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Infection, Genetics and Evolution

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https://www.readbyqxmd.com/read/29782933/whole-genome-sequencing-and-analyses-identify-high-genetic-heterogeneity-and-diversity-of-rotavirus-genotype-p-6-strains-circulating-in-africa
#1
Martin M Nyaga, Yi Tan, Mapaseka L Seheri, Rebecca A Halpin, Asmik Akopov, Karla M Stucker, Nadia B Fedorova, Susmita Shrivastava, A Duncan Steele, Jason M Mwenda, Brett E Pickett, Suman R Das, M Jeffery Mphahlele
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank...
May 18, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29778768/prevalence-of-g6pd-deficiency-and-associated-haematological-parameters-in-children-from-botswana
#2
Thato Motshoge, Grace Ababio, Larysa Aleksenko, Sajini Souda, Charles Waithaka Muthoga, Naledi Mutukwa, Leabaneng Tawe, Pleasure Ramatlho, Lesego Gabaitiri, Simon Chihanga, Tjantilili Mosweunyane, Shimeles Hamda, Kentse Moakofhi, Davies Ntebela, Elias Peloewetse, Loeto Mazhani, Jeffrey M Pernica, John Read, Isaac K Quaye, Giacomo Maria Paganotti
Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency is commonly seen in malaria endemic areas as it is known to confer a selective advantage against malaria. Recently, we reported a high proportion of asymptomatic reservoir of Plasmodium vivax in Botswana, that calls for intervention with primaquine to achieve radical cure of vivax malaria. Considering that individuals with this enzyme deficiency are at risk of haemolysis following primaquine treatment, assessment of the population for the relative frequency of G6PD deficiency is imperative...
May 17, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29778767/molecular-morphological-and-experimental-assessment-of-the-life-cycle-of-posthodiplostomum-nanum-trematoda-diplostomidae-from-brazil-with-phylogenetic-evidence-of-the-paraphyly-of-the-genus-posthodiplostomum-dubois-1936
#3
Danimar López-Hernández, Sean A Locke, Alan Lane de Melo, Élida Mara Leite Rabelo, Hudson Alves Pinto
Species of the genus Posthodiplostomum are intestinal parasites of piscivorous birds with worldwide distribution. Recent molecular surveys have focused on developmental stages from vertebrate hosts, with few sequences from larvae found in molluscs. Moreover, most published molecular data are from collections in North America, Europe and Asia, and there are no data for South American species. In the present study, cercariae found in the freshwater limpet Gundlachia ticaga from Brazil were used for morphological, experimental and molecular studies...
May 17, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29778766/first-genetic-characterization-of-usutu-virus-from-culex-pipiens-mosquitoes-serbia-2014
#4
Gábor Kemenesi, Dóra Buzás, Brigitta Zana, Kornélia Kurucz, Bosiljka Krtinic, Anett Kepner, Fanni Földes, Ferenc Jakab
Since its first appearance in Europe, Usutu virus (USUV) diverged to several different genetic lineages. The virus was reported to date from multiple countries across Europe (Hungary, Italy, Switzerland, Spain, Germany, Czech Republic and Belgium). Considering the more frequently published impact of the virus on humans it is crucial to investigate locally circulating genetic variants and trace its evolution. We retrospectively analyzed mosquito samples from Serbia Vojvodina region, collected during 2014. In this study we report the results of the screening of 23,753 female mosquitoes (753 pools) for USUV-specific nucleic-acid...
May 17, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29772399/characterization-of-a-g10p-14-rotavirus-strain-from-a-diarrheic-child-in-thailand-evidence-for-bovine-to-human-zoonotic-transmission
#5
Ratana Tacharoenmuang, Satoshi Komoto, Ratigorn Guntapong, Tomihiko Ide, Phakapun Singchai, Sompong Upachai, Saori Fukuda, Yumika Yoshida, Takayuki Murata, Tetsushi Yoshikawa, Kriangsak Ruchusatsawat, Kazushi Motomura, Naokazu Takeda, Somchai Sangkitporn, Koki Taniguchi
An unusual rotavirus strain, DB2015-066 with the G10P[14] genotype (RVA/Human-wt/THA/dB2015-066/2015/G10P[14]), was detected in a stool sample from a child hospitalized with acute gastroenteritis in Thailand. Here, we sequenced and characterized the full-genome of the strain DB2015-066. On whole genomic analysis, strain DB2015-066 was shown to have a unique genotype constellation: G10-P[14]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The backbone genes of this strain (I2-R2-C2-M2-A3-N2-T6-E2-H3) are commonly found in rotavirus strains from artiodactyls such as cattle...
May 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29772398/molecular-epidemiology-and-characterization-of-picobirnaviruses-in-small-ruminant-populations-in-india
#6
Yashpal Singh Malik, Shubhankar Sircar, Kuldeep Dhama, Rashmi Singh, Souvik Ghosh, Krisztián Bányai, Anastasia N Vlasova, Touil Nadia, Raj Kumar Singh
Picobirnavirus (PBV) is recognized as a putative cause of diarrhea and respiratory illnesses. Although PBV has been reported in several mammalian (including humans) and avian host species, data pertaining to its presence in small ruminants are limited. We report, here, PBV infection in small ruminants (ovine and caprine), in India. From January 2015 to December 2017, 400 samples were tested for the presence of PBV, using an RT-PCR assay specific for the genome segment-2. The overall rate of PBV infection was 35...
May 14, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29763671/searching-for-signals-of-recent-natural-selection-in-genes-of-the-innate-immune-response-ancient-dna-study
#7
Magda Lewandowska, Krystyna Jędrychowska-Dańska, Tomasz Płoszaj, Piotr Witas, Alicja Zamerska, Hanna Mańkowska-Pliszka, Henryk W Witas
The last decade has seen sharp progress in the field of human evolutionary genetics and a great amount of genetic evidence of natural selection has been provided so far. Since host-pathogen co-evolution is difficult to trace due to the polygenic nature of human susceptibility to microbial diseases, of particular interest is any signal of natural selection in response to the strong selective pressure exerted by pathogens. Analysis of ancient DNA allows for the direct insight into changes of a gene pool content over time and enables monitoring allele frequency fluctuations...
May 12, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29758354/isaba1-and-tn6168-acquisition-by-natural-transformation-leads-to-third-generation-cephalosporins-resistance-in-acinetobacter-baumannii
#8
Sara Domingues, Natasha Rosário, Hadhemi Ben Cheikh, Gabriela Jorge Da Silva
Acinetobacter baumannii has intrinsic beta-lactamase genes, namely ampC and blaOXA-51 -like, which are only strongly expressed when the ISAba1 insertion sequence is upstream the 5' end of the genes. A second ampC gene has also been identified in some clinical A. baumannii strains. The increased expression of these genes leads to resistance to beta-lactams, including third-generation cephalosporins and/or carbapenems. The aim of this work was to assess the involvement of natural transformation in the transfer of chromosomal ampC-associated mobile elements, and related changes in the resistance profile of recipient cells...
May 11, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29753903/detection-of-nineteen-enteric-viruses-in-raw-sewage-in-japan
#9
Aksara Thongprachum, Tsuguto Fujimoto, Sayaka Takanashi, Hiroyuki Saito, Shoko Okitsu, Hiroyuki Shimizu, Pattara Khamrin, Niwat Maneekarn, Satoshi Hayakawa, Hiroshi Ushijima
One-year surveillance for enteric viruses in raw sewage was conducted in Kansai area, central part of Japan from July 2015 to June 2016. The raw sewage was collected monthly from an inlet polluted pool and was concentrated by polyethylene glycol (PEG) precipitation. Twelve sewage samples were screened for nineteen kinds of enteric viruses by using RT-PCR method and further analyzed by nucleotide sequencing. Twelve enteric viruses were found in the investigative sewage samples. Rotavirus A and norovirus GI and GII with several genotypes were detected all year round...
May 10, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29753024/chemical-system-biology-based-molecular-interactions-to-identify-inhibitors-against-q151m-mutant-of-hiv-1-reverse-transcriptase
#10
Rajan Kumar Pandey, Drista Sharma, Rupal Ojha, Tarun Kumar Bhatt, Vijay Kumar Prajapati
The emergence of mutations leading to drug resistance is the main cause of therapeutic failure in the human HIV infection. Chemical system biology approach has drawn great attention to discover new antiretroviral hits with high efficacy and negligible toxicity, which can be used as a prerequisite for HIV drug resistance global action plan 2017-21. To discover potential hits, we docked 49 antiretroviral analogs (n = 6294) against HIV-1 reverse transcriptase Q151M mutant & its wild-type form and narrow downed their number in three sequential modes of docking using Schrödinger suite...
May 9, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29751196/the-significance-role-of-regulatory-t-cells-in-the-persistence-of-infections-by-intracellular-bacteria
#11
REVIEW
Parisa Sabbagh, Ahmad Karkhah, Hamid Reza Nouri, Mostafa Javanian, Soheil Ebrahimpour
Regulatory T cells (Treg cells), are considered as effective immune cells playing a key role in immune response during cancers, autoimmune and infectious diseases. Regulatory T lymphocytes are divided into two main subgroups: natural Treg cells that generated during maturation in the thymus and have the suppressive activity that is critical for the establishment and maintenance of homeostasis in the body and induced Treg cells (iTreg) that are originated from naive T cells following the self-antigen recognition...
May 8, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29751195/high-resolution-melting-pcr-analysis-for-rapid-genotyping-of-burkholderia-mallei
#12
G Girault, P Wattiau, M Saqib, B Martin, F Vorimore, H Singha, M Engelsma, H J Roest, S Spicic, R Grunow, N Vicari, S C J De Keersmaecker, N H C Roosens, M Fabbi, B N Tripathi, S Zientara, N Madani, K Laroucau
Burkholderia (B.) mallei is the causative agent of glanders. A previous work conducted on single-nucleotide polymorphisms (SNP) extracted from the whole genome sequences of 45 B. mallei isolates identified 3 lineages for this species. In this study, we designed a high-resolution melting (HRM) method for the screening of 15 phylogenetically informative SNPs within the genome of B. mallei that subtype the species into 3 lineages and 12 branches/sub-branches/groups. The present results demonstrate that SNP-based genotyping represent an interesting approach for the molecular epidemiology analysis of B...
May 8, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29733983/evolutionary-dynamics-of-hepatitis-c-virus-in-a-chronic-hiv-co-infected-patient-and-its-correlation-with-the-immune-status
#13
Andrés Carlos Alberto Culasso, María Cecilia Monzani, Patricia Baré, Rodolfo Hector Campos
The HCV evolutionary dynamics play a key role in the infection onset, maintenance of chronicity, pathogenicity, and drug resistance variants fixation, and are thought to be one of the main caveats in the development of an effective vaccine. Previous studies in HCV/HIV co-infected patients suggest that a decline in the immune status is related with increases in the HCV intra-host genetic diversity. However, these findings are based on single point sequence diversity measures or coalescence analyses in several virus-host interactions...
May 4, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29730275/comparative-ecology-of-escherichia-coli-in-endangered-australian-sea-lion-neophoca-cinerea-pups
#14
Mariel Fulham, Michelle Power, Rachael Gray
The dissemination of human-associated bacteria into the marine environment has the potential to expose wildlife populations to atypical microbes that can alter the composition of the gut microbiome or act as pathogens. The objective of the study was to determine whether endangered Australian sea lion (Neophoca cinerea) pups from two South Australian colonies, Seal Bay, Kangaroo Island and Dangerous Reef, Spencer Gulf, have been colonised by human-associated Escherichia coli. Faecal samples (n = 111) were collected to isolate E...
May 3, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29729386/global-analysis-of-plasmodium-falciparum-histidine-rich-protein-2-pfhrp2-and-pfhrp3-gene-deletions-using-whole-genome-sequencing-data-and-meta-analysis
#15
Nuno Sepúlveda, Jody Phelan, Ernest Diez-Benavente, Susana Campino, Taane G Clark, Heidi Hopkins, Colin Sutherland, Chris J Drakeley, Khalid B Beshir
Many rapid diagnostic tests (RDT) used on suspected malaria cases are based on the detection of the protein encoded by the Plasmodium falciparum histidine-rich protein-2 (pfhrp2) gene, which shares a high sequence homology with pfhrp3 in the 3D7 reference genome. Parasite isolates showing pfhrp2 and pfhrp3 gene deletions have been emerging over the years, but a comprehensive genetic analysis of these variants is still lacking. With this purpose, genomic data from experimental P. falciparum genetic crosses between different laboratory lines (3D7, HB3, DD2, 7G8 and GB4) were first analysed (n = 98)...
May 2, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29715528/functional-analysis-of-duck-goose-and-ostrich-2-5-oligoadenylate-synthetase
#16
Hassan T Tag-El-Din-Hassan, Masami Morimatsu, Takashi Agui
Up-to-date the flavivirus infection in avian taxa is not clearly defined. Several reports have demonstrated that many viruses belonging to Flaviviridae may cause diseases in poultry species; however, the susceptibility of other avian species is variable and still unclear. In human and mice, the 2'-5'-oligoadenylate synthetase (OAS) proteins are associated with resistance to the flavivirus infection as well as other virus infections. However, the avian OAS proteins are rarely studied. In our previous studies, we confirmed that the chicken OAS-like protein (chOASL) expressed OAS-enzymatic activity (the classical OAS/RNase L-dependent pathway) as well as the anti-flavivirus activity (the putative OAS/RNase L-independent pathway)...
April 28, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29715527/correlation-of-cd81-and-scarb1-polymorphisms-on-virological-responses-in-iranian-patients-with-chronic-hepatitis-c-virus-genotype-1
#17
Milad Nafari, Shiva Irani, Farzam Vaziri, Safoora Gharibzadeh, Mohammad Khazeni, Fatemeh Rahimi Jamnani, Seyed Davar Siadat, Abolfazl Fateh
The cluster of differentiation 81 (CD81) and scavenger receptor class B member 1 (SCARB1) plays an important role in the entry of hepatitis C virus (HCV). We assessed the correlation of five single nucleotide polymorphisms (SNPs) of CD81 (rs800136, rs2651842, rs2522012, rs800146, and rs708564) and SCARB1 rs10846744 polymorphisms with treatment responses in 395 treatment-naïve patients with chronic HCV (CHC) genotype 1 treated with pegylated interferon-α and ribavirin (pegIFN-α/RBV). The frequency of rapid virologic response (RVR), complete early virologic response (cEVR) and sustained virologic response (SVR) were 57...
April 28, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29715526/innate-immune-gene-polymorphisms-and-their-association-with-neonatal-sepsis
#18
Snehal L Martin, Saumil Desai, Ruchi Nanavati, Roshan B Colah, Kanjaksha Ghosh, Malay B Mukherjee
No abstract text is available yet for this article.
April 28, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29709693/metagenomic-identification-genetic-characterization-and-genotyping-of-porcine-sapoviruses
#19
Jingjiao Li, Wen Zhang, Li Cui, Quan Shen, Xiuguo Hua
Sapoviruses (SaVs), belonging to the genus Sapovirus of the family Caliciviridae, were known as the enteric pathogen causing acute gastroenteritis. SaVs have been detected in humans and several animals including pigs and some porcine SaVs showed close sequence relationship with human strains suggesting the possibility of interspecies transmission. Here, we sequenced the genomes of two porcine SaVs (with strain names of p38 and SH1703) using the metagenomic analyses and traditional RT-PCR methods. Phylogenetic trees were constructed based on the complete genome, the full-length VP 1 nucleotide and amino acid sequences to group those two strains...
April 27, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29706488/corrigendum-to-phylogenetic-analysis-of-a-newfound-bat-borne-hantavirus-supports-a-laurasiatherian-host-association-for-ancestral-mammalian-hantaviruses-infect-genet-evol-41-2016-113-119
#20
Peter T Witkowski, Jan F Drexler, René Kallies, Martina Ličková, Silvia Bokorová, Gael D Maganga, Tomáš Szemes, Eric M Leroy, Detlev H Krüger, Christian Drosten, Boris Klempa
No abstract text is available yet for this article.
April 26, 2018: Infection, Genetics and Evolution
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