Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs.
In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence" hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatmen...
Source: Infection, Genetics and Evolution - January 18, 2021 Category: Genetics & Stem Cells Authors: Sengupta A, Hassan SS, Choudhury PP Tags: Infect Genet Evol Source Type: research

Molecular detection and characterization of norovirus in asymptomatic food handlers in Chiang Mai, Thailand.
In conclusion, our data indicated that the patient was infected with GII.3 NoV and the virus was not directly transmitted to the patient by asymptomatic food handlers instead it might be transmitted by consumption of NoV-contaminated food provided by the restaurant. In addition, the existence of NoV in asymptomatic food handlers could be a potential source of NoV transmission. Therefore, strict adherence to hand hygiene practices should be reinforced to prevent foodborne outbreaks. PMID: 33465494 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 16, 2021 Category: Genetics & Stem Cells Authors: Kumthip K, Khamrin P, Ushijima H, Maneekarn N Tags: Infect Genet Evol Source Type: research

Bats are key hosts in the radiation of mammal-associated Bartonella bacteria.
Abstract Bats are notorious reservoirs of several zoonotic diseases and may be uniquely tolerant of infection among mammals. Broad sampling has revealed the importance of bats in the diversification and spread of viruses and eukaryotes to other animal hosts. Vector-borne bacteria of the genus Bartonella are prevalent and diverse in mammals globally and recent surveys have revealed numerous Bartonella lineages in bats. We assembled a sequence database of Bartonella strains, consisting of nine genetic loci from 209 previously characterized Bartonella lineages and 121 new cultured isolates from bats, and used these d...
Source: Infection, Genetics and Evolution - January 11, 2021 Category: Genetics & Stem Cells Authors: McKee CD, Bai Y, Webb CT, Kosoy MY Tags: Infect Genet Evol Source Type: research

Assessment of eugenol inhibitory effect on biofilm formation and biofilm gene expression in methicillin resistant Staphylococcus aureus clinical isolates in Egypt.
In this study, the aim was to estimate the effect of eugenol on biofilms of MRSA through quantifying the level of gene expression of three genes (IcaA, IcaD and SarA) involved in biofilm development.. Fifty MRSA biofilm producers collected from the microbiology lab at Theodor Bilharz Research Institute were incubated with different concentrations of eugenol for 24 h. The minimum inhibitory concentration of eugenol (MIC) that eradicates the biofilms growth was detected. mRNA was extracted from all isolates before and after the application of eugenol at 0.5 x MIC, and then subjected to quantitative real-time PCR (qPCR). Re...
Source: Infection, Genetics and Evolution - January 11, 2021 Category: Genetics & Stem Cells Authors: El Far A, Samir S, El-Gebaly E, Taha NY, Fahmy EM, Diab TM, El-Shenawy A Tags: Infect Genet Evol Source Type: research

Population structure and genetic diversity of Triatoma longipennis (Usinger, 1939) (Heteroptera: Reduviidae: Triatominae) in Mexico.
In this study, the intra-specific relationships between different T. longipennis populations were analyzed from seven states in Mexico using mitochondrial cyt B as a marker. Our results show that the population of Jalisco was the most diverse, with the highest genetic and haplotypic variation (Hd = 0.978, π = 0.099 and θ = 0.079), even 25 times higher than some other populations analyzed. Heterogeneous migration and gene flow were observed without relation to their geographical distribution, that is, nearby populations may present high values of gene flow with low migration. In contrast, remote populat...
Source: Infection, Genetics and Evolution - January 11, 2021 Category: Genetics & Stem Cells Authors: Martinez-Hernandez F, Villalobos G, Martínez-Ibarra JA Tags: Infect Genet Evol Source Type: research

Molecular characteristics of subgroup J avian Leukosis virus isolated from yellow breeder chickens in Guangdong, China, during 2016-2019.
This study provides the latest data on the molecular characteristics of ALV-J, which will help to reveal the evolution trend of ALV-J and develop relevant prevention and control measures. PMID: 33444858 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 11, 2021 Category: Genetics & Stem Cells Authors: Liu P, Li L, Jiang Z, Yu Y, Chen X, Xiang Y, Chen J, Li Y, Cao W Tags: Infect Genet Evol Source Type: research

Weighted gene co-expression network analysis and drug-gene interaction bioinformatics uncover key genes associated with various presentations of malaria infection in African children and major drug candidates.
Abstract Malaria is a fatal parasitic disease with unelucidated pathogenetic mechanism. Herein, we aimed to uncover genes associated with different clinical aspects of malaria based on the GSE1124 dataset that is publicly accessible by using WGCNA. We obtained 16 co-expression modules and their correlations with clinical features. Using the MCODE tool, we identified THEM4, STYX, VPS36, LCOR, KIAA1143, EEA1, RAPGEF6, LOC439994, ZBTB33, PTPN22, ESCO1, and KLF3 as hub genes positively associated with Plasmodium falciparum infection (ASPF). These hub genes were involved in the biological processes of endosomal transpo...
Source: Infection, Genetics and Evolution - January 11, 2021 Category: Genetics & Stem Cells Authors: Nambou K, Nie X, Tong Y, Anakpa M Tags: Infect Genet Evol Source Type: research

Contrasting association of Helicobacter pylori oipA genotype with risk of peptic ulceration and gastric cancer.
Abstract Helicobacter pylori OipA (outer inflammatory protein A) is an outer membrane protein that involves in the binding and colonization of the bacterium in the stomach. The oipA status is associated with the risk of peptic ulcerations (PUs) and gastric cancer (GC) diseases. However, the association trend with PUs compared to GC is often different and highly challenging. We therefore aimed to determine the presence of this genotype in Iranian strains and assess its association with the risk of PUs and GC in a larger number of samples. A total of 319 strains were obtained from 172 patients with non-atrophic gast...
Source: Infection, Genetics and Evolution - January 10, 2021 Category: Genetics & Stem Cells Authors: Feili O, Bakhti SZ, Latifi-Navid S, Zahri S, Yazdanbod A Tags: Infect Genet Evol Source Type: research

Bioinformatics features and immunogenic epitopes of Echinococcus granulosus Myophilin as a promising target for vaccination against cystic echinococcosis.
Abstract Cystic echinococcosis (CE) is a neglected zoonosis especially in underdeveloped countries around the world. Hence, immunization strategies are beneficial to avert the infection. The present investigation was aimed to predict the primary biochemical characteristics of the EgMyophilin and its potential B-cell and human leukocyte antigen (HLA)-binding epitopes as a promising vaccine candidate. Different web servers were used to predict physico-chemical, antigenic and allergenic profiles, transmembrane domain, subcellular localization, post-translational modification (PTM) sites, secondary and 3D structure, t...
Source: Infection, Genetics and Evolution - January 9, 2021 Category: Genetics & Stem Cells Authors: Shams M, Javanmardi E, Nosrati MC, Ghasemi E, Shamsinia S, Yousefi A, Kordi B, Majidiani H, Nourmohammadi H Tags: Infect Genet Evol Source Type: research

Isolation and whole protein characterization of bovine RVA and RVB from Chinese calves.
Abstract Rotaviruses (RVs) account for severe diarrhea in children and young animals globally. In the current study, the fecal samples of diarrheic calves from a beef farm in Inner Mongolia were screened for RVA by ELISA and RT-PCR, followed by culture of three positive RVA samples in the MA-104 cell line. After 10 blind passages, cytopathic effects (CPE) appeared as detachment, granulation, and clustering of the inoculated cells. The virus isolates were identified by RT-PCR (VP6 gene RVA) and ESI-LC-MS/MS for whole protein sequencing. The protein sequences demonstrated the presence of two strains from species A r...
Source: Infection, Genetics and Evolution - January 9, 2021 Category: Genetics & Stem Cells Authors: Elkady G, Zhu J, Peng Q, Chen M, Liu X, Chen Y, Hu C, Chen H, Guo A Tags: Infect Genet Evol Source Type: research

The plasmidome of multidrug-resistant emergent Salmonella serovars isolated from poultry.
In conclusion, the multidrug-resistant plasmids identified in S. enterica serovar Schwarzengrund and Newport isolated from poultry show a variety of antibiotic resistance and heavy metal tolerance genes, providing advantages for the bacteria to survive under extremely unfavorable conditions. PMID: 33429069 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 8, 2021 Category: Genetics & Stem Cells Authors: Galetti R, Filho RACP, Ferreira JC, Varani AM, Sazinas P, Jelsbak L, Darini ALC Tags: Infect Genet Evol Source Type: research

Gastrointestinal parasite burden in 4th-5th c. AD Florence highlighted by microscopy and paleogenetics.
This study strongly pleads for a systematic integrative approach combining microscopy and aDNA in paleoparasitology. PMID: 33429070 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 8, 2021 Category: Genetics & Stem Cells Authors: Kévin R, Nicolas C, Elsa P, Paolo L, Pasquino P, Raffaella B, Matthieu LB Tags: Infect Genet Evol Source Type: research

Identification of SARS-CoV-2 CTL epitopes for development of a multivalent subunit vaccine for COVID-19.
Abstract An immunoinformatics-based approach was used to identify potential multivalent subunit CTL vaccine candidates for SARS-CoV-2. Criteria for computational screening included antigen processing, antigenicity, allergenicity, and toxicity. A total of 2604 epitopes were found to be strong binders to MHC class I molecules when analyzed using IEDB tools. Further testing for antigen processing yielded 826 peptides of which 451 were 9-mers that were analyzed for potential antigenicity. Antigenic properties were predicted for 102 of the 461 peptides. Further assessment for potential allergenicity and toxicity narrow...
Source: Infection, Genetics and Evolution - January 7, 2021 Category: Genetics & Stem Cells Authors: Rencilin CF, Rosy JC, Mohan M, Coico R, Sundar K Tags: Infect Genet Evol Source Type: research

Restricted genetic heterogeneity of the Plasmodium vivax transmission-blocking vaccine (TBV) candidate Pvs48/45 in a low transmission setting: Implications for the Plasmodium vivax malaria vaccine development.
Abstract Plasmodium vivax is the most widespread malaria species parasitizing humans outside Africa, with approximately 100 million cases reported per year. Most human cases of P. vivax are asymptomatic with low parasitemia, making active case detection-based elimination programme challenging and less effective. Despite the widespread distribution of P. vivax, no effective vaccines are currently available. Transmission blocking vaccines have recently emerged as potential vaccine candidates to reduce transmission rates to below the essential levels required for the maintenance of the parasite life cycle. Here, we d...
Source: Infection, Genetics and Evolution - January 6, 2021 Category: Genetics & Stem Cells Authors: Asali S, Raz A, Turki H, Mafakher L, Razmjou E, Solaymani-Mohammadi S Tags: Infect Genet Evol Source Type: research

Topological analysis for sequence variability: Case study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countriesvin comparison with SARS-CoV-1 and MERS-CoV.
Abstract The pandemic due to novel coronavirus, SARS-CoV-2 is a serious global concern now. More than thousand new COVID-19 infections are getting reported daily for this virus across the globe. Thus, the medical research communities are trying to find the remedy to restrict the spreading of this virus, while the vaccine development work is still under research in parallel. In such critical situation, not only the medical research community, but also the scientists in different fields like microbiology, pharmacy, bioinformatics and data science are also sharing effort to accelerate the process of vaccine developme...
Source: Infection, Genetics and Evolution - January 6, 2021 Category: Genetics & Stem Cells Authors: Sarkar JP, Saha I, Seal A, Maity D, Maulik U Tags: Infect Genet Evol Source Type: research

Arboviruses in the Astrakhan region of Russia for 2018 season: The development of multiplex PCR assays and analysis of mosquitoes, ticks, and human blood sera.
Abstract The Astrakhan region of Russia is endemic for the number of arboviruses. In this paper, we describe the results of the detection of the list of neglected arboviruses in the Astrakhan region for the 2018 season. For the purpose of the study in-house PCR assays for detection of 18 arboviruses have been developed and validated using arboviruses obtained from Russian State Collection of Viruses. Pools of ticks (n = 463) and mosquitoes (n = 312) as well as 420 samples of human patients sera have been collected and analyzed. Using developed multiplex real-time PCR assays we were able to detect RNA of ei...
Source: Infection, Genetics and Evolution - January 6, 2021 Category: Genetics & Stem Cells Authors: Nikiforova MA, Kuznetsova NA, Shchetinin AM, Butenko AM, Kozlova AA, Larichev VP, Vakalova EV, Azarian AR, Rubalsky OV, Bashkina OA, Tkachuk AP, Gushchin VA, Gintsburg AL Tags: Infect Genet Evol Source Type: research

The association of the heterogeneity of HBV reverse transcriptase quasispecies with antiviral efficacy after treatment with nucleos(t)ide analogues for 10  years.
The association of the heterogeneity of HBV reverse transcriptase quasispecies with antiviral efficacy after treatment with nucleos(t)ide analogues for 10 years. Infect Genet Evol. 2021 Jan 05;:104706 Authors: Zhou TC, Liu FW, Fan JH, Zhang SH, Lv SQ, Yu ZY, Zhang YM, Zhang L, Wei J Abstract To assess the heterogeneity of HBV reverse transcriptase (RT) quasispecies during 10 years of antiviral therapy and their association with antiviral efficacy. Nineteen patients with chronic hepatitis B (CHB) infection receiving nucleos(t)ide analogues (NAs) were enrolled. Based on the antiviral efficacy after ...
Source: Infection, Genetics and Evolution - January 5, 2021 Category: Genetics & Stem Cells Authors: Zhou TC, Liu FW, Fan JH, Zhang SH, Lv SQ, Yu ZY, Zhang YM, Zhang L, Wei J Tags: Infect Genet Evol Source Type: research

Discovery and genetic characterization of a novel orthonairovirus in Ixodes ricinus ticks from Danube Delta.
In this study, a collection of ticks obtained in 2016 directly from mammal and bird hosts from several rural and natural sites of Danube Delta was subjected to transcriptome sequencing and amplification assays. Vector surveillance revealed the presence of a novel orthonairovirus species, designated Sulina virus, in Ixodes ricinus ticks. Phylogenetic clustering of each viral protein consistently placed the new virus in the Orthonairovirus genus as a new genogroup closely related to Tamdy orthonairovirus, a genogroup comprising both pathogenic and tick-associated orthonairoviruses. The serological testing of engorged ticks a...
Source: Infection, Genetics and Evolution - January 5, 2021 Category: Genetics & Stem Cells Authors: Tomazatos A, von Possel R, Pekarek N, Holm T, Rieger T, Baum H, Bialonski A, Maranda I, Erdelyi-Molnár I, Spînu M, Lühken R, Jansen S, Emmerich P, Schmidt-Chanasit J, Cadar D Tags: Infect Genet Evol Source Type: research

Cefoperazone/sulbactam: New composites against multiresistant gram negative bacteria?
In conclusion, appropriate composites of cefoperazone and β-lactamase inhibitor sulbactam may expand the clinical use if the pharmacokinetic optimization could be achieved in the human serum. PMID: 33418147 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - January 5, 2021 Category: Genetics & Stem Cells Authors: Ku YH, Yu WL Tags: Infect Genet Evol Source Type: research

Divergence at mitochondrial and ribosomal loci indicates the split between Asian and European populations of Trichinella spiralis occurred prior to swine domestication.
al BM Abstract Available evidence suggests that Trichinella spiralis first originated in Asia and subsequently spread to the rest of the world. Notably limited genetic diversity in European T. spiralis isolates indicates that the parasite went through a dramatic genetic bottleneck at some point in its history. Did this genetic bottleneck result from the transport of a limited number of T. spiralis infected pigs from Asian centers of domestication, or was the parasite resident in Europe far earlier than the domestication of pigs there? In order to explore this hypothesis, we generated complete mitochondrial genomes...
Source: Infection, Genetics and Evolution - January 5, 2021 Category: Genetics & Stem Cells Authors: Thompson PC, Bilska-Zajac E, Zarlenga DS, Mingyuan L, Cencek T, Różycki M, Rosenthal BM Tags: Infect Genet Evol Source Type: research

Prevalence and phylogenetic analysis of spike gene of porcine epidemic diarrhea virus in Henan province, China in 2015-2019.
Abstract Porcine epidemic diarrhea virus (PEDV) causes diarrhea, dehydration and a high morbidity and mortality in piglets. To investigate the prevalence and molecular characteristics of the spike (S) gene of the PEDV strains, 575 faecal and intestinal samples were collected from individual pigs with diarrhea in 18 regions in Henan, China from April 2015 to March 2019. The detection results showed that PEDV infection was high up to 51.65% in Henan pigs. The PEDV positive rate in suckling piglets was the highest (60.47%), and it existed widely both in PEDV-vaccine immunized (25.00%) and non-immunized pigs (62.29%)....
Source: Infection, Genetics and Evolution - January 4, 2021 Category: Genetics & Stem Cells Authors: Zhang H, Han F, Yan X, Liu L, Shu X, Hu H Tags: Infect Genet Evol Source Type: research

Molecular epidemiology and genetic diversity of norovirus infection in children hospitalized with acute gastroenteritis in East Java, Indonesia in 2015-2019.
Abstract Noroviruses are recognized as a leading cause of outbreaks and sporadic cases of acute gastroenteritis (AGE) among individuals of all ages worldwide, especially in children
Source: Infection, Genetics and Evolution - January 2, 2021 Category: Genetics & Stem Cells Authors: Utsumi T, Lusida MI, Dinana Z, Wahyuni RM, Soegijanto S, Soetjipto, Athiyyah AF, Sudarmo SM, Ranuh RG, Darma A, Juniastuti, Yamani LN, Doan YH, Shimizu H, Ishii K, Matsui C, Deng L, Abe T, Katayama K, Shoji I Tags: Infect Genet Evol Source Type: research

Integrated meta-analysis and machine learning approach identifies acyl-CoA thioesterase with other novel genes responsible for biofilm development in Staphylococcus aureus.
Abstract Biofilm forming Staphylococcus aureus is a major threat to the health-care industry. It is important to understand the differences between planktonic and biofilm growth forms in the pathogen since conventional treatments targeting the planktonic forms are not effective against biofilms. The current study conducts a meta-analysis of three public transcriptomic profiles to examine the differences in gene expression between the planktonic and biofilm states of S. aureus using random-effects modeling. Mean effect sizes were calculated for 2847 genes among which 726 differentially expressed genes were taken fo...
Source: Infection, Genetics and Evolution - December 31, 2020 Category: Genetics & Stem Cells Authors: Subramanian D, Natarajan J Tags: Infect Genet Evol Source Type: research

Using PacBio SMRT data for identification of class I MHC alleles in a wildlife species, Zalophus californianus (California sea lion).
Abstract High allelic polymorphism and association with disease susceptibility has made the genes encoding major histocompatibility complex (MHC) antigen presentation molecules in humans, domesticated animals, and wildlife species of wide interest to ecologists, evolutionary biologists, and health specialists. The often multifaceted polygenism and extreme polymorphism of this immunogenetic system have made it especially difficult to characterize in non-model species. Here we compare and contrast the workflows of traditional Sanger sequencing of plasmid-cloned amplicons to Pacific Biosciences SMRT circular consensu...
Source: Infection, Genetics and Evolution - December 30, 2020 Category: Genetics & Stem Cells Authors: Duckworth EEM, Romoser KR, Ott JA, Deiss TC, Gulland FMD, Criscitiello MF Tags: Infect Genet Evol Source Type: research

COVID-19 spatiotemporal research with workflow-based data analysis.
Abstract Given the pertinence and acceleration of the spread of COVID-19, there is an increased need for the replicability of data models to verify the veracity of models and visualize important data. Most of these visualizations lack reproducibility, credibility, or accuracy, and are static, which makes it difficult to analyze the spread over time. Furthermore, most current visualizations depicting the spread of COVID-19 are at a global or country level, meaning there is a dearth of regional analysis within a country. Keeping these issues in mind, a replicable, efficient, and simple method to generate regional CO...
Source: Infection, Genetics and Evolution - December 30, 2020 Category: Genetics & Stem Cells Authors: Chintala S, Dutta R, Tadmor D Tags: Infect Genet Evol Source Type: research

Pharmacoinformatics based elucidation and designing of potential inhibitors against Plasmodium falciparum to target importin α/β mediated nuclear importation.
Pharmacoinformatics based elucidation and designing of potential inhibitors against Plasmodium falciparum to target importin α/β mediated nuclear importation. Infect Genet Evol. 2020 Dec 29;:104699 Authors: Oany AR, Pervin T, Moni MA Abstract Plasmodium falciparum, the prime causative agent of malaria, is responsible for 4, 05,000 deaths per year and fatality rates are higher among the children aged below 5 years. The emerging distribution of the multi-drug resistant P. falciparum becomes a worldwide concern, so the identification of unique targets and novel inhibitors is a prime need now...
Source: Infection, Genetics and Evolution - December 29, 2020 Category: Genetics & Stem Cells Authors: Oany AR, Pervin T, Moni MA Tags: Infect Genet Evol Source Type: research

Into the sea: Antimicrobial resistance determinants in the microbiota of little penguins (Eudyptula minor).
This study contrasts the occurrence of class 1 integrons and associated antimicrobial resistance genes in wild and captive little penguins (Eudyptula minor), an Australian seabird with local population declines. PCR screening of faecal samples (n = 448) revealed a significant difference in the prevalence of class 1 integrons in wild and captive groups, 3.2% and 44.7% respectively, with genes that confer resistance to streptomycin, spectinomycin, trimethoprim and multidrug efflux pumps detected. Class 1 integrons were not detected in two clinically relevant bacterial species, Klebsiella pneumoniae or Escherichia coli, i...
Source: Infection, Genetics and Evolution - December 25, 2020 Category: Genetics & Stem Cells Authors: Lundbäck IC, McDougall FK, Dann P, Slip DJ, Gray R, Power ML Tags: Infect Genet Evol Source Type: research

Age reduces resistance and tolerance in malaria-infected mice.
vre B Abstract Once infected, hosts can rely on two strategies to cope with parasites: fight them (resist the infection) or minimize the damage they induce (tolerate the infection). While there is evidence that aging reduces resistance, how tolerance varies as hosts become old has been barely studied. Here, we used a rodent malaria parasite (Plasmodium yoelii) to investigate whether 2- and 12-month old house mice differ in their capacity to resist and tolerate the infection. We found that 12-month old mice harbored higher parasitemia, showing that age reduces resistance to malaria. Infection-induced deterioration ...
Source: Infection, Genetics and Evolution - December 25, 2020 Category: Genetics & Stem Cells Authors: Sorci G, Léchenault-Bergerot C, Faivre B Tags: Infect Genet Evol Source Type: research

HLA-DRB1* and DQB1* allele and haplotype diversity in eight tribal populations: Global affinities and genetic basis of diseases in south India.
CONCLUSION: The HLA immunogenetic study of south Indian tribes has revealed the presence of globally shared haplotypes that are implicated in health and diseases in respective populations. The dendrogram based phylogenetic analyses have revealed the Caucasian affinity of Urali and palaeo-Mediterranean and Indo-European affinity of Malasar tribes. The presence of globally shared susceptible and protective haplotypes revealed the mosaic immunogenetic fabric of south Indian tribes. PMID: 33359263 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - December 22, 2020 Category: Genetics & Stem Cells Authors: Rangasamy N, Chinniah R, Vijayan M, Sivanadham R, Ravi PM, Darsa KV, Pandi S, Sevak V, Krishnan P, Karuppiah B Tags: Infect Genet Evol Source Type: research

Silent mutations in ribosomal protein genes are associated with high-risk clones of carbapenem-resistant Acinetobacter baumannii prevalent in Brazil.
CONCLUSIONS: By comparing the nucleotide and amino acid sequences of diversified A. baumannii, and Bruker Biotyper profiles, we showed that silent mutations in ribosomal RNA nucleotides are associated with clonal complexes, but since most of the mutations were silent, MALDI-TOF MS raw data was not a useful tool for typing the high-risk clones of this species. PMID: 33359045 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - December 21, 2020 Category: Genetics & Stem Cells Authors: de Barcellos TAF, Bueno MS, Cunha MPV, Nagamori FO, de Carvalho E, Takagi EH, Moreno LZ, Moreno AM, Chimara E, Tiba-Casas MR, Camargo CH Tags: Infect Genet Evol Source Type: research

Two prolonged viremic SARS-CoV-2 infections with conserved viral genome for two months.
tollini R Abstract We document two cases of viremic and prolonged active infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) where the viral genome was conserved for two months, but infection was with little or no symptoms. The first infection persisted for 80 days and the second for 62 days. Clearance of infection occurred 40 and 41 days, respectively, after development of detectable antibodies. Both cases were identified incidentally in an investigation of reinfection in a cohort of 133,266 laboratory-confirmed infected persons. PMID: 33352320 [PubMed - as supplied by publi...
Source: Infection, Genetics and Evolution - December 19, 2020 Category: Genetics & Stem Cells Authors: Abu-Raddad LJ, Chemaitelly H, Malek JA, Ahmed AA, Mohamoud YA, Younuskunju S, Al Kanaani Z, Al Khal A, Al Kuwari E, Butt AA, Coyle P, Jeremijenko A, Kaleeckal AH, Latif AN, Shaik RM, Abdul Rahim HF, Yassine HM, Al Kuwari MG, Al Romaihi HE, Al-Thani MH, Be Tags: Infect Genet Evol Source Type: research

Circulating cell-free mitochondrial DNA fragment: A possible marker for early detection of Schistosoma japonicum.
In this study, we explored the usefulness of the mitochondrial cfDNA markers for the diagnosis of schistosomiasis from the experimentally infected hosts (rabbits and mice). In this study we found mitochondrial DNA fragment cytochrome B gene as persistent and useful cfDNA marker for the early detection of schistosomiasis. We evaluated the sensitivity of cfDNA marker with varying numbers of cercaria. Overall, our results suggest that cfDNA markers can be useful for developing a diagnostic tool for the detection of S. japonicum infection. PMID: 33348056 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - December 18, 2020 Category: Genetics & Stem Cells Authors: Ullah H, Arbab S, Khan MIU, Li K, Muhammad N, Suleman, Qadeer A, Wangdan, Sato MO Tags: Infect Genet Evol Source Type: research

Ethnic and age-specific acute lung injury/acute respiratory distress syndrome risk associated with angiotensin-converting enzyme insertion/deletion polymorphisms, implications for COVID-19: A meta-analysis.
CONCLUSIONS: Significant associations of the ACE I/D polymorphism with the risk of ALI/ARDS were indicated in Caucasians and children as well as in Asians in mortality analysis. These findings were underpinned by high significance, high statistical power and robustness. ACE genotypes may be useful for ALI/ARDS therapy for patients with COVID-19. PMID: 33338639 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - December 15, 2020 Category: Genetics & Stem Cells Authors: Pabalan N, Tharabenjasin P, Suntornsaratoon P, Jarjanazi H, Muanprasat C Tags: Infect Genet Evol Source Type: research

microRNA-103a-3p confers protection against lipopolysaccharide-induced sepsis and consequent multiple organ dysfunction syndrome by targeting HMGB1.
CONCLUSIONS: Taken together, our results demonstrated the inhibitory role of miR-103a-3p in sepsis via inhibiting HMGB1 expression. PMID: 33333289 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - December 14, 2020 Category: Genetics & Stem Cells Authors: Li Y, Zhu H, Pan L, Zhang B, Che H Tags: Infect Genet Evol Source Type: research

Metagenomic identification, sequencing, and genome analysis of porcine hepe-astroviruses (bastroviruses) in porcine feces inn Japan.
In this study, we determined nearly complete genome sequences of four BastVs in the feces of healthy pigs. Genetic characterization revealed that these porcine BastVs (PBastVs) and BastVs from other animals including humans, had the same genome organization, that is, they contained three predicted conserved domains of viral methyltransferase, RNA helicase, and RdRp in the nonstructural ORF1 and the astrovirus capsid domain in the structural ORF2. Phylogenetic analyses using RNA-dependent RNA polymerase and the capsid region revealed that PBastVs branched with bat and rat BastVs; however, the groups formed by each host were...
Source: Infection, Genetics and Evolution - December 14, 2020 Category: Genetics & Stem Cells Authors: Nagai M, Okabayashi T, Akagami M, Matsuu A, Fujimoto Y, Hashem MA, Mekata H, Nakao R, Matsuno K, Katayama Y, Oba M, Omatsu T, Asai T, Nakagawa K, Ito H, Madarame H, Kawai K, Ito T, Nonaka N, Tsukiyama-Kohara K, Inoshima Y, Mizutani T, Misawa N Tags: Infect Genet Evol Source Type: research

Evolution and epidemiologic dynamics of dengue virus in Nicaragua during the emergence of chikungunya and Zika viruses.
Abstract Arthropod-borne viruses (arboviruses) comprise a significant and ongoing threat to human health, infecting hundreds of millions annually. Three such arboviruses include circumtropical dengue, Zika, and chikungunya viruses, exhibiting continuous emergence primarily via Aedes mosquito vectors. Nicaragua has experienced endemic dengue virus (DENV) transmission involving multiple serotypes since 1985, with chikungunya virus (CHIKV) reported in 2014-2015, followed by Zika virus (ZIKV) first reported in 2016. In order to identify patterns of genetic variation and selection pressures shaping the evolution of co-...
Source: Infection, Genetics and Evolution - December 13, 2020 Category: Genetics & Stem Cells Authors: Edgerton SV, Thongsripong P, Wang C, Montaya M, Balmaseda A, Harris E, Bennett SN Tags: Infect Genet Evol Source Type: research

Molecular characterization of invasive Staphylococcus aureus strains isolated from patients with diabetes in Iran: USA300 emerges as the major type.
Abstract There have been few studies focused on the molecular characterization of invasive Staphylococcus aureus strains in patients with diabetes in Iran. In the present study, 20 invasive S. aureus strains recovered from the patients with diabetes characterized by the virulence and resistance analysis, biofilm formation, staphylocoagulase (SC) typing, S. aureus protein A locus (spa) typing staphylococcal cassette chromosome mec (SCCmec) typing, and multilocus sequence typing (MLST). Virulence gene detection indicated a high prevalence of strains encoding the pvl genes (50%), a low prevalence of the tst and seg g...
Source: Infection, Genetics and Evolution - December 13, 2020 Category: Genetics & Stem Cells Authors: Tayebi Z, Fazeli M, Hashemi A, Abdi S, Dadashi M, Nasiri MJ, Goudarzi M Tags: Infect Genet Evol Source Type: research

Rapid detection of the New Delhi metallo- β-lactamase (NDM) gene by recombinase polymerase amplification.
In this study, recombinase polymerase amplification assays using a basic detection (Basic-RPA) and a real-time fluorescent detection (Exo-RPA) were established for detecting blaNDM gene. The RPA reactions were performed at 39 °C and finished within 20 min. Using different copy numbers of pMD18T-NDM plasmid DNA as templates, we identified the detection limit of Basic-RPA assay (1.85 × 103 copies/μL), conventional PCR assay (1.85 × 104 copies/μL), Exo-RPA assay (1.85 × 10 copies/μL) and real-time PCR assay (1.85 × 102 copies/μL). Both Basic-RPA and Exo-RPA assays we...
Source: Infection, Genetics and Evolution - December 12, 2020 Category: Genetics & Stem Cells Authors: Wang X, Xu LL, Zuo XY, Lin JW, Jin Z, Shen R, Du D, Tang YZ Tags: Infect Genet Evol Source Type: research

Wing geometry and genetic analyses reveal contrasting spatial structures between male and female Aedes aegypti (L.) (Diptera: Culicidae) populations in metropolitan Manila, Philippines.
Abstract The population genetic structure of Aedes aegypti (Linnaeus, 1762) has been studied in order to understand its role as an efficient vector. Several studies utilized an integrative approach; to combine genetic and phenotypic data to determine its population structure but these studies have only focused on female populations. To address this particular gap, our study compared the population variability and structuring between its male and female populations using phenotypic and genetic data from a highly-urbanized and dengue-endemic region of the Philippines, Metropolitan Manila. Five mosquito populations c...
Source: Infection, Genetics and Evolution - December 12, 2020 Category: Genetics & Stem Cells Authors: Carvajal TM, Amalin DM, Watanabe K Tags: Infect Genet Evol Source Type: research

Non-B variants of HIV-1 in San Francisco, California.
We describe the diversity of non-B variants and present evidence of local transmission of non-B HIV in San Francisco. Viral sequences collected from patients between 2000 and 2016 were matched to the San Francisco HIV/AIDS case registry. HIV subtype was determined using COMET. Phylogenies were reconstructed using the pol region of subtypes A, C, D, G, CRF01_AE, CRF02_AG, and CRF07_BC, with reference sequences from the LANL HIV database. Associations of non-B subtypes and circulating recombinant forms (CRFs) with patient characteristics were assessed using multivariable logistic regression. Out of 11,381 sequences, 10,669 w...
Source: Infection, Genetics and Evolution - December 12, 2020 Category: Genetics & Stem Cells Authors: O'Keefe KJ, Pipkin S, Fatch R, Scheer S, Liegler T, McFarland W, Grant RM, Truong HM Tags: Infect Genet Evol Source Type: research

Genome sequences of antibiotic-resistant Streptococcus suis strains isolated from human patients and diseased and asymptomatic pigs in Thailand.
In this study, whole-genome sequences of antibiotic-resistant S. suis strains isolated from human patients (2 strains), diseased pigs (4 strains), and asymptomatic pigs (3 strains) in Thailand were compared with known genomes of 1186 S. suis strains. Single-nucleotide polymorphism-based phylogenetic analysis indicated that the Thai-isolated S. suis strains have close genetic relatedness to S. suis strains isolated from Canada, China, Denmark, Netherlands, United Kingdom, and United States of America. The genome analysis revealed genes conferring antibiotic resistance (aad(6), ant(6)-Ia, ermB, tet(O), patB, and sat4) and ...
Source: Infection, Genetics and Evolution - December 11, 2020 Category: Genetics & Stem Cells Authors: Yongkiettrakul S, Wongsurawat T, Jenjaroenpun P, Acheampong DA, Srimanote P, Maneerat K, Visessanguan W, Nookaew I Tags: Infect Genet Evol Source Type: research

Association of variants in IL1B, TLR9, TREM1, IL10RA, and CD3G and Native American ancestry on malaria susceptibility in Colombian populations.
In this study, the association of mild malaria with 28 variants in 16 genes previously reported in other populations and/or close to ancestry-informative markers (AIMs) selected was evaluated in an admixed 736 Colombian population sample. Additionally, the effect of genetic ancestry on phenotype expression was explored. For this purpose, the ancestral genetic composition of Turbo and El Bagre was determined. A higher Native American ancestry trend was found in the population with lower malaria susceptibility [odds ratio (OR) = 0.416, 95% confidence interval (95% CI) = 0.234-0.740, P = 0.003]. Three AIMs presented significa...
Source: Infection, Genetics and Evolution - December 11, 2020 Category: Genetics & Stem Cells Authors: Mario-Vásquez JE, Naranjo-González CA, Montiel J, Zuluaga LM, Vásquez AM, Tobón-Castaño A, Bedoya G, Segura C Tags: Infect Genet Evol Source Type: research

Deep sequencing of the transcriptome from murine lung infected with H5N8 subtype avian influenza virus with combined substitutions I283M and K526R in PB2 gene.
Abstract H5N8 subtype highly pathogenic avian influenza viruses (HPAIVs) pose a huge threat to poultry industry and general public health. Our previous study demonstrated that synergistic effect of 283M and 526R in PB2 gene was a critical factor for viral high pathogenicity in mammals. However, the potential pathogenic mechanism of the mutant virus is still unclear. Here, RNA-seq method was used to analyze the global host response of murine lungs after infecting with parental r-JY virus and JY-PB2-I283M-K526R mutant virus. We found that both amounts and the expression levels of host differentially expressed genes ...
Source: Infection, Genetics and Evolution - December 9, 2020 Category: Genetics & Stem Cells Authors: Chen S, Wang X, Su X, Miao X, Qin T, Peng D, Liu X Tags: Infect Genet Evol Source Type: research

Complicated genotypes circulating among treatment na ïve HIV-1 patients in Guangzhou, China.
Complicated genotypes circulating among treatment naïve HIV-1 patients in Guangzhou, China. Infect Genet Evol. 2020 Dec 09;:104673 Authors: Lan Y, He X, Li L, Zhou P, Huang X, Deng X, Li J, Fan Q, Li F, Tang X, Cai W, Hu F Abstract Guangzhou city is the political, economic, and cultural center of the Guangdong Province, China. The molecular epidemiological characteristics of HIV-1 in Guangzhou are not widely known. The aim of this study was to explore the characteristics of HIV-1 genotypes among treatment naïve HIV/AIDS patients living in Guangzhou. HIV-1 RNA was extracted from serum specime...
Source: Infection, Genetics and Evolution - December 9, 2020 Category: Genetics & Stem Cells Authors: Lan Y, He X, Li L, Zhou P, Huang X, Deng X, Li J, Fan Q, Li F, Tang X, Cai W, Hu F Tags: Infect Genet Evol Source Type: research

Host range projection of SARS-CoV-2: South Asia perspective.
Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causing agent of Coronavirus Disease-2019 (COVID-19), is likely to be originated from bat and transmitted through intermediate hosts. However, the immediate source species of SARS-CoV-2 have not yet been confirmed. Here, we used diversity analysis of the angiotensin I converting enzyme 2 (ACE2) that serves as cellular receptor for SARS-CoV-2 and transmembrane protease serine 2 (TMPRSS2), which has been proved to be utilized by SARS-CoV-2 for spike protein priming. We also simulated the structure of receptor-binding domain of SARS-CoV-2 spik...
Source: Infection, Genetics and Evolution - December 7, 2020 Category: Genetics & Stem Cells Authors: Ahmed R, Hasan R, Siddiki AMAMZ, Islam MS Tags: Infect Genet Evol Source Type: research

Covid-19 pathogenesis in prostatic cancer and TMPRSS2-ERG regulatory genetic pathway.
Abstract Members of Coronaviridae family have been the source of respiratory illnesses. The outbreak of SARS-CoV-2 that produced a severe lung disease in afflicted patients in China and other countries was the reason for the incredible attention paid toward this viral infection. It is known that SARS-CoV-2 is dependent on TMPRSS2 activity for entrance and subsequent infection of the host cells and TMPRSS2 is a host cell molecule that is important for the spread of viruses such as coronaviruses. Different factors can increase the risk of prostate cancer, including older age, a family history of the disease. Androge...
Source: Infection, Genetics and Evolution - December 7, 2020 Category: Genetics & Stem Cells Authors: Afshari A, Janfeshan S, Yaghobi R, Roozbeh J, Azarpira N Tags: Infect Genet Evol Source Type: research

Polymorphism in the catalytic subunit of the PI3K γ gene is associated with Trypanosoma cruzi-induced chronic chagasic cardiomyopathy.
In conclusion, the presence of the T allele at single or double doses may differentiate the cardiac from other clinical manifestations of Chagas disease. This finding should help in further studies to evaluate the mechanisms underlying the differential association of PIK3CG in Chagas disease. PMID: 33301989 [PubMed - as supplied by publisher] (Source: Infection, Genetics and Evolution)
Source: Infection, Genetics and Evolution - December 7, 2020 Category: Genetics & Stem Cells Authors: Silva MC, da Silva Medina T, Fuzo CA, Dias FC, Freitas-Castro F, Fukutani KF, Donadi EA, Cunha-Neto E, Cunha TM, Silva JS Tags: Infect Genet Evol Source Type: research

Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways.
Abstract Apicomplexans are alveolate parasites which include Plasmodium falciparum, the main cause of malaria, one of the world's biggest killers from infectious disease. Apicomplexans are characterized by a reduction in proteome size, which appears to result from metabolic and functional simplification, commensurate with their parasitic lifestyle. However, other factors may also help to explain gene loss such as population bottlenecks experienced during transmission, and the effect of reducing the overall genomic information content. The latter constitutes an 'informational constraint', which is proposed to exert...
Source: Infection, Genetics and Evolution - December 6, 2020 Category: Genetics & Stem Cells Authors: Derilus D, Rahman MZ, Serrano AE, Massey SE Tags: Infect Genet Evol Source Type: research

Scrutinizing the spread of COVID-19 in Madagascar.
Abstract We scrutinize the evolution of COVID-19 in Madagascar by comparing results from three approaches (cubic polynomial, semi-gaussian and gaussian-like models) which we use to provide an analytical form of the spread of the pandemic. In so doing, we introduce (for the first time) the ratio ℛI/Tc, d of the cumulative and daily numbers of infected persons over the corresponding one of tests which are expected to be less sensitive to the number of the tests because the credibility of the results based only on the absolute numbers often raises some criticisms. We also give and compare the effective reproduction...
Source: Infection, Genetics and Evolution - December 5, 2020 Category: Genetics & Stem Cells Authors: Narison S, Maltezos S Tags: Infect Genet Evol Source Type: research

Genomic characterization of a novel G3P[10] rotavirus strain from a diarrheic child in Thailand: Evidence for bat-to-human zoonotic transmission.
Abstract An unusual rotavirus strain with the G3P[10] genotype (RVA/Human-wt/THA/MS2015-1-0001/2015/G3P[10]) was identified in a stool sample from a hospitalized child aged 11 months with severe gastroenteritis in Thailand. In the current study, we sequenced and characterized the full genome of strain MS2015-1-0001. On full-genomic analysis, strain MS2015-1-0001 exhibited the following genotype configuration: G3-P[10]-I8-R3-C3-M3-A9-N3-T3-E3-H6, which is identical or closely related to those of bat and bat-like rotavirus strains (MYAS33-like). Furthermore, phylogenetic analysis revealed that all 11 genes of stra...
Source: Infection, Genetics and Evolution - December 4, 2020 Category: Genetics & Stem Cells Authors: Komoto S, Tacharoenmuang R, Guntapong R, Upachai S, Singchai P, Ide T, Fukuda S, Hatazawa R, Sutthiwarakom K, Kongjorn S, Onvimala N, Luechakham T, Sriwanthana B, Murata T, Uppapong B, Taniguchi K Tags: Infect Genet Evol Source Type: research