Infection and molecular identification of ascaridoid nematodes from the important marine food fish Japanese threadfin bream Nemipterus japonicus (Bloch) (Perciformes: Nemipteridae) in China.
Abstract The Japanese threadfin bream N. japonicus (Bloch) (Perciformes: Nemipteridae) is an important marine food fish in Asia. However, our present knowledge of the occurrence of its nematode parasites is still limited. In the present study, the species composition and infection rate of ascaridoid nematodes in N. japonicus from the South China Sea, were studied for the first time. Five ascaridoid species, namely Anisakis typica (L3), Hysterothylacium amoyense (L3), Hysterothylacium sp. IV-A (L3), adult of H. thalassini and Raphidascaris lophii (L3), were identified using integrative taxonomy. Hysterothylacium am...
Source: Infection, Genetics and Evolution - September 19, 2020 Category: Genetics & Stem Cells Authors: Guo N, Chen HX, Zhang LP, Zhang JY, Yang LY, Li L Tags: Infect Genet Evol Source Type: research

Enterocytozoon bieneusi genotypes in farmed goats and sheep in Ningxia, China.
Abstract Enterocytozoon bieneusi is reported to be a common microsporidian of humans and animals in various countries. However, scarce information on E. bieneusi has been recorded in farmed goats and sheep in China. As such, we undertook molecular epidemiological investigation of E. bieneusi in farmed goats (Capra aegagrus hircus) and sheep (Ovis aries) in Ningxia, China. A total of 660 genomic DNAs were extracted from individual faecal samples from famed goats (n = 300) and sheep (n = 360), and then tested using a nested PCR-based sequencing approach employing internal transcribed spacer (ITS) of nuclear ...
Source: Infection, Genetics and Evolution - September 19, 2020 Category: Genetics & Stem Cells Authors: Zhang Y, Mi R, Yang J, Wang J, Gong H, Huang Y, Wang X, Han X, Zhou H, Chen Z Tags: Infect Genet Evol Source Type: research

Insect-specific viruses and arboviruses in adult male culicids from Midwestern Brazil.
Abstract Viruses were identified from male anthropophilic mosquitoes from Mato Grosso (MT) State, Midwest Brazil from February 2017 to January 2018. Mosquitoes tested included Aedes (Stegomyia) aegypti (1139 males; 84 pools), Culex quinquefasciatus (9426 males; 179 pools), Culex sp. (3 males; 3 pools) and Psorophora albigenu (1 male; 1 pool) collected from four cities of MT. Pools were subjected to viral RNA extraction followed by RT-PCRs specific for ten flaviviruses, five alphaviruses and Simbu serogroup of orthobunyaviruses. Positive pools were passaged three times in VERO cells (alphavirus and orthobunyavirus)...
Source: Infection, Genetics and Evolution - September 19, 2020 Category: Genetics & Stem Cells Authors: da Silva Ferreira R, de Toni Aquino da Cruz LC, Souza VJ, da Silva Neves NA, de Souza VC, Filho LCF, da Silva Lemos P, de Lima CPS, Naveca FG, Atanaka M, Nunes MRT, Slhessarenko RD Tags: Infect Genet Evol Source Type: research

Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in South America.
The objective of this study was to describe the substitution frequency of the S and N proteins of SARS-CoV-2 in South America. A total of 504 amino acid and nucleotide sequences of the S and N proteins of SARS-CoV-2 from seven South American countries (Argentina, Brazil, Chile, Ecuador, Peru, Uruguay, and Colombia), reported as of June 3, and corresponding to samples collected between March and April 2020, were compared through substitution matrices using the Muscle algorithm in MEGA X. Forty-three sequences from 13 Colombian departments were obtained in this study using the Oxford Nanopore and Illumina MiSeq technologies,...
Source: Infection, Genetics and Evolution - September 17, 2020 Category: Genetics & Stem Cells Authors: Franco-Muñoz C, Álvarez-Díaz DA, Laiton-Donato K, Wiesner M, Escandón P, Usme-Ciro JA, Franco-Sierra ND, Flórez-Sánchez AC, Gómez-Rangel S, Rodríguez-Calderon LD, Barbosa-Ramirez J, Ospitia-Baez E, Walteros DM, Ospina-Martinez ML, Mercado-Reyes M Tags: Infect Genet Evol Source Type: research

Egg transcriptome profile responds to maternal virus infection in honey bees, Apis mellifera.
Abstract Trans-generational disease effects include vertical pathogen transmission but also immune priming to enhance offspring immunity. Accordingly, the survival consequences of maternal virus infection can vary and its molecular consequences during early development are poorly understood. The honey bee queen is long-lived and represents the central hub for vertical virus transmission as the sole reproductive individual in her colony. Even though virus symptoms in queens are mild, viral infection may have severe consequences for the offspring. Thus, transcriptome patterns during early developmental are predicted...
Source: Infection, Genetics and Evolution - September 15, 2020 Category: Genetics & Stem Cells Authors: Amiri E, Herman JJ, Strand MK, Tarpy DR, Rueppell O Tags: Infect Genet Evol Source Type: research

Quasi-species nature and differential gene expression of severe acute respiratory syndrome coronavirus 2 and phylogenetic analysis of a novel Iranian strain.
Abstract A novel coronavirus related to severe acute respiratory syndrome virus, (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. Despite the genetic mutations across the SARS-CoV-2 genome being recently investigated, its transcriptomic genetic polymorphisms at inter-host level and the viral gene expression level based on each Open Reading Frame (ORF) remains unclear. Using available High Throughput Sequencing (HTS) data and based on SARS-CoV-2 infected human transcriptomic data, this study presents a high-resolution map of SARS-CoV-2 single nucleotide polymorphism (SNP) hotspots in a viral population at...
Source: Infection, Genetics and Evolution - September 13, 2020 Category: Genetics & Stem Cells Authors: Ghorbani A, Samarfard S, Ramezani A, Izadpanah K, Afsharifar A, Eskandari MH, Karbanowicz TP, Peters JR Tags: Infect Genet Evol Source Type: research

Near-complete genome of Cosavirus A from a child hospitalized with acute gastroenteritis, Brazil.
This report characterized the first complete genome of a Cosavirus A strain (AM326) from a child hospitalized with AG in Brazil. Sequencing was performed using the HiSeq™ 2500 platform (Illumina) in one fecal specimen collected from the Surveillance of Rotavirus Network of Evandro Chagas Institute collected in 2017. Sequence reads were assembled using De Novo approach with IDBA-UD, Spades, and MegaHit. HCosV-AM326 assembled with 7735 nt (GenBank MT023104) and showed a new variant strain from Brazil, highlighting the association of HCosV-A as a possible pathogen in this patient. This finding demonstrates the need fo...
Source: Infection, Genetics and Evolution - September 12, 2020 Category: Genetics & Stem Cells Authors: Lobo PS, Cardoso JF, Barata RR, Lemos PS, Guerra SFS, Soares LS, Nunes MRT, Mascarenhas JDP Tags: Infect Genet Evol Source Type: research

Subtractive proteomics and immunoinformatics approaches to explore Bartonella bacilliformis proteome (virulence factors) to design B and T cell multi-epitope subunit vaccine.
Abstract Bartonella bacilliformis a gram-negative facultative aerobe responsible for the Carrion's disease widely distributed in Ecuador, Peru, and Colombia with a high mortality rate when no specific treatment is received. B bacilliformis is transmitted by Sand fly (Lutzomyia verrucarum) to healthy individuals. Immunoinformatic and subtractive proteomics approaches were employed in this study to prioritize the best candidates for vaccine designing. These approaches resulted in five vaccine candidates, flagellar biosynthetic protein (Uniprot ID: A1UTU1), heme exporter protein C (UniProt ID: A1UU82), Cytochrome c-t...
Source: Infection, Genetics and Evolution - September 12, 2020 Category: Genetics & Stem Cells Authors: Gul H, Ali SS, Saleem S, Khan S, Khan J, Wadood A, Rehman AU, Ullah Z, Ali S, Khan H, Hussain Z, Akbar F, Khan A, Wei DQ Tags: Infect Genet Evol Source Type: research

Molecular characterisation of canine parvoviruses from clinical samples and vaccines in Nigeria.
PMID: 32927118 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 11, 2020 Category: Genetics & Stem Cells Authors: Shima FK, Omobowale TO, Adesina RD, Nottidge HO, Fagbohun OA Tags: Infect Genet Evol Source Type: research

Phylogenetic and biological characterizations of a GI.3 norovirus.
In this study, we report the isolation, near-complete genome sequencing, and expression and biological characterization of the major capsid protein (VP1) of a GI.3 NoV isolated from a child presenting acute gastroenteritis. The genome of the GI.3 NoV is 7746 bp in length, not including the poly-adenylation tail. Phylogenetic analysis based on the complete VP1 nucleotide sequences indicates that GI.3 NoVs could be divided into four clusters, with 4.6%, 5.3%, 6.6%, 1.9% intracluster variations in nucleotide and 4.8%, 3.8%, 6.1%, 1.7% intracluster variations in amino acid sequences, respectively. A Bayesian evolutionary ana...
Source: Infection, Genetics and Evolution - September 11, 2020 Category: Genetics & Stem Cells Authors: Zheng L, Zhang H, Ma J, Liu J, Ma S, Wang M, Huo Y Tags: Infect Genet Evol Source Type: research

MALDI-TOF MS identification of Cimex lectularius and Cimex hemipterus bedbugs.
In this study, we assess the use of MALDI-TOF MS for the identification of laboratory and wild strains of C. lectularius and C. hemipterus. Several body parts of laboratory reared C. lectularius specimens were used to develop a MALDI-TOF MS protocol for bedbug identification, which was later validated using five other laboratory and wild populations of C. hemipterus and C. lectularius. A total of 167C. lectularius and C. hemipterus bedbug specimens (98 laboratory specimens and 69 wild specimens) were submitted to MALDI-TOF MS analysis. 143/167 (85.63%) provided high quality MS spectra. The in-lab database was then upgraded...
Source: Infection, Genetics and Evolution - September 11, 2020 Category: Genetics & Stem Cells Authors: Benkacimi L, Gazelle G, El Hamzaoui B, Bérenger JM, Parola P, Laroche M Tags: Infect Genet Evol Source Type: research

Characterization of Mycobacterium tuberculosis var. africanum isolated from a patient with pulmonary tuberculosis in Brazil.
SEG, Uwezeye C, de Jong BC, Junqueira-Kipnis AP, Suffys PN Abstract Human tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis complex (MTBC), including Mycobacterium tuberculosis var. tuberculosis (MTB) and Mycobacterium tuberculosis var. africanum (MAF). While MTB is isolated worldwide, MAF is almost completely restricted to the African continent, and despite the historical proximity between Brazil and Africa during the slave trade, no case of TB being caused by MAF has been reported in Brazil to date. We hereby describe the first case of TB caused by MAF in Brazil comparing its genome again...
Source: Infection, Genetics and Evolution - September 10, 2020 Category: Genetics & Stem Cells Authors: Rabahi MF, Conceição EC, de Paiva LO, Souto MVML, Sisco MC, de Waard J, de Souza Caldas PC, Fandinho F, Ramos JP, de Carvalho LD, Campos CED, Lima KVB, da Silva SP, Sharma A, Robledo J, Paez UAH, Duarte RS, da Silva MG, Gomes LL, Vasconcellos SEG, Uweze Tags: Infect Genet Evol Source Type: research

Genetic diversification of acanthocephalans of the genus Floridosentis Ward 1953 (Acanthocephala: Neoechinorhynchidae), parasites of mullets from the Americas.
iacute;a-Varela M Abstract Adult worms of the genus Floridosentis are endoparasites of marine fishes of the genus Mugil and are broadly distributed in the Americas. Currently, Floridosentis includes two species, F. mugilis, distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, restricted to the Pacific Ocean coast. The aim of this study was to explore the species limit of both species of the genus Floridosentis, collected in 37 localities in eight countries: Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, Ecuador and Venezuela. We sequenced 253 specimens to build a...
Source: Infection, Genetics and Evolution - September 10, 2020 Category: Genetics & Stem Cells Authors: Rosas-Valdez R, Morrone JJ, Pinacho-Pinacho CD, Domínguez-Domínguez O, García-Varela M Tags: Infect Genet Evol Source Type: research

The role of animals as a source of antimicrobial resistant nontyphoidal Salmonella causing invasive and non-invasive human disease in Vietnam.
Abstract BACKGROUND: Nontyphoidal Salmonella (NTS) are associated with both diarrhea and bacteremia. Antimicrobial resistance (AMR) is common in NTS in low-middle income countries, but the major source(s) of AMR NTS in humans are not known. Here, we aimed to assess the role of animals as a source of AMR in human NTS infections in Vietnam. We retrospectively combined and analyzed 672 NTS human and animal isolates from four studies in southern Vietnam and compared serovars, sequence types (ST), and AMR profiles. We generated a population structure of circulating organisms and aimed to attribute sources of AMR in NTS...
Source: Infection, Genetics and Evolution - September 10, 2020 Category: Genetics & Stem Cells Authors: Parisi A, Phuong TLT, Mather AE, Jombart T, Tuyen HT, Lan NPH, Trang NHT, Carrique-Mas J, Campbell JI, Trung NV, Glass K, Kirk MD, Baker S Tags: Infect Genet Evol Source Type: research

Knockdown of fatty acid binding protein 4 exacerbates Bacillus Calmette-Guerin infection-induced RAW264.7 cell apoptosis via the endoplasmic reticulum stress pathway.
Abstract Mycobacterial infection can induce alveolar macrophage apoptosis, which plays a vital role in the pathogenesis of tuberculosis. Accumulating evidence has demonstrated that fatty acid oxidation is involved in apoptosis during various pathological processes, including bacterial infection. However, whether fatty acid oxidation regulates mycobacterial infection-induced macrophage apoptosis remains unclear. Hence, the present study aimed to investigate the role of fatty acid binding protein 4 (FABP4) which is a carrier protein for fatty acids, in regulating apoptosis in RAW264.7 cells infected with Bacillus Ca...
Source: Infection, Genetics and Evolution - September 10, 2020 Category: Genetics & Stem Cells Authors: Yu J, Ma C, Xu Y, Han L, Wu X, Wang Y, Deng G Tags: Infect Genet Evol Source Type: research

Multilocus sequence typing analysis of Leishmania clinical isolates from cutaneous leishmaniasis patients of Iran.
This study represents the first successful application of MLST approach to L. tropica and L. major strains in Iran. PMID: 32919066 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 9, 2020 Category: Genetics & Stem Cells Authors: Hosseini M, Rostami MN, Doust RH, Khamesipour A Tags: Infect Genet Evol Source Type: research

Differential expression of cytokine genes in THP-1-derived macrophages infected with mild and virulence strains of Shigella flexneri 2a.
Abstract Shigella is an intracellular bacterial pathogen that causes bacterial dysentery called shigellosis. The assessment of pro- and anti-inflammatory mediators produced by immune cells against this bacteria are vital in identifying the effectiveness of the immune reaction in protecting the host. In Malaysia, Shigella is ranked as the third most common bacteria causing diarrheal disease among children below 5 years old. In the present study, we aim to examine the differential cytokine gene expressions of macrophages in response to two types of clinical strains of Shigella flexneri 2a (S. flexneri 2a) isolated...
Source: Infection, Genetics and Evolution - September 7, 2020 Category: Genetics & Stem Cells Authors: Shabani NRM, Mokhtar M, Leow CH, Lean QY, Candy C, Singh KKB, Leow CY Tags: Infect Genet Evol Source Type: research

The emergence of hypervirulent blaNDM-1-positive Klebsiella pneumoniae sequence type 395 in an oncology hospital.
Abstract Fifteen hypermucoviscous isolates (13 blaNDM-1-positive) obtained from 11 oncology patients were analyzed by whole genome sequencing, and selected isolates were assessed in a murine model of sepsis. ST395/K2 isolates harboring rmpA, rmpA2, peg-344, aerobactin, enterobactin, yersiniabactin, type I fimbriae, etc. displayed maximal virulence in the mouse lethality assay (LD50 = 102 CFU). ST147/K20 isolates lacking yersiniabactins were relatively less virulent (LD50 = 104 CFU), ST395/K2 isolates lacking rmpA, rmpA2, peg-344, and aerobactin, but harboring yersiniabactin demonstrated minimal virulen...
Source: Infection, Genetics and Evolution - September 5, 2020 Category: Genetics & Stem Cells Authors: Lazareva I, Ageevets V, Sopova J, Lebedeva M, Starkova P, Likholetova D, Lebedeva M, Gostev V, Moiseenko V, Egorenkov V, Navatskaya A, Mitroshina G, Myasnikova E, Tsvetkova I, Lobzin Y, Sidorenko S Tags: Infect Genet Evol Source Type: research

Allelic variation of msp-3 α gene in Plasmodium vivax isolates and its correlation with the severity of disease in vivax malaria.
This study aims to correlate the severity of clinical symptoms with parasite load, genotype of P. vivax and multiplicity of infection. Based on clinical symptoms classification, 31 (67.9%) out of 46 cases were found to be severe while 15 (32.6%) were non-severe and correlation of the severity of vivax infection with parasite load was not observed. Analysis of msp3-α allele genotype showed that out of 31 severe cases, 19 (61.2%) were single-clone infection cases whereas 12 (38.7%) were multi-clone infections. Similarly, out of 15 non-severe cases, 9 (60%) were single clone and 6 (40%) were multi-clone infections indic...
Source: Infection, Genetics and Evolution - September 4, 2020 Category: Genetics & Stem Cells Authors: Upmanyu K, Matlani M, Yadav P, Rathi U, Mallick PK, Singh R Tags: Infect Genet Evol Source Type: research

EV-transported microRNAs of Schistosoma mansoni and Fasciola hepatica: Potential targets in definitive hosts.
Abstract Trematodes are widespread parasitic flatworms that significantly affect mankind either directly as human parasites, or indirectly via the infection of livestock and the related economic damage. The two most important trematode taxa are the blood flukes Schistosoma and the liver flukes Fasciola, but detection and differentiation of these parasites remains a challenge. Recently, microRNAs (miRNAs) were described from extracellular vesicles (EV) for both parasites secreted into respective hosts. These molecules have been proposed as mediators of parasite-host communication, and potential biomarkers for the d...
Source: Infection, Genetics and Evolution - September 3, 2020 Category: Genetics & Stem Cells Authors: Ovchinnikov VY, Kashina EV, Mordvinov VA, Fromm B Tags: Infect Genet Evol Source Type: research

Phlebovirus sequences detected in ticks collected in Russia: Novel phleboviruses, distinguish criteria and high tick specificity.
F, Vakalova EV, Lukashev AN, Karganova GG, Gmyl AP Abstract Phlebovirus is an abundant and rather heterogeneous genus within the Phenuiviridae family (order Bunyavirales). The genus Phlebovirus is divided into two antigenic complexes, which also correspond to the main vector: sandflies/mosquitoes and ticks. Previously, only sandfly/mosquito-borne phleboviruses were associated with human disease, such as Rift Valley fever virus, Toscana virus, Sicilian and Naples Sandfly fever viruses and others. Until recently, tick-borne phleboviruses were not considered as human pathogens. After the discovery of severe fever wit...
Source: Infection, Genetics and Evolution - September 3, 2020 Category: Genetics & Stem Cells Authors: Klimentov AS, Belova OA, Kholodilov IS, Butenko AM, Bespyatova LA, Bugmyrin SV, Chernetsov N, Ivannikova AY, Kovalchuk IV, Nafeev AA, Oorzhak ND, Pilikova OM, Polienko AE, Purmak KA, Romanenko EN, Romanova LI, Saryglar AA, Solomashchenko NI, Shamsutdinov Tags: Infect Genet Evol Source Type: research

Co-harboring of mcr-1 and β-lactamase genes in Pseudomonas aeruginosa by high-resolution melting curve analysis (HRMA): Molecular typing of superbug strains in bloodstream infections (BSI).
CONCLUSION: CRPA strains play an essential role in the spread of antibiotic resistance in BSI. Likewise, the HRMA method was sensitive and specific for the detection of superbugs. Moreover, MLST analysis of a diverse collection of P. aeruginosa from blood culture suggests that particular strains or clonal complexes are associated with antibiotic resistance profile. PMID: 32891877 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 3, 2020 Category: Genetics & Stem Cells Authors: Tahmasebi H, Dehbashi S, Arabestani MR Tags: Infect Genet Evol Source Type: research

Diversity of L1/L2 genes and molecular epidemiology of high-level carbapenem resistance Stenotrophomonas maltophilia isolates from animal production environment in China.
Abstract Stenotrophomonas maltophilia is emerging as a significant cause of human and animal disease worldwide. A total of 3400 samples were collected from animal farms and adjacent environments in China. The blaL1 and blaL2 genes were identified using whole genome sequence analyses and examined by phylogenetics. Isolates were also tested for susceptibility to 18 antibiotics. We isolated 118 strains of S. maltophilia from 3400 samples. The positive rates of blaL1 and blaL2 genes were 75% (89/118) and 22% (26/118) and we identified 11 L1 and 6 L2 amino acid sequence variants. S. maltophilia has at least two inducib...
Source: Infection, Genetics and Evolution - September 3, 2020 Category: Genetics & Stem Cells Authors: Han L, Zhang RM, Jia L, Bai SC, Liu XW, Wei R, Cui CY, Sun RY, Wang MG, Cai DT, Liao XP, Liu YH, Sun J Tags: Infect Genet Evol Source Type: research

Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene.
Abstract The new SARS-CoV-2 poses a significant threat to human health but many aspects of its basic biology remain unknown. Its genome encodes accessory genes that differ significantly within coronaviruses and contribute to the virus pathogenicity. Among accessory genes, open reading frame 8 (ORF8) stands out by being highly variable and showing structural changes suspected to be related with the virus ability to spread. However, the function of ORF8 remains to be elucidated, making it less studied than other SARS-CoV-2 genes. Here I show that ORF8 is poorly conserved among related coronaviruses. The ORF8 phyloge...
Source: Infection, Genetics and Evolution - September 2, 2020 Category: Genetics & Stem Cells Authors: Pereira F Tags: Infect Genet Evol Source Type: research

Diagnostic accuracy of hepatocyte growth factor, Fas/CD95 and Endostatin for non-invasive assessment of hepatic fibrosis in biopsy-proven hepatitis C virus patients.
CONCLUSION: FHEPA-Test is considered a novel non-invasive test which could be applied in assessment of liver fibrosis in HCV infected patients. Our novel score was more efficient than Immune Fibrosis Index, Fibrosis Index and FibroQ and thus it could be more applicable, feasible & economic for Egyptian HCV patients. Our Novel Scoring system could be globalized to other populations to confirm its advantageous use in early diagnosis of liver fibrosis. PMID: 32890764 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 2, 2020 Category: Genetics & Stem Cells Authors: Abdelgawad ME, El-Zakzok H, Salah M, El-Mezayen HA Tags: Infect Genet Evol Source Type: research

Molecular characterization of Cachavirus firstly detected in dogs in China.
This study confirms the presence of Cachavirus in pet dogs in China and provides novel findings on its molecular characteristics. PMID: 32890765 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 2, 2020 Category: Genetics & Stem Cells Authors: Hu W, Liu Q, Chen Q, Ji J Tags: Infect Genet Evol Source Type: research

Genetic diversity and phylogeographic analysis of human herpesvirus type 8 (HHV-8) in two distant regions of Argentina: Association with the genetic ancestry of the population.
;nchez M, González C, Rivello HG, Corach D, Caputo M, Trinks J Abstract BACKGROUND: The genetic diversity of persistent infectious agents, such as HHV-8, correlates closely with the migration of modern humans out of East Africa which makes them useful to trace human migrations. However, there is scarce data about the evolutionary history of HHV-8 particularly in multiethnic Latin American populations. OBJECTIVES: The aims of this study were to characterize the genetic diversity and the phylogeography of HHV-8 in two distant geographic regions of Argentina, and to establish potential associations with p...
Source: Infection, Genetics and Evolution - September 2, 2020 Category: Genetics & Stem Cells Authors: Hulaniuk ML, Mojsiejczuk L, Jauk F, Remondegui C, Mammana L, Bouzas MB, Zapiola I, Ferro MV, Ajalla C, Blejer J, Alter A, Acevedo ME, Rodríguez E, Fernández R, Bartoli S, Volonteri V, Kohan D, Elsner B, Bürgesser MV, Reynaud AL, Sánchez M, González C Tags: Infect Genet Evol Source Type: research

Identification of a novel hantavirus strain in the root vole (Microtus oeconomus) in Lithuania, Eastern Europe.
In conclusion, the detection of Rusne virus RNA in multiple root voles at the same trapping site during three years and its absence in sympatric field voles suggests root voles as the reservoir host of this novel virus. Future investigations should evaluate host association of TRAV, TATV, Kielder virus and the novel Rusne virus and their evolutionary relationships. PMID: 32890767 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - September 2, 2020 Category: Genetics & Stem Cells Authors: Drewes S, Jeske K, Straková P, Balčiauskas L, Ryll R, Balčiauskienė L, Kohlhause D, Schnidrig GA, Hiltbrunner M, Špakova A, Insodaitė R, Petraitytė-Burneikienė R, Heckel G, Ulrich RG Tags: Infect Genet Evol Source Type: research

Genome based evolutionary lineage of SARS-CoV-2 towards the development of novel chimeric vaccine.
Abstract The present study aimed to predict a novel chimeric vaccine by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein, membrane protein, envelope protein and nucleocapsid protein were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were gen...
Source: Infection, Genetics and Evolution - September 1, 2020 Category: Genetics & Stem Cells Authors: Akhand MRN, Azim KF, Hoque SF, Moli MA, Joy BD, Akter H, Afif IK, Ahmed N, Hasan M Tags: Infect Genet Evol Source Type: research

Inferring the genetic variability in Indian SARS-CoV-2 genomes using consensus of multiple sequence alignment techniques.
Abstract Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a threat to the human population and has created a worldwide pandemic. Daily thousands of people are getting affected by the SARS-CoV-2 virus; India being no exception. In this situation, there is no doubt that vaccine is the primary prevention strategy to contain the wave of COVID-19 pandemic. In this regard, genome-wide analysis of SARS-CoV-2 is important to understand its genetical variability. This has motivated us to analyse the 566 Indian SARS-CoV-2 sequences using multiple sequence alignment techniques viz. ClustalW, MUSCLE, ClustalO a...
Source: Infection, Genetics and Evolution - September 1, 2020 Category: Genetics & Stem Cells Authors: Saha I, Ghosh N, Maity D, Sharma N, Mitra K Tags: Infect Genet Evol Source Type: research

NS1-based DNA vaccination via in vivo electroporation confers mouse protective immunity against ZIKV challenge.
Abstract The recent pandemic of Zika virus (ZIKV) infections highlights the urgent need for the development of a safe and efficacious ZIKV vaccine. We previously demonstrated that robust humoral and cellular immunity was elicited in BALB/c mice by ZIKV DNA vaccine encoding the precursor membrane (prM) and envelope (E) proteins while the protective efficacies were not evaluated against ZIKV challenge. To further explore the protective immunity elicited by various targets of ZIKV, we constructed a novel DNA-based vaccine expressing nonstructural protein 1 (NS1), named as VRC-NS1, and evaluated and compared immune re...
Source: Infection, Genetics and Evolution - August 31, 2020 Category: Genetics & Stem Cells Authors: Zhan Y, Pang Z, Du Y, Wang W, Yang Y, Wang W, Gao GF, Huang B, Deng Y, Tan W Tags: Infect Genet Evol Source Type: research

Emergence of high-risk multidrug-resistant Enterococcus faecalis CC2 (ST181) and CC87 (ST28) causing healthcare-associated infections in India.
This study aimed to establish the epidemiology and clonal composition of 134 clinical E. faecalis isolates and to link molecular typing data with antimicrobial resistance and virulence determinants. All isolates were identified by conventional methods and confirmed by PCR (16srRNA and ddl gene of E. faecalis) in 5 years. Disk diffusion test performed on all strains. We screened all E. faecalis for aac(6')-aph(2″), vanA, and vanB resistance genes, and aggregation substance-asa1, cytolysin-cylA, collagen-binding protein-ace, enterococcal surface protein-esp, gelatinase-gelE, and hyaluronidase-hyl virulence genes by P...
Source: Infection, Genetics and Evolution - August 30, 2020 Category: Genetics & Stem Cells Authors: Rao C, Dhawan B, Vishnubhatla S, Kapil A, Das B, Sood S Tags: Infect Genet Evol Source Type: research

Novel association of genetic variants in non-coding regulatory regions with HIV-1 infection.
Abstract Host genetic variability interplays with the environment and variegating viral factors to determine the outcome in HIV-1/AIDS. Several GWAS studies have reported that genetic heterogeneity of individuals leads to differential HIV susceptibility. Proxy SNPs that are in Linkage Disequilibrium to the GWAS SNPs could be important targets in HIV pathogenesis and need to be analyzed further for their potential regulatory role. Current study thus aimed to identify novel proxy SNPs that may play a critical role in HIV susceptibility and disease progression. 372 SNPs, associated with HIV-1/AIDS pathogenesis, were ...
Source: Infection, Genetics and Evolution - August 27, 2020 Category: Genetics & Stem Cells Authors: Waqar W, Altaf S, Nazir S, Javed A Tags: Infect Genet Evol Source Type: research

Developing and quality testing of microsatellite loci for four species of Glossina.
;s T Abstract Microsatellite loci still represent valuable resources for the study of the population biology of non-model organisms. Discovering or adapting new suitable microsatellite markers in species of interest still represents a useful task, especially so for non-model organisms as tsetse flies (genus Glossina), which remain a serious threat to the health of humans and animals in sub-Saharan Africa. In this paper, we present the development of new microsatellite loci for four species of Glossina: two from the Morsitans group, G. morsitans morsitans (Gmm) from Zimbabwe, G. pallidipes (Gpalli) from Tanzania; a...
Source: Infection, Genetics and Evolution - August 27, 2020 Category: Genetics & Stem Cells Authors: Ravel S, Sere M, Manangwa O, Kagbadouno M, Mahamat MH, Shereni W, Okeyo WA, Argiles-Herrero R, De Meeûs T Tags: Infect Genet Evol Source Type: research

First whole genome sequence of Peanalcaligenes suwonensis bearing blaVIM-5 Metallo- β-lactamase: A clinical isolate responsible for acute gastroenteritis.
First whole genome sequence of Peanalcaligenes suwonensis bearing blaVIM-5 Metallo-β-lactamase: A clinical isolate responsible for acute gastroenteritis. Infect Genet Evol. 2020 Aug 26;:104513 Authors: Olowo-Okere A, Ibrahim YKE, Olayinka BO, Ehinmidu JO, Mohammed Y, Nabti LZ, Rolain JM, Diene SM Abstract Carbapenemase-producing Alcaligenes species has been described in only few studies, with none so far from the African continent. Here, we report the whole genome sequence of Peanalcaligenes suwonensis bearing blaVIM-5 metallo-β-lactamase and first detection of carbapenemase producing Alcali...
Source: Infection, Genetics and Evolution - August 26, 2020 Category: Genetics & Stem Cells Authors: Olowo-Okere A, Ibrahim YKE, Olayinka BO, Ehinmidu JO, Mohammed Y, Nabti LZ, Rolain JM, Diene SM Tags: Infect Genet Evol Source Type: research

Possible transmission of Strongyloides fuelleborni between working Southern pig-tailed macaques (Macaca nemestrina) and their owners in Southern Thailand: Molecular identification and diversity.
Abstract Human strongyloidiasis is caused by Strongyloides stercoralis, S. fuelleborni fuelleborni and Strongyloides f. kellyi. Strongyloides fuelleborni is a soil-transmitted nematode parasite typically infecting non-human primates. The southern pig-tailed macaque (Macaca nemestrina) is distributed throughout the southern part of Thailand and could be a source of zoonotic transmission of this nematode. Here, we extracted DNA from Strongyloides species cultured from the feces of southern pig-tailed macaques and their owners. Using PCR and sequencing of the extracted DNA, we compared the nucleotide sequences of the...
Source: Infection, Genetics and Evolution - August 26, 2020 Category: Genetics & Stem Cells Authors: Janwan P, Rodpai R, Intapan PM, Sanpool O, Tourtip S, Maleewong W, Thanchomnang T Tags: Infect Genet Evol Source Type: research

Differences of inflammatory and non-inflammatory indicators in Coronavirus disease-19 (COVID-19) with different severity.
Abstract Background A variety of inflammatory and non-inflammatory indicators were increased in severe and critical Coronavirus disease-19 (COVID-19) and some of them were used to evaluate the severity and predict prognosis of community-acquired pneumonia. The aim of this study was to investigate the association of these indicators in COVID-19 with different severity. Methods Clinical data of 46 patients with severe COVID-19 and 31 patients with critical COVID-19 were collected. The general characteristics and comorbidities of the patients were retrospectively analyzed. The initial and peak concentrations of serum...
Source: Infection, Genetics and Evolution - August 25, 2020 Category: Genetics & Stem Cells Authors: Wang M, Zhu Q, Fu J, Liu L, Xiao M, Du Y Tags: Infect Genet Evol Source Type: research

Chemokine receptor gene polymorphisms and COVID-19: Could knowledge gained from HIV/AIDS be important?
Abstract Emerging results indicate that an uncontrolled host immune response, leading to a life-threatening condition called cytokine release syndrome (also termed "cytokine storm"), is the major driver of pathology in severe COVID-19. In this pandemic, considerable effort is being focused on identifying host genomic factors that increase susceptibility or resistance to the complications of COVID-19 and translating these findings to improved patient care. In this regard, the chemokine receptor-ligand nexus has been reported as potentially important in severe COVID-19 disease pathogenesis and its treatmen...
Source: Infection, Genetics and Evolution - August 25, 2020 Category: Genetics & Stem Cells Authors: Mehlotra RK Tags: Infect Genet Evol Source Type: research

A survey of genetic variants in SARS-CoV-2 interacting domains of ACE2, TMPRSS2 and TLR3/7/8 across populations.
Abstract The COVID-19 pandemic highlighted healthcare disparities in multiple countries. As such morbidity and mortality vary significantly around the globe between populations and ethnic groups. Underlying medical conditions and environmental factors contribute higher incidence in some populations and a genetic predisposition may play a role for severe cases with respiratory failure. Here we investigated whether genetic variation in the key genes for viral entry to host cells-ACE2 and TMPRSS2-and sensing of viral genomic RNAs (i.e., TLR3/7/8) could explain the variation in incidence across diverse ethnic groups. ...
Source: Infection, Genetics and Evolution - August 25, 2020 Category: Genetics & Stem Cells Authors: Lee IH, Lee JW, Kong SW Tags: Infect Genet Evol Source Type: research

Intrinsic disorder perspective of an interplay between the renin-angiotensin-aldosterone system and SARS-CoV-2.
Abstract The novel severe acute respiratory syndrome (SARS) coronavirus SARS-CoV-2 walks the planet causing the rapid spread of the CoV disease 2019 (COVID-19) that has especially deleterious consequences for the patients with underlying cardiovascular diseases (CVDs). Entry of the SARS-CoV-2 into the host cell involves interaction of the virus (via the receptor-binding domain (RBD) of its spike glycoprotein) with the membrane-bound form of angiotensin-converting enzyme 2 (ACE2) followed by the virus-ACE2 complex internalization by the cell. Since ACE2 is expressed in various tissues, such as brain, gut, heart, ki...
Source: Infection, Genetics and Evolution - August 24, 2020 Category: Genetics & Stem Cells Authors: Elrashdy F, Redwan EM, Uversky VN Tags: Infect Genet Evol Source Type: research

Heterologous expression of the Salmonella enterica serovar Paratyphi A stk fimbrial operon suggests a potential for repeat sequence-mediated low-frequency phase variation.
In this study, BlastN-based interrogation of the NCBI bacterial genome database and PCR investigation of Salmonella serovars have shown that the S. Paratyphi A stkF gene and/or the whole stk fimbrial gene cluster is present in about ~30% of S. enterica serovars investigated up to date. Furthermore, bioinformatics and phenotypic characterization have revealed that the stk fimbrial operon belongs to the chaperone/usher-γ4- fimbrial clade and that it encodes a mannose-sensitive hemagglutinating fimbrial structure. The latter trait is typical of type 1 fimbriae, in which fimbrial phase variation is common. The observed i...
Source: Infection, Genetics and Evolution - August 21, 2020 Category: Genetics & Stem Cells Authors: Tawfick MM, Rosser A, Rajakumar K Tags: Infect Genet Evol Source Type: research

The effect of Staphylococcus aureus on the antibiotic resistance and pathogenicity of Pseudomonas aeruginosa based on crc gene as a metabolism regulator: An in vitro wound model study.
CONCLUSION: In polymicrobial wound infection, Staphylococcus aureus plays a vital role in the metabolic changes of Pseudomonas aeruginosa. However, the levels of antibiotic susceptibility and pathogenicity of Pseudomonas aeruginosa also changed due to metabolism. PMID: 32835876 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - August 21, 2020 Category: Genetics & Stem Cells Authors: Dehbashi S, Pourmand MR, Alikhani MY, Asl SS, Arabestani MR Tags: Infect Genet Evol Source Type: research

The first months of COVID-19 in Madagascar.
Abstract Using the officially published data and aware of the uncertain source and insufficient number of samples, we present a first and (for the moment) unique attempt to study the first two months spread of the pandemic COVID-19 in Madagascar. The approach has been tested by predicting the number of contaminated persons for the next week after fitting the inputs data collected within 7 or 15 days using standard least χ2-fit method. Encouraged by this first test, we study systematically during 67 days, 1-2 weeks new data and predict the contaminated persons for the coming week. We find that the first m...
Source: Infection, Genetics and Evolution - August 20, 2020 Category: Genetics & Stem Cells Authors: Narison S Tags: Infect Genet Evol Source Type: research

Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs.
Abstract Isolation and cultivation of wild-type viruses in model organism cells or tissues is standard practice in virology. Oftentimes, the virus host species is distantly related to the species from which the culture system was developed. Thus, virus culture in these tissues and cells basically constitutes a host jump, which can lead to genomic changes through genetic drift and/or adaptation to the culture system. We directly sequenced 70 avian influenza virus (Orthomyxoviridae) genomes from oropharyngeal/cloacal swabs collected from wild bird species and paired virus isolates propagated from the same samples fo...
Source: Infection, Genetics and Evolution - August 19, 2020 Category: Genetics & Stem Cells Authors: Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Pierce C, Abdo Z Tags: Infect Genet Evol Source Type: research

Molecular characterization of Staphylococcus aureus complex from fomites in Nigeria.
In this study, we describe the S. aureus complex from inanimate surfaces in Nigeria. Fomite samples in Obafemi Awolowo University were initially screened for S. aureus and species differentiation was determined by MALDI-TOF, PCR of the S. aureus specific thermonuclease and the nonribosomal peptide synthetase genes. Characterization of the isolates was based on antimicrobial susceptibility, spa typing, multilocus sequence typing and virulence gene detection (lukS/lukF-PV, chp, sak, scn). Whole-genome sequencing was done for selected isolates. Of the 239 fomites samples, 14 S. aureus and two S. schweitzeri isolates were id...
Source: Infection, Genetics and Evolution - August 14, 2020 Category: Genetics & Stem Cells Authors: Shittu AO, Mellmann A, Schaumburg F Tags: Infect Genet Evol Source Type: research

Analysis of sulphadoxine-pyrimethamine resistance-associated mutations in Plasmodium falciparum isolates obtained from asymptomatic pregnant women in Ogun State, Southwest Nigeria.
This study determined the prevalence of pfdhfr and pfdhps mutations in isolates obtained from pregnant women with asymptomatic P. falciparum infection in Nigerian. Additionally, P. falciparum genetic diversity and multiplicity of infection (MOI) was assessed by genotyping the P. falciparum merozoite surface Protein 1 and 2 (pfmsp-1 and pfmsp-2) genes. The pfdhfr and pfdhps were genotyped by direct sequencing, and the pfmsp-1 and pfmsp-2 fragment analysis by polymerase chain reaction was used to determine P. falciparum genetic diversity. Of the 406 pregnant women recruited, 123 had P. falciparum infection by PCR, and of the...
Source: Infection, Genetics and Evolution - August 14, 2020 Category: Genetics & Stem Cells Authors: Fagbemi KA, Adebusuyi SA, Nderu D, Adedokun SA, Pallerla SR, Amoo AOJ, Thomas BN, Velavan TP, Ojurongbe O Tags: Infect Genet Evol Source Type: research

From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses.
Abstract Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) - diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes repaid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target ...
Source: Infection, Genetics and Evolution - August 13, 2020 Category: Genetics & Stem Cells Authors: Kirtipal N, Bharadwaj S, Kang SG Tags: Infect Genet Evol Source Type: research

Going back to the roots: Evaluating Bayesian phylogeographic models with discrete trait uncertainty.
Abstract Phylogeography is a popular way to analyze virus sequences annotated with discrete, epidemiologically-relevant, trait data. For applied public health surveillance, a key quantity of interest is often the state at the root of the inferred phylogeny. In epidemiological terms, this represents the geographic origin of the observed outbreak. Since determining the origin of an outbreak is often critical for public health intervention, it is prudent to understand how well phylogeographic models perform this root state classification task under various analytical scenarios. Specifically, we investigate how discre...
Source: Infection, Genetics and Evolution - August 12, 2020 Category: Genetics & Stem Cells Authors: Vaiente MA, Scotch M Tags: Infect Genet Evol Source Type: research

Toward integrative 'omics of the barber's pole worm and related parasitic nematodes.
Abstract Advances in nucleic acid sequencing, mass spectrometry and computational biology have facilitated the identification, annotation and analysis of genes, transcripts, proteins and metabolites in model nematodes (Caenorhabditis elegans and Pristionchus pacificus) and socioeconomically important parasitic nematodes (Clades I, III, IV and V). Significant progress has been made in genomics and transcriptomics as well as in the proteomics and lipidomics of Haemonchus contortus (the barber's pole worm) - one of the most pathogenic representatives of the order Strongylida. Here, we review salient aspects of genomi...
Source: Infection, Genetics and Evolution - August 11, 2020 Category: Genetics & Stem Cells Authors: Ma G, Gasser RB, Wang T, Korhonen PK, Young ND Tags: Infect Genet Evol Source Type: research

Genomic features of an Escherichia coli ST156 strain harboring chromosome-located mcr-1 and plasmid-mediated blaNDM-5.
This study reports the emergence of an E. coli strain GZEC065 isolated from blood sample of a patient in China with both chromosome-located mcr-1 and plasmid-mediated blaNDM-5 genes. Antimicrobial susceptibility testing showed that GZEC065 was resistant to most tested antimicrobials, including imipenem and polymyxin B. S1-nuclease-pulsed-field gel electrophoresis, Southern blotting analysis and conjugation assay was performed to determine the location and conjugative ability of mcr-1 and blaNDM-5 genes. Whole genome sequencing and analysis showed that GZEC065 belonged to sequence type ST156 and contained three different pl...
Source: Infection, Genetics and Evolution - August 10, 2020 Category: Genetics & Stem Cells Authors: Lin Y, Yang L, Lu L, Wang K, Li J, Li P, Liu Y, Liu X, Li P, Song H Tags: Infect Genet Evol Source Type: research