Bartonella diversity and zoonotic potential in indigenous Tete Veld rats (Aethomys ineptus) from South Africa.
Abstract Bartonellosis is a vector-borne disease that is often misdiagnosed due to a broad range of clinical symptoms, compounded by a lack of awareness regarding the prevalence, diversity and public health impacts of regional strains. Despite recent PCR-based confirmation of Bartonella in 9.7% of non-malarial, acute febrile patients in South Africa, data regarding reservoirs of infection are limited. As the majority of Bartonella species described to date are associated with rodent species globally, including zoonotic species such as B. elizabethae, and as rodent biodiversity is high in southern Africa, we evalua...
Source: Infection, Genetics and Evolution - April 17, 2019 Category: Genetics & Stem Cells Authors: Hatyoka LM, Brettschneider H, Bennett NC, Kleynhans DJ, Muteka SP, Bastos ADS Tags: Infect Genet Evol Source Type: research

Microsatellite markers reveal two genetic groups in European populations of the carrot cyst nematode Heterodera carotae.
Abstract The cyst nematode Heterodera carotae, which parasitizes carrot roots, has been recorded in many countries in Europe (Italy, The Netherlands, Switzerland, France, Denmark, …), in South Africa and in North America (Canada, USA). To date, there is a lack of knowledge about the genetic structure of the populations of this economically important nematode. The aim of this work was to study the structuration of the genetic diversity of the carrot cyst nematode at the European scale. We have developed a set of thirteen polymorphic microsatellite markers and used it to genotype seventeen European population...
Source: Infection, Genetics and Evolution - April 16, 2019 Category: Genetics & Stem Cells Authors: Camille G, Magali E, Sylvain F, Christophe P, Jean-Claude Y, Eric NO, Eric G, Josselin M Tags: Infect Genet Evol Source Type: research

Genetic diversity of zoonotic malaria parasites from mosquito vector and vertebrate hosts.
This study provides a preliminary snapshot of the structure of these populations, that was insufficient to answer our aim. Thus, collection of parasites from their various hosts and over time, associated with a systematic analysis of a set of genetical loci is strongly advocated in order to obtain a clear picture of the parasite population and the flow between different hosts. This is important to devise measures that will minimise the risk of transmission to humans, because zoonotic malaria impedes malaria elimination. PMID: 30999059 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 15, 2019 Category: Genetics & Stem Cells Authors: Wong ML, Ahmed MA, Sulaiman WYW, Manin BO, Leong CS, Quan FS, Chua TH, Drakeley C, Snounou G, Vythilingam I Tags: Infect Genet Evol Source Type: research

Human papillomavirus type 16 E6 and E7 gene variations associated with cervical cancer in a Han Chinese population.
CONCLUSION: Our study will provide a good reference for further functional studies of the relationship between cervical cancer carcinogenesis and the HPV16 E6 and E7 genes. PMID: 30981880 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - April 11, 2019 Category: Genetics & Stem Cells Authors: Zhou Z, Yang H, Yang L, Yao Y, Dai S, Shi L, Li C, Yang L, Yan Z, Yao Y Tags: Infect Genet Evol Source Type: research

Carrying a 112  bp-segment in Helicobacter pylori dupA may associate with increased risk of duodenal ulcer.
Carrying a 112 bp-segment in Helicobacter pylori dupA may associate with increased risk of duodenal ulcer. Infect Genet Evol. 2019 Apr 11;: Authors: Fatahi G, Abadi ATB, Peerayeh SN, Forootan M Abstract The discovery of Helicobacter pylori in 1983 challenged researchers around the world to identify this pathogen's major virulence factors. The main rationale for this kind of research was to identify a biomarker associated with specific diseases following H. pylori colonization. Among different investigated virulence factors, duodenal ulcer promoting gene A (dupA) has been found to be associated with ...
Source: Infection, Genetics and Evolution - April 11, 2019 Category: Genetics & Stem Cells Authors: Fatahi G, Abadi ATB, Peerayeh SN, Forootan M Tags: Infect Genet Evol Source Type: research

Whole genome characterization of feline-like G3P[8] reassortant rotavirus A strains bearing the DS-1-like backbone genes detected in Vietnam, 2016.
Abstract While conducting rotavirus gastroenteritis surveillance in Vietnam, two G3P[8] rotavirus A specimens possessing an identical short RNA electropherotype were detected. They were RVA/Human-wt/VNM/0232/2016/G3P[8] and RVA/Human-wt/VNM/0248/2016/G3P[8], and recovered from 9 and 23 months old boys, respectively. The patients developed diarrhoea within one-week interval in March 2016 but in places>100 km apart in northern Vietnam. Whole genome sequencing of the two G3P[8] rotavirus A strains revealed that their genomic RNA sequences were identical across the 11 genome segments, suggesting that they deriv...
Source: Infection, Genetics and Evolution - April 9, 2019 Category: Genetics & Stem Cells Authors: Hoa-Tran TN, Nakagomi T, Vu HM, Kataoka C, Nguyen TTT, Dao ATH, Nguyen AT, Takemura T, Hasebe F, Dang AD, Nakagomi O Tags: Infect Genet Evol Source Type: research

A first insight into the application of high discriminatory MIRU-VNTR typing using QIAxcel technology for genotyping Mycobacterium bovis isolated from the Delta area in Egypt.
This study aimed to evaluate the discrimination ability of 15 mycobacterial interspersed repetitive unit-variable number tandem repeats (MIRU-VNTR) loci and to assess the extremely efficient loci subset for molecular epidemiological investigations of M.bovis from farms in the Delta area of Egypt. The discriminating ability of MIRU-VNTR genotyping using 15 loci {2 exact tandem repeat (ETR) loci, 6 MIRU loci, 4 Mtub loci, and 3 Queen's University of Belfast (QUB) group loci)} were evaluated on 61 M.bovis isolates from cattle (Holstein Frisian) and buffaloes. The results indicate that there are 48 genotypes: 3 unique genoty...
Source: Infection, Genetics and Evolution - April 8, 2019 Category: Genetics & Stem Cells Authors: Elsayed MSAE Tags: Infect Genet Evol Source Type: research

Time-scaled phylogeography of complete Zika virus genomes using discrete and continuous space diffusion models.
Abstract Zika virus (ZIKV), a vector-borne infectious agent that has recently been associated with neurological diseases and congenital microcephaly, was first reported in the Western hemisphere in early 2015. A number of authors have reconstructed its epidemiological history using advanced phylogenetic approaches, and the majority of Zika phylogeography studies have used discrete diffusion models. Continuous space diffusion models make it possible to infer the possible origin of the virus in real space by reconstructing its ancestral location on the basis of geographical coordinates deduced from the latitude and ...
Source: Infection, Genetics and Evolution - April 8, 2019 Category: Genetics & Stem Cells Authors: Ebranati E, Veo C, Carta V, Percivalle E, Rovida F, Frati ER, Amendola A, Ciccozzi M, Tanzi E, Galli M, Baldanti F, Zehender G Tags: Infect Genet Evol Source Type: research

Chronology of emergence of the genus Leptospira and over-representation of gene families enriched by vitamin B2, B12 biosynthesis, cell adhesion and external encapsulating structure in L. interrogans isolates from asymptomatic dogs.
In this study, we performed chronology analysis to look for insight into the emergence of Leptospira species, focusing on L. interrogans, and investigated gene gain and loss related to their adaptation in strains isolated from asymptomatic dogs. Chronology analysis revealed that the emergence of L. interrogans was around 53.7 million years ago (MYA), corresponding to the Paleogene period that coincided with an optimal climatic temperature and the evolution of suitable mammalian hosts. Gene families encoding for vitamin B2, B12 biosynthesis, cell adhesion and external encapsulating structure were found to be enriched in L. ...
Source: Infection, Genetics and Evolution - April 8, 2019 Category: Genetics & Stem Cells Authors: Kurilung A, Keeratipusana C, Horiike T, Suriyaphol P, Hampson DJ, Prapasarakul N Tags: Infect Genet Evol Source Type: research

Genetically highly divergent RNA virus with astrovirus-like (5'-end) and hepevirus-like (3'-end) genome organization in carnivorous birds, European roller (Coracias garrulus).
In this study, a novel astrovirus/hepevirus-like virus with +ssRNA genome (Er/SZAL5/HUN/2011, MK450332) was serendipitously identified and characterized from 3 (8.5%) out of 35 European roller (Coracias garrulus) faecal samples by RT-PCR in Hungary. The complete genome of Er/SZAL5/HUN/2011 (MK450332) is 8402 nt-long and potentially composed three non-overlapping open reading frames (ORFs): ORF1a (4449 nt/1482aa), ORF1b (1206 nt/401aa) and ORF2 (1491 nt/496aa). The ORF1ab has an astrovirus-like genome organization containing the non-structural conserved elements (TM, CC, NLS, VPg) and enzyme residues (trypsine-like ...
Source: Infection, Genetics and Evolution - April 5, 2019 Category: Genetics & Stem Cells Authors: Pankovics P, Boros Á, Kiss T, Engelmann P, Reuter G Tags: Infect Genet Evol Source Type: research

Survivorship of wild caught Mepraia spinolai nymphs: The effect of seasonality and Trypanosoma cruzi infection after feeding and fasting in the laboratory.
C, Solari A Abstract Chagas disease is caused by Trypanosoma cruzi. Vector survival is an important variable affecting vectorial capacity to determine parasite transmission risk. The aims of this study are to evaluate vector survival under fasting/starvation conditions of wild-caught Mepraia spinolai after feeding and fasting, the pathogenicity of T. cruzi infection, the parasite burden and seasonal variation in parasite discrete typing units (DTU). The survivorship of M. spinolai nymphs after two continuous artificial feedings was evaluated, assessing their infection with microscopic observation of fecal samples ...
Source: Infection, Genetics and Evolution - April 3, 2019 Category: Genetics & Stem Cells Authors: Cabe AM, Yañez F, Pinto R, López A, Ortiz S, Martin CM, Botto-Mahan C, Solari A Tags: Infect Genet Evol Source Type: research

Analysis of Apical Membrane Antigen (AMA)-1 characteristics using bioinformatics tools in order to vaccine design against Plasmodium vivax.
Abstract Plasmodium vivax, an intracellular protozoan, causes malaria which is characterized by fever, anemia, respiratory distress, liver and spleen enlargement. In spite of attempts to design an efficient vaccine, there is not a vaccine against P. vivax. Notable advances have recently achieved in the development of malaria vaccines targeting the surface antigens such as Apical Membrane Antigens (AMA)-1. AMA-1 is a micronemal protein synthesized during the erythrocyte-stage of Plasmodium species and plays a significant role in the invasion process of the parasite into host cells. P. vivax AMA-1 (PvAMA-1) can ...
Source: Infection, Genetics and Evolution - April 3, 2019 Category: Genetics & Stem Cells Authors: Jahangiri F, Jalallou N, Ebrahimi M Tags: Infect Genet Evol Source Type: research

Potential immune escape mutations under inferred selection pressure in HIV-1 strains circulating in Medell ín, Colombia.
Potential immune escape mutations under inferred selection pressure in HIV-1 strains circulating in Medellín, Colombia. Infect Genet Evol. 2019 Apr;69:267-278 Authors: Arcia D, Ochoa R, Hernández JC, Álvarez CM, Díaz FJ, Velilla PA, Acevedo-Sáenz L Abstract The introduction of highly active antiretroviral therapy (HAART) has significantly improved life expectancy of HIV-infected patients; nevertheless, it does not eliminate the virus from hosts, so a cure for this infection is crucial. Some strategies have employed the induction of anti-HIV CD8+ T cells. However, the...
Source: Infection, Genetics and Evolution - March 1, 2019 Category: Genetics & Stem Cells Authors: Arcia D, Ochoa R, Hernández JC, Álvarez CM, Díaz FJ, Velilla PA, Acevedo-Sáenz L Tags: Infect Genet Evol Source Type: research

KlcAHS genes are ubiquitous in clinical, blaKPC-2-positive, Klebsiella pneumoniae isolates.
Abstract Carbapenemase-producing Klebsiella pneumoniae has emerged and spread widely throughout the world. The mechanisms involved remain unclear. To provide insight, five plasmids were obtained from carbapenemase-producing K. pneumoniae clinical isolates. The five sequences were acquired, aligned and analyzed. In addition to the blaKPC-2 gene, which encodes beta lactamase, essentially all the plasmids contained a putative anti-restriction protein-encoding gene, KlcAHS. The KlcAHS gene was found in 98.2% of the blaKPC-2-positive, imipenem-resistant K. pneumoniae clinical isolates and in
Source: Infection, Genetics and Evolution - February 23, 2019 Category: Genetics & Stem Cells Authors: Liang W, Tang Y, Li G, Shen P, Tian Y, Jiang H, Jiang X, Lu Y Tags: Infect Genet Evol Source Type: research

Identification of a novel cluster of PCV2 isolates from Meghalaya, India indicates possible recombination along with changes in capsid protein.
Abstract Documentation of the emergence of Porcine circovirus 2 (PCV2) infection and economic losses incurred due to high mortality has been reported worldwide. The prevalence and genetic diversity of the virus has been reported in Northeast India including the possible chances of Classical swine fever virus (CSFV) vaccine failure in pig population in this region resulting in major disease outbreak. Irrespective of the genetic variability, the emergence of a novel cluster (based on the ORF2 phylogeny) was reported last year. The present study describes a state-wide (Meghalaya, India) molecular epidemiological inve...
Source: Infection, Genetics and Evolution - February 23, 2019 Category: Genetics & Stem Cells Authors: Mukherjee P, Karam A, Chakraborty AK, Baruah S, Pegu R, Das S, Milton AAP, Puro K, Sanjukta R, Ghatak S, Shakuntala I, Laha RG, Sen A Tags: Infect Genet Evol Source Type: research

Inconsistent temporal patterns of genetic variation of HCV among high-risk subjects may impact inference of transmission networks.
Abstract Hepatitis-C Virus (HCV) sequences are often used to establish networks of people who inject drugs (PWID). However, the degree to which within-host evolutionary dynamics affect those inferences has not been carefully studied. Here, we analyzed 702 longitudinally-sampled HCV E1 sequences from 88 HCV+ people who inject drugs (PWID) in the Baltimore Before and After Acute Study of Hepatitis (BBAASH) cohort. Individuals were tested for HCV RNA over multiple visits to the clinic, and the HCV E1 gene was sequenced for HCV+ samples. Genetic clustering was performed on the full set of sequences using a 3% genetic ...
Source: Infection, Genetics and Evolution - February 22, 2019 Category: Genetics & Stem Cells Authors: Rose R, Rodriguez C, Dollar JJ, Lamers SL, Massaccesi G, Osburn W, Ray SC, Thomas DL, Cox AL, Laeyendecker O Tags: Infect Genet Evol Source Type: research

Molecular identification of Puumala orthohantavirus in Bulgaria.
Abstract In Bulgaria, only Dobrava orthohantavirus has been detected in patients and in rodents. In order to elucidate possible Puumala orthohantavirus (PUUV) circulation, 131 bank voles (Myodes glareolus) were captured. PUUV RNA was detected in 14 (10.7%). Partial L segment sequences were recovered from six M. glareolus. Phylogenetic analysis showed that all PUUV sequences from this study clustered together among the Alpe-Adrian lineage. It is the first genetic evidence of the virus circulation in a Balkan country outside north-western Balkans. The findings in this study extended the known edge of virus distribut...
Source: Infection, Genetics and Evolution - February 21, 2019 Category: Genetics & Stem Cells Authors: Christova I, Trifonova I, Panayotova E, Dimitrov H, Gladnishka T Tags: Infect Genet Evol Source Type: research

Prevalence and mulilocus genotypes of Giardia duodenalis infecting pigs in Ogun state, Nigeria.
Abstract Giardia duodenalis is an intestinal flagellated protozoan parasite that is infectious to humans and a wide range of animals worldwide. While varying prevalence rates have been reported in pigs worldwide, there are currently no published reports on the genotypes of Giardia infecting pigs in any African country. The present study is on the prevalence and genotypes of G. duodenalis in 209 pigs raised on four farms in Ogun State Nigeria. Using an enzyme-linked immunosorbent assay (ELISA) kit, Giardia duodenalis coproantigens were detected on all farms and in 25.4% (53/209) of pigs sampled. However, there was ...
Source: Infection, Genetics and Evolution - February 21, 2019 Category: Genetics & Stem Cells Authors: Akinkuotu OA, Takeet MI, Otesile EB, Olufemi F, Greenwood SJ, McClure JT Tags: Infect Genet Evol Source Type: research

Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus).
Abstract Increasing reports of antimicrobial resistance in wildlife highlight the significance of a One Health approach to managing resistance. We investigated the prevalence and diversity of class 1 integrons, a genetic determinant of resistance, in grey-headed flying foxes, a large fruit bat species belonging to the order Chiroptera. Class 1 integrons were detected in both wild flying foxes (5.3%) and captive flying foxes (41.2%) housed in wildlife rehabilitation facilities. Genes encoding resistance to aminoglycosides, trimethoprim and beta-lactams, and Qac efflux pumps were detected. Analysis of conserved inte...
Source: Infection, Genetics and Evolution - February 21, 2019 Category: Genetics & Stem Cells Authors: McDougall F, Boardman W, Gillings M, Power M Tags: Infect Genet Evol Source Type: research

Co-circulation of dengue virus serotypes in Central India: Evidence of prolonged viremia in DENV-2.
Abstract In view of paucity of information on serotype distribution of Dengue virus (DENV) in Central India, we undertook a cross-sectional study to identify clinical and virological characteristics of DENV serotypes that circulated in this region during the 2016 outbreak. Suspected cases were screened by ELISA for NS1 antigen and anti-DENV IgM antibodies. Serologically confirmed cases were subjected to RT-PCR based detection and serotyping. The RT-PCR results were confirmed by nucleotide sequencing. Genome-wide association was undertaken with DENV sequences from ViPR database and the immune evasion potential of i...
Source: Infection, Genetics and Evolution - February 21, 2019 Category: Genetics & Stem Cells Authors: Agarwal A, Gupta S, Chincholkar T, Singh V, Umare IK, Ansari K, Paliya S, Yadav AK, Chowdhary R, Purwar S, Biswas D Tags: Infect Genet Evol Source Type: research

Genome analysis of a G9P[23] group A rotavirus isolated from a dog with diarrhea in China.
In this study, an RVA strain designated RVA/Dog-tc/CHN/SCCD-A/2017/G9P[23] was isolated in cell culture from a pet dog stool sample with acute diarrhea, and its whole genome was sequenced. The genotype constellation of SCCD-A was G9-P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. All genome segments except the VP1 gene were closely related to the genes from porcine RVA strains or porcine-like human RVA strains. On the other hand, the VP1 gene clustered in a distinct lineage only with that of a G5P[6] porcine-like human RVA, preventing the identification of the exact host species origin, but very unlikely to be originated from human RVA....
Source: Infection, Genetics and Evolution - February 20, 2019 Category: Genetics & Stem Cells Authors: Yan N, Tang C, Kan R, Feng F, Yue H Tags: Infect Genet Evol Source Type: research

Geometric morphometrics in the cloud.
Abstract XYOM, for XY Online Morphometrics, is an online implementation of the geometric morphometric (GM) approach. It is a platform-independent product, and is presented here as an optional alternative software to client side morphometrics software. From the point of view of the user, the interesting features of a web application are: no download, no installation, no configuration, and automatic updating. Because XYOM is accessible through a standard web interface, it is expected to allow an easier and faster learning process. Additional benefits are that users will have their own highly secured cloud storage, w...
Source: Infection, Genetics and Evolution - February 19, 2019 Category: Genetics & Stem Cells Authors: Dujardin S, Dujardin JP Tags: Infect Genet Evol Source Type: research

Clinical and genetic characteristics of unusual G12P [11] rotavirus strains recovered from neonates: A study from Pune, Western India.
Abstract Rotavirus infections in neonates are generally nosocomial, and differ from pediatric infections both clinically and epidemiologically. These infections are predominantly asymptomatic and often associated with unusual strains. Globally, so far limited data is available on rotavirus infections in neonates admitted at Neonatal Intensive Care Unit. The aim of the present study is to determine the prevalence of rotavirus among neonates and to study their genetic characteristics. Stool specimens (n = 701) collected from neonates (n = 621) admitted during April 2016 to March 2018 mainly for prematurity, ...
Source: Infection, Genetics and Evolution - February 19, 2019 Category: Genetics & Stem Cells Authors: Ranshing SS, Bavdekar AR, Vaidya UV, Behera MK, Walimbe AM, Gopalkrishna V Tags: Infect Genet Evol Source Type: research

The effect of released new synthetic peptide from nanofibrous scaffold of peptide/Poly (Vinyl Alcohol)/Poly l-Lactic Acid on expression of Secretory aspartyl proteinases 4 to 6 genes of Candida albicans.
In this study we have established the nanofibrous scaffold of new synthetic peptide/Poly (Vinyl Alcohol)/Poly l-Lactic Acid on expression of Secretory aspartyl proteinases 4 to 6 genes of C. albicans in comparison with free peptide. We designed new synthetic Antimicrobial peptide (AMPs) used bioinformatics tools to predict structure and stabilities. The electrospinning method was used to produce the polymeric nanofibers. Scanning Electron Microscopy (SEM) was used to measure the nanofibers diameters and morphology. To analyze the expression of SAP4, SAP5 and SAP6 genes, RNA was extracted from clinical isolates of C. albica...
Source: Infection, Genetics and Evolution - February 18, 2019 Category: Genetics & Stem Cells Authors: Keikha N, Yadegari MH, Rajabibazl M, Amani J, Hosseinzadeh S Tags: Infect Genet Evol Source Type: research

Association between hepatic steatosis and MTP gene -493G/T polymorphism in the patients with HCV genotype 1 infection.
kkız H Abstract AIM: Hepatitis C virus (HCV) affects approximately 250 million people worldwide. If patients are untreated, 80% of patients with chronic HCV develop liver failure, liver cirrhosis (LC), and hepatocellular carcinoma (HCC). HCV genotype 1 is the most prevalent among the infected individuals with HCV. Hepatic steatosis is known as accumulation of lipid molecules in hepatocytes, and its prevalence is approximately 55% in CHC infection. The reason of HCV-related hepatic steatosis in CHC infection is mainly HCV core protein. HCV core protein inhibits activities of microsomal triglyceride transfer protei...
Source: Infection, Genetics and Evolution - February 18, 2019 Category: Genetics & Stem Cells Authors: Akgöllü E, Akkız H Tags: Infect Genet Evol Source Type: research

Phenotyping of Lewis and secretor HBGA from saliva and detection of new FUT2 gene SNPs from young children from the Amazon presenting acute gastroenteritis and respiratory infection.
In this study, Lewis and secretor HBGA phenotyping was performed using 352 saliva samples collected from children between three months and five years old born in the Amazon (Brazil, Venezuela and English Guyana) presenting AGE or acute respiratory infection (ARI), the latter considered as control samples. The total of children phenotyped as secretors was 323, corresponding to 91.80%. From these, 207 (58.80%) had a Le (a + b+) profile. The HBGA profiles were equally found in children with AGE as well as with ARI. The rs1047781 of the FUT2 gene was not detected in DNA from saliva cells with a Le (a+b+) profile. However, ...
Source: Infection, Genetics and Evolution - February 18, 2019 Category: Genetics & Stem Cells Authors: de Moraes MTB, Olivares AIO, Fialho AM, Malta FC, da Silva E Mouta Junior S, de Souza Bispo R, Velloso AJ, Leitão GA, Cantelli CP, Nordgren J, Svenson L, Miagostovich MP, Leite JPG Tags: Infect Genet Evol Source Type: research

The population structure of Ochrobactrum isolated from entomopathogenic nematodes indicates interactions with the symbiotic system.
This study describe the population structure and the diversity in Ochrobactrum natural populations isolated from EPNs in the Caribbean basin in order to question the existence of EPN-specialized clones and to gain a better insight into Ochrobactrum-EPNs relationships. EPN-associated Ochrobactrum and Photorhabdus strains were characterized by multi-locus sequence typing, Pulsed-Field Gel Electrophoresis fingerprinting and phenotypic traits. Population study showed the absence of EPN-specialized clones in O. intermedium and O. anthropi but suggested the success of some particular lineages. A low level of genetic and genomic ...
Source: Infection, Genetics and Evolution - February 18, 2019 Category: Genetics & Stem Cells Authors: Aujoulat F, Pagès S, Masnou A, Emboulé L, Teyssier C, Marchandin H, Gaudriault S, Givaudan A, Jumas-Bilak E Tags: Infect Genet Evol Source Type: research

Porcine epidemic diarrhea virus in Asia: An alarming threat to the global pig industry.
PMID: 30779958 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 16, 2019 Category: Genetics & Stem Cells Authors: Sun Y, Chen Y, Han X, Yu Z, Wei Y, Zhang G Tags: Infect Genet Evol Source Type: research

Genetic diversity of Alkhurma hemorrhagic fever virus in Western Asia.
Abstract Alkhurma hemorrhagic fever, caused by Alkhurma hemorrhagic fever virus (ALKV), is an arboviral infection which is further expanding in tropical and subtropical regions of the Western Asia. A number of Alkhurma hemorrhagic fever virus (ALKV) strains have been isolated from clinical cases representing Saudi Arabia and Egypt; however, the phylogenetic relationship of these particular isolates to those reported previously elsewhere in the world remains elusive. Based on the analysis of the envelope (E), and non-structural gene (NS3 and NS5), the phylogenetic and PASC analysis revealed the circulation of three...
Source: Infection, Genetics and Evolution - February 16, 2019 Category: Genetics & Stem Cells Authors: Ul-Rahman A Tags: Infect Genet Evol Source Type: research

Genome characterization and temporal evolution analysis of a non-epidemic norovirus variant GII.8.
In this study, we assembled the first GII.8 norovirus genome from China and clarified the temporal evolutionary process of this non-epidemic variant. Using the "4+1+1" application strategy with newly designed primer sets, the genome of one GII.8 strain GZ2017-L601 from China was firstly sequenced that comprised 7476 nucleotides. The homology of the new genome and the previous only GII.8 genome reached 93.8% identity at the nucleotide level, but only 10, 6, 7 amino acid mutations occurred in three ORFs. When compared the new strain with other GII reference strains, p22 and P2 were calculated as the variable encodi...
Source: Infection, Genetics and Evolution - February 15, 2019 Category: Genetics & Stem Cells Authors: Xue L, Cai W, Gao J, Zhang L, Wu H, Pang R, Li Y, Wang J, Zhang J, Wu S, Ye Q, Lei T, Wu Q Tags: Infect Genet Evol Source Type: research

Mitochondrial diversity and phylogeographic analysis of Pediculus humanus reveals a new Amazonian clade "F".
This study analyzed genetic diversity at three mitochondrial genes (cytochrome b [cytb], cytochrome oxidase subunit 1 [cox1] and 12S ribosomal RNA [12S]) in 98 head lice collected from an isolated Native American population from the Wayampi community in Trois-Sauts, French Guiana. These results are integrated with all prior data of P. humanus (1402 cytb, 743 cox1 and 344 12S) from other parts of the world. The phylogenetic analysis revealed six highly divergent and well-supported monophyletic clades. Five clades corresponded to the previously recognized mitochondrial clades A, D, B, C and E, while the sixth (clade F) was...
Source: Infection, Genetics and Evolution - February 12, 2019 Category: Genetics & Stem Cells Authors: Amanzougaghene N, Fenollar F, Davoust B, Djossou F, Ashfaq M, Bitam I, Raoult D, Mediannikov O Tags: Infect Genet Evol Source Type: research

Whole genome characterisation of G11P[25] and G9P[19] rotavirus A strains from adult patients with diarrhoea in Nepal.
This study aimed to characterise the RVA strains detected from adult patients with diarrhoea in Nepal. A total of 47 RVA positive stool samples from adult patients with diarrhoea in Kathmandu, Nepal during 2007-2008 were examined for the G and P genotypes by sequencing. Nearly half (49%) of the samples were genotyped as G9P[8] (n = 23), G1P[8], G2P[4] (n = 5 each), G12P[8] (n = 4), G12P[6] (n = 3), G1P[6] (n = 2), G3P[8] and G9P[6] (n = 1 each). Interestingly, two G11P[25] and one G9P[19] strains detected were further subjected to Illumina MiSeq next generation sequencing to determine their whole ge...
Source: Infection, Genetics and Evolution - February 11, 2019 Category: Genetics & Stem Cells Authors: Takatsuki H, Agbemabiese CA, Nakagomi T, Pun SB, Gauchan P, Muto H, Masumoto H, Atarashi R, Nakagomi O, Pandey BD Tags: Infect Genet Evol Source Type: research

G1P[8] Rotavirus in children with severe diarrhea in the post-vaccine introduction era in Brazil: Evidence of reassortments and structural modifications of the antigenic VP7 and VP4 regions.
Abstract Worldwide rotaviruses A (RVA) are responsible for approximately 215,000 deaths annually among children aged 50% of gastroenteritis cases in this age group. The aim of this study was to assess the genetic variability of G1P[8] strains detected in children with severe diarrhea in Belém, Pará, Brazil, during the post-rotavirus vaccine introduction era. Phylogenetic analysis clustered the VP4 and VP7 genes of 40 samples selected between 2009 and 2011 into lineages found to be different from the Rotarix® vaccine strain. A detailed investigation of their complete genotype constellations identi...
Source: Infection, Genetics and Evolution - February 11, 2019 Category: Genetics & Stem Cells Authors: Santos FS, Sousa Junior EC, Guerra SFS, Lobo PS, Penha Junior ET, Lima ABF, Vinente CBG, Chagas EHN, Justino MCA, Linhares AC, Matthijnssens J, Soares LS, Mascarenhas JDP Tags: Infect Genet Evol Source Type: research

Plasmodium ovale curtisi and Plasmodium ovale wallikeri in Chinese travelers: Prevalence of novel genotypes of circumsporozoite protein in the African continent.
We report novel genotypes, their prevalence and the predominant haplotypes of P. ovale curtisi and P. ovale wallikeri circumsporozoite protein (CSP) from 20 African countries in Chinese travelers. These genotypes should be considered while designing a CSP-based vaccine against P. ovale malaria. PMID: 30763775 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 11, 2019 Category: Genetics & Stem Cells Authors: Lu F, Ahmed MA, Xu S, Xu S, Han JH, Liu Q, Chen J, Zhu G, Zhou H, Cao J, Han ET Tags: Infect Genet Evol Source Type: research

Optimizing molecular surveillance of mumps genotype G viruses.
Abstract Mumps viruses continue to cause sporadic cases and outbreaks in countries with a high vaccination coverage for mumps. Molecular surveillance of mumps viruses can be supportive to elucidate the origin and transmission routes of mumps virus in case of an outbreak. Currently, molecular surveillance is worldwide primarily focused on sequencing of the small hydrophobic (SH) gene. However, few studies have already shown that additional genes or regions contribute to the resolution of the sequence data in such a way that mumps cases that seem to be linked to the same source on basis of the SH sequence, appear to...
Source: Infection, Genetics and Evolution - February 7, 2019 Category: Genetics & Stem Cells Authors: Bodewes R, van Rooijen K, Cremer J, Veldhuijzen IK, van Binnendijk R Tags: Infect Genet Evol Source Type: research

The complete coding region of the maxicircle as a superior phylogenetic marker for exploring evolutionary relationships between members of the Leishmaniinae.
Abstract The mitochondrial DNA (mtDNA) is a potentially valuable phylogenetic marker given its presence across all eukaryotic taxa and its relative conservation in structure and sequence. In trypanosomatids, a homologue of the mtDNA referred to as the maxicircle DNA, is located within a specialised structure in the single mitochondrion of the trypanosomatids called the kinetoplast; a high molecular weight network of DNA composed of thousands of catenated minicircles and a smaller number of larger maxicircles. Unique to the kinetoplastid protists, the maxicircle component of this complex network could represent a d...
Source: Infection, Genetics and Evolution - February 6, 2019 Category: Genetics & Stem Cells Authors: Kaufer A, Barratt J, Stark D, Ellis J Tags: Infect Genet Evol Source Type: research

Protection induced by Leishmania Major antigens and the imiquimod adjuvant encapsulated on liposomes in experimental cutaneous leishmaniasis.
Abstract There is a need for new, effective, and less expensive and toxic treatment for Leishmaniasis. It seems that the use of a suitable adjuvant and a delivery system is effective in inducing immune reactions for protection. Liposomes can be applied as immunoadjuvants to trigger immune reactions to different antigens. The adjuvant effects of imiquimod using DSPC liposomes containing SLA (soluble Leishmania antigens) were studied on the type and intensity of the produced immune reaction to the challenge of Leishmania major in BALB/c mice. Liposomes were produced by the lipid film procedure. BALB/C mice were immu...
Source: Infection, Genetics and Evolution - February 6, 2019 Category: Genetics & Stem Cells Authors: Mehravaran A, Nasab MR, Mirahmadi H, Sharifi I, Alijani E, Nikpoor AR, Akhtari J Tags: Infect Genet Evol Source Type: research

Geographical structure of bat SARS-related coronaviruses.
Abstract Bats are the natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) which caused the outbreak of human SARS in 2002-2003. We introduce the genetic diversity of SARS-related coronaviruses (SARSr-CoVs) discovered in bats and provide insights on the bat origin of human SARS. We also analyze the viral geographical structure that may improve our understanding of the evolution of bat SARSr-CoVs. PMID: 30735813 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - February 5, 2019 Category: Genetics & Stem Cells Authors: Yu P, Hu B, Shi ZL, Cui J Tags: Infect Genet Evol Source Type: research

Few Plasmodium falciparum merozoite ligand and erythrocyte receptor pairs show evidence of balancing selection.
We examined six merozoite ligands EBA175, EBL1, EBA140, MSP1, Rh4 and Rh5, and their corresponding erythrocyte receptors, glycophorin (Gyp) A, GypB, GypC, band 3, complement receptor (CR) 1 and basigin, focusing on the regions involved in the ligand-receptor interactions. Positive Tajima's D values (>1) were observed only in the MSP1 C-terminal region and EBA175 region II, while negative values (
Source: Infection, Genetics and Evolution - February 5, 2019 Category: Genetics & Stem Cells Authors: Ochola-Oyier LI, Wamae K, Omedo I, Ogola C, Matharu A, Musayibimana JP, Njogu FK, Marsh K Tags: Infect Genet Evol Source Type: research

Malaria infection rates in Anopheles albimanus (Diptera: Culicidae) at Ipet í-Guna, a village within a region targeted for malaria elimination in Panamá.
Malaria infection rates in Anopheles albimanus (Diptera: Culicidae) at Ipetí-Guna, a village within a region targeted for malaria elimination in Panamá. Infect Genet Evol. 2019 Feb 04;: Authors: Rigg CA, Hurtado LA, Calzada JE, Chaves LF Abstract The Panamá Canal construction encompassed one of the first examples of malaria elimination. Nevertheless, malaria has uninterruptedly persisted in Native American populations living within a few kilometers of the Panamá Canal. Here, we present results from a monthly longitudinal study (May 2016 to March 2018), whose goal was to qua...
Source: Infection, Genetics and Evolution - February 4, 2019 Category: Genetics & Stem Cells Authors: Rigg CA, Hurtado LA, Calzada JE, Chaves LF Tags: Infect Genet Evol Source Type: research

ampD homologs in biotypes of Yersinia enterocolitica: Implications in regulation of chromosomal AmpC-type cephalosporinases.
Abstract Inducible 'AmpC-type' chromosomal cephalosporinases have been reported to be differentially expressed in different biotypes of Yersinia entercolocolitica. AmpD amidases are key regulators of the expression of ampC genes in Y. entercolocolitica as their inactivation results in hyper production of AmpC. To understand the differences in regulation of ampC expression in different biotypes of Y. enterocolitica, characteristics of ampD homologs were studied in strains of Y. enterocolitica belonging to five biotypes namely 1A, 1B, 2, 3 and 4. Our results indicated that the mechanisms which regulate expression of...
Source: Infection, Genetics and Evolution - January 30, 2019 Category: Genetics & Stem Cells Authors: Singhal N, Pandey D, Singh NS, Kumar M, Virdi JS Tags: Infect Genet Evol Source Type: research

A ten year study of prevalence, antimicrobial susceptibility pattern, and genotypic characterization of Methicillin resistant Staphylococcus aureus causing ocular infections in a tertiary eye care hospital in South India.
This study aimed to determine the prevalence and antimicrobial susceptibility pattern of MRSA and their genotypic characterization in ocular infections. The study period was from January 2007 to December 2017 in Aravind Eye Hospital, Madurai. Retrospective analysis of clinical records found a total of 1306 Staphylococcus aureus in various ocular infections. Among these, 274 (21%) were found to be MRSA with an increased incidence from 9% in 2007 to 38% in 2017 (P = .007). MRSA was isolated commonly from lacrimal sac infection 89 (32%), lid infection 55 (20%), keratitis 45 (16%) and orbital infection 34 (12%). MRSA isola...
Source: Infection, Genetics and Evolution - January 29, 2019 Category: Genetics & Stem Cells Authors: Nithya V, Rathinam S, Karthikeyan RSG, Lalitha P Tags: Infect Genet Evol Source Type: research

Phylogenetic analysis based on the 16S rDNA, gltA, gatB, and hcpA gene sequences of Wolbachia sp. from the novel host Ceratozetes thienemanni (Acari: Oribatida).
Abstract We determined the occurrence of intracellular endosymbionts (Wolbachia sp., Cardinium sp., Arsenophonus sp., Rickettsia sp., Spiroplasma sp., Hamiltonella sp., Flavobacterium, and microsporidia) in oribatid mites (Acari: Oribatida) with the use of PCR technique. For the first time we looked for and detected Wolbachia sp. in parthenogenetic oribatid mite Ceratozetes thienemanni Willmann, 1943. The 16S rDNA, gatB, hcpA, and gltA sequences of Wolbachia sp. in C. thienemanni showed the highest similarity (≥ 90%) to the genes of Wolbachia sp. from springtails Collembola and oribatid mite Gustavia microc...
Source: Infection, Genetics and Evolution - January 29, 2019 Category: Genetics & Stem Cells Authors: Konecka E, Olszanowski Z Tags: Infect Genet Evol Source Type: research

Zika virus outbreak in Rajasthan, India in 2018 was caused by a virus endemic to Asia.
Abstract Zika virus (ZIKV) infection in human has been reported from Gujarat and Tamil Nadu states during the year 2016 and 2017 respectively. In paucity of complete genome data of ZIKV, the analysis and prediction were not possible. Zika cases were reported in Jaipur city, Rajasthan, India during the period of 21st September 2018 to 29th October 2018. In order to understand the circulating ZIKV strain in Rajasthan state about ten human serum samples from the positive cases of Jaipur city, Rajasthan state considering the locality and clustering variations were sequenced using next-generation sequencing (NGS) platf...
Source: Infection, Genetics and Evolution - January 28, 2019 Category: Genetics & Stem Cells Authors: Yadav PD, Malhotra B, Sapkal G, Nyayanit DA, Deshpande G, Gupta N, Ullas PT, Sharma H, Sahay RR, Sharma P, Mourya DT Tags: Infect Genet Evol Source Type: research

First report of New Delhi metallo- β-lactamase-6 (NDM-6) among Klebsiella pneumoniae ST147 strains isolated from dialysis patients in Iran.
First report of New Delhi metallo-β-lactamase-6 (NDM-6) among Klebsiella pneumoniae ST147 strains isolated from dialysis patients in Iran. Infect Genet Evol. 2019 Jan 23;: Authors: Bahramian A, Shariati A, Azimi T, Sharahi JY, Bostanghadiri N, Gachkar L, Ghalavand Z, Chirani AS, Erfanimanesh S, Hashemi A Abstract There has been an alarming health-related concern about the growth of New Delhi metallo-β-lactamase. The aims of this study include the phenotypic detection of β-lactamases and molecular characterization of NDM in Klebsiella pneumoniae isolates in Tehran, Iran. A total of 120 K...
Source: Infection, Genetics and Evolution - January 23, 2019 Category: Genetics & Stem Cells Authors: Bahramian A, Shariati A, Azimi T, Sharahi JY, Bostanghadiri N, Gachkar L, Ghalavand Z, Chirani AS, Erfanimanesh S, Hashemi A Tags: Infect Genet Evol Source Type: research

Sequestration inside the yeast vacuole may enhance Helicobacter pylori survival against stressful condition.
In this study, occurrence of H. pylori inside the vacuole of Candida yeast was studied and the role of vacuolating cytotoxin A (VacA) in constructing the vacuole was discussed. One gastric Candida yeast was used for Live/Dead stain and fluorescence in situ hybridization (FISH) with universal bacterial probe. Yeast total DNA was used for amplification of full-length bacterial 16S rDNA as well as H. pylori-specific 16S rDNA and vacA alleles. Vacuoles were isolated from yeast cells and stained with fluorescent yeast vacuole membrane marker MDY-64. DNA extracted from vacuoles was used for amplification of H. pylori-specific 16...
Source: Infection, Genetics and Evolution - January 22, 2019 Category: Genetics & Stem Cells Authors: Siavoshi F, Heydari S, Shafiee M, Ahmadi S, Saniee P, Sarrafnejad A, Kolahdoozan S Tags: Infect Genet Evol Source Type: research

Sequence ambiguity determined from routine pol sequencing is a reliable tool for real-time surveillance of HIV incidence trends.
This study explores the utility of SA defined as a proportion of ambiguous nucleotides detected in baseline pol sequences as a tool for routine real-time surveillance of HIV incidence trends at a national level. A total of 353 partial HIV-1 pol sequences obtained from persons diagnosed with HIV infection in Slovenia from 2000 to 2012 were studied, and SA was reported as a percentage of ambiguous base calls. Patients were characterized as recently infected by examining anti-HIV serological patterns and/or using commercial HIV-1 incidence assays (BED and/or LAg-Avidity assay). A mean SA of 0.29%, 0.14%, and 0.19% was observe...
Source: Infection, Genetics and Evolution - January 22, 2019 Category: Genetics & Stem Cells Authors: Lunar MM, Lepej SŽ, Poljak M Tags: Infect Genet Evol Source Type: research

Molecular detection of a novel Babesia sp. and pathogenic spotted fever group rickettsiae in ticks collected from hedgehogs in Turkey: Haemaphysalis erinacei, a novel candidate vector for the genus Babesia.
In this study, a total of 319 ticks were obtained from hedgehogs (Erinaceus concolor). All ticks were pooled into groups and screened by PCR for tick-borne pathogens (TBPs). PCR and sequence analyses identified the presence of a novel Babesia sp. in adult Haemaphysalis erinacei. In addition, the presence of natural transovarial transmission of this novel Babesia sp. was detected in Ha. erinacei. According to the 18S rRNA (nearly complete) and partial rRNA locus (ITS-1/5.8S/ITS-2) phylogeny, it was determined that this new species is located within the Babesia sensu stricto clade and is closely related to Babesia spp. found...
Source: Infection, Genetics and Evolution - January 22, 2019 Category: Genetics & Stem Cells Authors: Orkun Ö, Çakmak A, Nalbantoğlu S, Karaer Z Tags: Infect Genet Evol Source Type: research

Genotypic persistence of dengue virus in the Philippines.
Abstract The Philippines is known to have one of the world's highest prevalences of dengue infection. The disease has been endemic in the country since 1956 and the severe form was first reported during an outbreak in Manila in 1954. Among all of the countries in the world, the Philippines had the highest case fatality rate from 2008 to 2012. With the increasing rate of international travel, the country is also considered one of the primary sources of imported dengue cases in non-endemic areas in Asia, Australia, and Europe. Despite this high prevalence, there is a dearth of literature describing the circulating s...
Source: Infection, Genetics and Evolution - January 22, 2019 Category: Genetics & Stem Cells Authors: Jowina Galarion M, Schwem B, Pangilinan C, Dela Tonga A, Petronio-Santos JA, Reyes ED, Destura R Tags: Infect Genet Evol Source Type: research

Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis.
PMID: 30682552 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 22, 2019 Category: Genetics & Stem Cells Authors: de Viedma DG Tags: Infect Genet Evol Source Type: research