pathogenesis, and reveals promising candidate for future investigation. PMID: 30391720 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - November 1, 2018 Category: Genetics & Stem Cells Authors: Ji S, Zhu M, Zhang J, Cai Y, Zhai X, Wang D, Li G, Su S, Zhou J Tags: Infect Genet Evol Source Type: research

Characterization of a multidrug resistant Citrobacter amalonaticus clinical isolate harboring blaNDM-1 and mcr-1.5 genes.
rso A Abstract A multidrug resistant isolate, identified as Citrobacter amalonaticus using MALDI-TOF MS and confirmed by genomic analysis, was recovered from a pediatric patient in a hospital from Buenos Aires, Argentina. By whole-genome sequencing a total of 16 resistance genes were detected, including blaNDM-1 and mcr-1.5. To the best of our knowledge this is the first description of these two genes together in a clinical isolate of the Citrobacter genus. PMID: 30389546 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 31, 2018 Category: Genetics & Stem Cells Authors: Faccone D, Albornoz E, Tijet N, Biondi E, Gomez S, Pasterán F, Vazquez M, Melano RG, Corso A Tags: Infect Genet Evol Source Type: research

Human CCR5 Δ32 (rs333) polymorphism has no influence on severity and mortality of influenza A(H1N1)pdm09 infection in Brazilian patients from the post pandemic period.
CONCLUSIONS: The CCR5Δ32 variant does not influence the susceptibility to influenza A(H1N1)pdm09 severe disease or mortality in individuals from Brazil. PMID: 30389547 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 31, 2018 Category: Genetics & Stem Cells Authors: Matos AR, Martins JSCC, Oliveira MLA, Garcia CC, Siqueira MM Tags: Infect Genet Evol Source Type: research

Insights into the population structure and pan-genome of Haemophilus influenzae.
vado MP, Gomes JP Abstract The human-restricted bacterium Haemophilus influenzae is responsible for respiratory infections in both children and adults. While colonization begins in the upper airways, it can spread throughout the respiratory tract potentially leading to invasive infections. Although the spread of H. influenzae serotype b (Hib) has been prevented by vaccination, the emergence of infections by other serotypes as well as by non-typeable isolates (NTHi) have been observed, prompting the need for novel prevention strategies. Here, we aimed to study the population structure of H. influenzae and to get so...
Source: Infection, Genetics and Evolution - October 31, 2018 Category: Genetics & Stem Cells Authors: Pinto M, González-Díaz A, Machado MP, Duarte S, Vieira L, Carriço JA, Marti S, Bajanca-Lavado MP, Gomes JP Tags: Infect Genet Evol Source Type: research

Incidence of antiviral drug resistance markers among human influenza A viruses in the Eastern Mediterranean Region, 2005-2016.
CONCLUSION: Our study reveals the emergence and spread of antiviral drug resistant influenza A viruses in the EMR and emphasizes the importance of continuous surveillance to maintain the effective use of the current antivirals. PMID: 30389548 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 30, 2018 Category: Genetics & Stem Cells Authors: Moasser E, Moasser A, Zaraket H Tags: Infect Genet Evol Source Type: research

Distinct role of outer membrane protein A in the intrinsic resistance of Acinetobacter baumannii and Acinetobacter nosocomialis.
Abstract Acinetobacter baumannii outer membrane protein A (AbOmpA) contributes to the intrinsic resistance of A. baumannii through the OmpA-like domain. The present study investigated the role of Acinetobacter nosocomialis OmpA (AnOmpA) in the intrinsic resistance of A. nosocomialis and compared it with the role of AbOmpA. The minimal inhibitory concentrations (MICs) of antimicrobial agents against wild-type A. nosocomialis ATCC 17903, ∆AnompA mutant, and single-copy AnompA-complemented strains were determined by performing E-test or agar dilution. Single-copy ompA cross-complemented strains were constructed by ...
Source: Infection, Genetics and Evolution - October 29, 2018 Category: Genetics & Stem Cells Authors: Kwon HI, Kim S, Oh MH, Shin M, Lee JC Tags: Infect Genet Evol Source Type: research

Development and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.
Abstract Brucellosis is a zoonotic disease caused by Brucella spp. Brucella spp. can be sub-typed by multilocus sequence typing (MLST) method, which targets a set of housekeeping genes. We have developed a core genome MLST (cgMLST) typing scheme to distinguish and differentiate species of Brucella up to biovar level. A total of 407 whole (complete and draft) genome sequences of different Brucella strains were used in this study. Genome sequences were filtered using the BLAST score ratio (BSR)-based allele calling algorithm, and we found that 164 cgMLST target loci are shared in all the 407 genome sequences. These ...
Source: Infection, Genetics and Evolution - October 29, 2018 Category: Genetics & Stem Cells Authors: Sankarasubramanian J, Vishnu US, Gunasekaran P, Rajendhran J Tags: Infect Genet Evol Source Type: research

DNA compositional dynamics and codon usage patterns of M1 and M2 matrix protein genes in influenza A virus.
This study is carried out to unravel the key features of the genes encoding the matrix proteins that manoeuvre the codon usage profile in the H3N2 strains. The findings reveal differential codon choice for both matrix protein 1 and matrix protein 2. The overall codon usage bias is less pronounced in both the datasets which is evident from higher value of effective number of codons (>55). Comparison of the codon usage for both the genes under study with that of humans revealed that the viral codon usage is not fully optimized for the human host conditions. Both the genes enrolled in the study showed variation which was r...
Source: Infection, Genetics and Evolution - October 24, 2018 Category: Genetics & Stem Cells Authors: Deka H, Nath D, Uddin A, Chakraborty S Tags: Infect Genet Evol Source Type: research

Emergence of dengue virus type 1 and type 3 as dominant serotypes during 2017 in Pune and Nashik regions of Maharashtra, Western India.
Abstract India witnessed dengue outbreaks during 2017 in different parts with more than 180000 cases. There is no data on the serotypes/genotypes of dengue virus (DENV) associated with the 2017 outbreak season. The present study investigated DENV circulating in Pune and Nashik regions of Maharashtra, Western India at molecular level. IgM negative samples that were collected before 6th post onset days of illness were tested for DENV RNA and serotyped by real time RT-PCR based methods. Representative samples of each serotype were processed for virus isolation and envelope (E) gene sequencing. Among the 472 samples t...
Source: Infection, Genetics and Evolution - October 23, 2018 Category: Genetics & Stem Cells Authors: Patil JA, Alagarasu K, Kakade MB, More AM, Gadekar KA, Jadhav SM, Parashar D, Shah PS Tags: Infect Genet Evol Source Type: research

Genome analysis of newly emerging goose-origin nephrotic astrovirus in China reveals it belongs to a novel genetically distinct astrovirus.
Abstract Since 2017, a new type of goose-origin astrovirus (GoAstV) disease occurred in China. This disease can cause joint swelling of sick geese, and the anatomy shows a clear urate precipitation in the viscera. The rate of death or amputation can reach more than 30%, revealing its severe pathogenicity. One novel goose-origin astrovirus strain, designated as CXZ18, was isolated from diseased geese with a fatal infection characterized by visceral urate deposition. Similar clinical anatomy symptoms were partially reproduced by attacking infection of healthy geese. The CXZ18 has no hemagglutination with chicken ery...
Source: Infection, Genetics and Evolution - October 23, 2018 Category: Genetics & Stem Cells Authors: Yuan X, Meng K, Zhang Y, Yu Z, Ai W, Wang Y Tags: Infect Genet Evol Source Type: research

Molecular characterization of enterovirus 71 sibling strains for thermal adaption in Vero cells with adaptive laboratory evolution.
In this study, we investigated the variations of enterovirus 71 in thermal adaption, using the method of adaptive laboratory evolution. The sibling virus strains were isolated from a 2-year-old severe case of HFMD (#100) and her symptomless close contact (#101). Both strains were cultured in Vero cells by serial passage of 36 generations at the temperatures of 28.0 °C, 33.0 °C and 39.5 °C to construct adaptive lineages. According to the comparative analysis of phenotypes between adapted strains and parental strains, differences in growth rate were observed in the sibling lineages and a larger plaque was f...
Source: Infection, Genetics and Evolution - October 19, 2018 Category: Genetics & Stem Cells Authors: Chen H, Cheng Y, Liang X, Meng JT, Zuo HJ, Su LY, Wang XX, Yang CB, Luan RS Tags: Infect Genet Evol Source Type: research

Hybrids and hybridization in the Cryptococcus neoformans and Cryptococcus gattii species complexes.
Abstract The basidiomycetous yeasts of the Cryptococcus neoformans and Cryptococcus gattii species complexes (CNSC and CGSC respectively) are the causative agents of cryptococcosis, a set of life-threatening diseases affecting the central nervous system, lungs, skin, and other body sites of humans and other mammals. Both the CNSC and CGSC can be subdivided into varieties, serotypes, molecular types, and lineages based on structural variations, molecular characteristics and genetic sequences. Hybridization between the haploid lineages within and between the two species complexes is known to occur in natural and cli...
Source: Infection, Genetics and Evolution - October 17, 2018 Category: Genetics & Stem Cells Authors: Samarasinghe H, Xu J Tags: Infect Genet Evol Source Type: research

Highly pathogenic avian influenza H5N8 Clade 2.3.4.4B virus in Uganda, 2017.
Abstract In early January 2017, outbreaks of H5N8 highly pathogenic avian influenza (HPAI) were reported for the first time in wild and domestic birds along the shores and on some islands of Lake Victoria, in central-southern Uganda. Our whole-genome phylogenetic analyses revealed that the H5N8 viruses recovered from the outbreak in Uganda belonged to genetic clade 2.3.4.4 group-B and clustered with viruses collected in 2017 in the Democratic Republic of the Congo and in West Africa. Our results suggested that infected migratory wild birds might have played a crucial role in the introduction of HPAI H5N8 into this...
Source: Infection, Genetics and Evolution - October 17, 2018 Category: Genetics & Stem Cells Authors: Ndumu D, Zecchin B, Fusaro A, Arinaitwe E, Erechu R, Kidega E, Kayiwa J, Muwanga E, Kirumira M, Kirembe G, Lutwama J, Monne I Tags: Infect Genet Evol Source Type: research

Genetic characterization of Plasmodium vivax in the Kyrgyz Republic.
Abstract At the end of 2016, Kyrgyz Republic was certified by the World Health Organization as a malaria-free country, while only a decade ago this disease posed a serious health threat.. The progress achieved by Kyrgyz Republic provides a unique example of tertian (Plasmodium vivax) malaria elimination. This success was based on an integrated approach, including measures for the treatment of infected people and disease prevention, vector control and the development of an effective national epidemiological surveillance system. Lower P. vivax msp-1, msp-3α, csp and dbpII genes polymorphism was revealed in Kyr...
Source: Infection, Genetics and Evolution - October 16, 2018 Category: Genetics & Stem Cells Authors: Goryacheva II, Baranova AM, Lukashev AN, Gordeev MI, Usenbaev NT, Schaikevich EV Tags: Infect Genet Evol Source Type: research

Genetic variants upstream of TNFAIP3 in the 6q23 region are associated with liver disease severity in HIV/HCV-coinfected patients: A cross-sectional study.
CONCLUSIONS: Genetic variants upstream of TNFAIP3 were associated with the liver fibrosis severity and inflammation in HIV/HCV-coinfected patients. PMID: 30336268 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 15, 2018 Category: Genetics & Stem Cells Authors: Jiménez-Sousa MA, Berenguer J, Rodríguez AF, Medrano LM, Aldámiz-Echevarria T, Pérez-Latorre L, Díez C, Martín-Vicente M, Gutiérrez-Rivas M, Martínez I, Resino S Tags: Infect Genet Evol Source Type: research

Improving diagnosis and case management of patients with tuberculosis: A review of gaps, needs and potential solutions in accessing laboratory diagnostics.
Abstract Tuberculosis (TB) recently surpassed HIV/AIDS as the deadliest infectious disease. Despite some advancements in technologies and programs, TB remains a global health epidemic that, without significant gains in better diagnostic and management, will not abate. This review describes the molecular diagnostic gaps, needs, and potential solutions for improving access to diagnosis and management of patients with drug susceptible and drug resistant TB. The ultimate goal is to improve laboratory diagnostics and better individualized managementof detected TB, and make an important contribution toward eliminating t...
Source: Infection, Genetics and Evolution - October 13, 2018 Category: Genetics & Stem Cells Authors: Andama A, Somoskovi A, Mandel B, Bell D, Gutierrez C Tags: Infect Genet Evol Source Type: research

Molecular epidemiology and evolution of drug-resistant genes in the malaria parasite Plasmodium falciparum in southwestern Nigeria.
Abstract Malaria is an age-old disease of human kind living in the tropical and sub-tropical regions of the globe, with Africa contributing the highest incidence of morbidity and mortality. Among many hurdles, evolution and spread of drug-resistant Plasmodium falciparum parasites constitute major challenges to malaria control and elimination. Information on molecular epidemiology and pattern of evolution of genes conferring resistance to different antimalarials are needed to track the route of the spread of resistant parasites and also to inform if the drug-resistant genes are adapted in the population following t...
Source: Infection, Genetics and Evolution - October 11, 2018 Category: Genetics & Stem Cells Authors: Oboh MA, Singh US, Antony HA, Ndiaye DA, Badiane AS, Ali NA, Bharti PK, Das A Tags: Infect Genet Evol Source Type: research

The association between BACH1 polymorphisms and anti-tuberculosis drug-induced hepatotoxicity in a Chinese cohort.
CONCLUSIONS: This is the first study to explore the relationship between tagSNPs of BACH1 and ATDH in a Chinese cohort. Based on this cohort, genetic polymorphisms of BACH1 may be associated with susceptibility to ATDH in the Chinese population. PMID: 30316884 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 11, 2018 Category: Genetics & Stem Cells Authors: Zhang H, Qian H, Tao B, Yang M, Gong J, Yi H, Tang S Tags: Infect Genet Evol Source Type: research

Metagenomic identification and sequence analysis of a Teschovirus A-related virus in porcine feces in Japan, 2014-2016.
Abstract Porcine Teschoviruses (PTVs) are associated with polioencephalomyelitis and various diseases, including reproductive and gastrointestinal disorders, of pigs and wild boars, and are also detected in the feces of healthy pigs. The genus Teschovirus contains a single species Teschovirus A that currently includes 13 serotypes. In the present study, we identified novel PTVs that are distantly related to Teschovirus A and were found in fecal samples of pigs with or without diarrhea in Japan. Phylogenetic analysis of amino acid (aa) sequences of the complete coding region revealed that these newly identified vir...
Source: Infection, Genetics and Evolution - October 11, 2018 Category: Genetics & Stem Cells Authors: Oba M, Naoi Y, Ito M, Masuda T, Katayama Y, Sakaguchi S, Omatsu T, Furuya T, Yamasato H, Sunaga F, Makino S, Mizutani T, Nagai M Tags: Infect Genet Evol Source Type: research

Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases.
Abstract Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM di...
Source: Infection, Genetics and Evolution - October 10, 2018 Category: Genetics & Stem Cells Authors: Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ Tags: Infect Genet Evol Source Type: research

Identification of sparganosis based on next-generation sequencing.
We present, for the first time, a study of human sparganosis diagnosed using NGS, which provided a clinically actionable diagnosis of a specific infectious disease from an uncommon pathogen. PMID: 30315893 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 10, 2018 Category: Genetics & Stem Cells Authors: Du B, Tao Y, Ma J, Weng X, Gong Y, Lin Y, Shen N, Mo X, Cao Q Tags: Infect Genet Evol Source Type: research

New human isolates of Trypanosoma cruzi confirm the predominance of hybrid lineages in domestic transmission cycle of the Argentinean Chaco.
MV Abstract Trypanosoma cruzi, the etiological agent of Chagas disease, was initially classified into 6 Discrete Typing Units (DTUs). The hybrid DTUs TcV and TcVI are the most frequent in domestic transmission cycles throughout the Southern Cone countries of South America. Here, we genotyped parasite isolates from human residents in Pampa del Indio municipality, Chaco, to further characterize the structure of T. cruzi populations, and to assess the degree of overlapping between the domestic and sylvatic transmission cycles. Artificial xenodiagnostic tests were performed to blood samples from 125 T. cruzi-seropo...
Source: Infection, Genetics and Evolution - October 5, 2018 Category: Genetics & Stem Cells Authors: Macchiaverna NP, Enriquez GF, Buscaglia CA, Balouz V, Gürtler RE, Cardinal MV Tags: Infect Genet Evol Source Type: research

Diversity of aminoglycoside modifying enzymes and 16S rRNA methylases in Acinetobacter baumannii and Acinetobacter nosocomialis species in Iran; wide distribution of aadA1 and armA.
CONCLUSION: The overall high-level carriage of ARGs in Acinetobacter species may limited usage of this class of antibacterials as a treatment option. PMID: 30292703 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - October 4, 2018 Category: Genetics & Stem Cells Authors: Salimizand H, Zomorodi AR, Mansury D, Khakshoor M, Azizi O, Khodaparast S, Baseri Z, Karami P, Zamanlou S, Farsiani H, Amini Y, Moradi B, Meshkat Z, Salimizand H, Sadeghian H Tags: Infect Genet Evol Source Type: research

Virus detection in high-throughput sequencing data without a reference genome of the host.
We present a new modular, computational pipeline for discovery of novel viruses in host samples. While existing pipelines rely on the availability of the hosts reference genome for filtering sequence reads, our new pipeline can also cope with cases for which no reference genome is available. As a further novelty of our method a decoy module is used to assess false classification rates in the discovery process. Additionally, viruses with a low read coverage can be identified and visually reviewed. We validate our pipeline on simulated data as well as two experimental samples with known virus content. For the experimental sa...
Source: Infection, Genetics and Evolution - October 3, 2018 Category: Genetics & Stem Cells Authors: Kruppa J, Jo WK, van der Vries E, Ludlow M, Osterhaus A, Baumgaertner W, Jung K Tags: Infect Genet Evol Source Type: research

Mutations of Mycobacterium tuberculosis induced by anti-tuberculosis treatment result in metabolism changes and elevation of ethambutol resistance.
Abstract Selective pressure from antibiotic use is one of the most important risk factors associated with the development of drug resistance in Mycobacterium tuberculosis (MTB). However, the mechanisms underlying drug resistance at the molecular level remain partly unclear. Therefore, the purpose of this study was to investigate the potential functional effect of novel mutations arising from anti-tuberculosis treatment. We analyzed two multidrug-resistant TB (MDR-TB) isolates from the same patient; one collected before and one almost a year after commencing MDR-TB treatment. The post-treatment isolate exhibited el...
Source: Infection, Genetics and Evolution - October 3, 2018 Category: Genetics & Stem Cells Authors: Sun L, Zhang L, Wang T, Jiao W, Li Q, Yin Q, Li J, Qi H, Xu F, Shen C, Xiao J, Liu S, Mokrousov I, Huang H, Shen A Tags: Infect Genet Evol Source Type: research

Microsatellite-based genetic diversity of Dermacentor reticulatus in Europe.
Abstract Dermacentor reticulatus, also known as ornate dog tick, is an important vector of the causative agents of various tick-borne diseases in humans, livestock and wild animals. The geographical range of D. reticulatus in Europe is fragmented and divided into two main zones: The Western European and the Eastern European zone. To investigate D. reticulatus population structure through its distribution range we used microsatellite markers and compared the genetic diversity of D. reticulatus in 26 selected sites in the western and eastern European distribution areas. A total of 254 unfed adult D. reticulatus tick...
Source: Infection, Genetics and Evolution - October 2, 2018 Category: Genetics & Stem Cells Authors: Paulauskas A, Galdikas M, Galdikaitė-Brazienė E, Stanko M, Kahl O, Karbowiak G, Radzijevskaja J Tags: Infect Genet Evol Source Type: research

Tigecycline resistance caused by rpsJ evolution in a 59-year-old male patient infected with KPC-producing Klebsiella pneumoniae during tigecycline treatment.
In this study, curative effect of tigecycline therapy was monitored in a 59-year-old male patient infected with KPC-producing K. pneumoniae. Consecutive clonal consistent K. pneumoniae isolates were cultured during tigecycline treatment. Whole genome sequencing of the isolates was performed, and bioinformatics analysis was further performed. Five isolates, four of which were susceptible and one resistant were collected. All of the isolates belong to Sequence Type 11 (ST11), and harbouring 11 gene sequences relevant to antibiotic resistance including blaKPC-2. One amino acid substitution V57L in rpsJ was identified in the t...
Source: Infection, Genetics and Evolution - September 27, 2018 Category: Genetics & Stem Cells Authors: He F, Shi Q, Fu Y, Xu J, Yu Y, Du X Tags: Infect Genet Evol Source Type: research

Evolutionary analysis of six isolates of porcine reproductive and respiratory syndrome virus from a single pig farm: MLV-evolved and recombinant viruses.
This study stresses the necessity for pig producers to restrain the use of HP-PRRSV MLV vaccines in the field. PMID: 30261264 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 24, 2018 Category: Genetics & Stem Cells Authors: Zhang Z, Zhou L, Ge X, Guo X, Han J, Yang H Tags: Infect Genet Evol Source Type: research

Longitudinal genotyping surveillance of Mycobacterium tuberculosis in an area with high tuberculosis incidence shows high transmission rate of the modern Beijing subfamily in Japan.
This study used a molecular epidemiological approach to investigate the transmissibility of the modern Beijing subfamily in the Airin area of Osaka City, Japan. During 2006-2016, we collected 596 M. tuberculosis clinical isolates in the Airin area, Osaka city, Japan. We analyzed the 24-locus variable number of tandem repeats typing optimized for the Beijing family of isolates, M. tuberculosis lineage, and patient epidemiological data. The proportion of the modern Beijing subfamily was significantly higher not only than previously obtained data for the Airin area: it was also higher than the nationwide in Japan. The rate ...
Source: Infection, Genetics and Evolution - September 24, 2018 Category: Genetics & Stem Cells Authors: Yamamoto K, Takeuchi S, Seto J, Shimouchi A, Komukai J, Hase A, Nakamura H, Umeda K, Hirai Y, Matsumoto K, Ogasawara J, Wada T, Yamamoto T Tags: Infect Genet Evol Source Type: research

Genetics and roadblocks of drug resistant tuberculosis.
This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms tha...
Source: Infection, Genetics and Evolution - September 24, 2018 Category: Genetics & Stem Cells Authors: Perdigão J, Portugal I Tags: Infect Genet Evol Source Type: research