scholarly journals Phylogenetic and Molecular Analyses of More Prevalent HCV1b Subtype in the Calabria Region, Southern Italy

2021 ◽  
Vol 10 (8) ◽  
pp. 1655
Author(s):  
Nadia Marascio ◽  
Angela Costantino ◽  
Stefania Taffon ◽  
Alessandra Lo Presti ◽  
Michele Equestre ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dental Treatment ◽  
Treatment Success ◽  
Antiviral Agents ◽  
Likelihood Method ◽  
Calabria Region ◽  
Eradication Of Infection ◽  
Prevalent Subtype ◽  
Genomic Regions ◽  
Subtype 1B

Hepatitis C virus subtype 1b (HCV1b) is still the most prevalent subtype worldwide, with massive expansion due to poor health care standards, such as blood transfusion and iatrogenic procedures. Despite safe and effective new direct antiviral agents (DAA), treatment success can depend on resistance-associated substitutions (RASs) carried in target genomic regions. Herein we investigated transmission clusters and RASs among isolates from HCV1b positive subjects in the Calabria Region. Forty-one NS5B and twenty-two NS5A sequences were obtained by Sanger sequencing. Phylogenetic analysis was performed using the maximum likelihood method and resistance substitutions were analyzed with the Geno2pheno tool. Phylogenetic analysis showed sixteen statistically supported clusters, with twelve containing Italian sequences mixed with foreign HCV1b isolates and four monophyletic clusters including only sequences from Calabria. Interestingly, HCV1b spread has been maintained by sporadic infections in geographically limited areas and by dental treatment or surgical intervention in the metropolitan area. The L159F NS5B RAS was found in 15 isolates and in particular 8/15 also showed the C316N substitution. The Y93H and L31M NS5A RASs were detected in three and one isolates, respectively. The A92T NS5A RAS was found in one isolate. Overall, frequencies of detected NS5B and NS5A RASs were 36.6% and 22.7%, respectively. For the eradication of infection, improved screening policies should be considered and the prevalence of natural RASs carried on viral strains.

scholarly journals Role of Endoscopic Sinus Surgery and Dental Treatment in the Management of Odontogenic Sinusitis Due to Endodontic Disease and Oroantral Fistula

2021 ◽  
Vol 10 (12) ◽  
pp. 2712
Author(s):  
Anda Gâta ◽  
Corneliu Toader ◽  
Dan Valean ◽  
Veronica Elena Trombitaș ◽  
Silviu Albu
Keyword(s):  
Endoscopic Sinus Surgery ◽  
Dental Treatment ◽  
Treatment Success ◽  
Sinus Surgery ◽  
Rank Test ◽  
Oroantral Fistula ◽  
Surgical Closure ◽  
Communication Time ◽  
Odontogenic Sinusitis ◽  
Mean Time

Background: Odontogenic sinusitis (ODS) is frequently encountered in ENT practice; however, there are no guidelines regarding its management. This study aims to analyse the results of endoscopic sinus surgery versus dental treatment in ODS. Additionally, we aim to demonstrate the benefit of associating endoscopic sinus surgery (ESS) to surgical closure of chronic oroantral fistulas (OAF) by comparing mean time to healing in patients who opted or not for concurrent ESS. Methods: Records of patients with ODS were reviewed. Group one consisted of patients with ODS caused by periapical pathology undergoing either endoscopic sinus surgery (ESS) or dental treatment. Resolution of ODS was considered treatment success and was compared between the two treatment strategies. Group two included patients with ODS and associated chronic oroantral communication. Time to healing was compared between patients undergoing OAF closure alone versus patients receiving associated ESS, using the Log-Rank test to correlate Kaplan–Meier curves. Results: 25 patients from a total of 45 in group one underwent dental treatment alone, and 20 opted for exclusive ESS treatment. The failure rate was 40% for patients treated with ESS compared to 4% (one patient) for dental treatment. ODS resolved in all patients in the second group, but the mean time to healing was half (10 days) when ESS was complementary to OAF closure. Conclusion: The present study represents the first estimator of the role ESS plays in OAF treatment. Nonetheless, it provides proof of the importance of first addressing dental problems in odontogenic sinusitis.

Phylogeny and Polymorphism in the Long Control Region, E6, and L1 of Human Papillomavirus Types 53, 56, and 66 in Central Brazil

2011 ◽  
Vol 21 (2) ◽  
pp. 222-229 ◽  
Author(s):  
Patrícia Soares Wyant ◽  
Daniela Marreco Cerqueira ◽  
Daniella Sousa Moraes ◽  
José Paulo Gagliardi Leite ◽  
Cláudia Renata Fernandes Martins ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genetic Variability ◽  
Binding Sites ◽  
Long Control Region ◽  
Amino Acid Substitutions ◽  
Nucleotide Substitutions ◽  
Central Brazil ◽  
Hpv Types ◽  
Genomic Regions

Introduction:Several studies related that different human papillomavirus (HPV) types and intratype variants can present different oncogenic potential. In opposite to HPVs 16 and 18 variants, information about variants of other carcinogenic HPV types is still scarce. The aim of this study was to investigate the genetic variability of HPVs 53, 56, and 66 from Central Brazil isolates.Methods:The long control region (LCR), E6, and L1 genomic regions were amplified and sequenced. We evaluate for nucleotide variations in relation to the reference sequence of each HPV type and also the conservation of physicochemical properties of the deduced amino acid substitutions. In silico analysis was performed to locate binding sites for transcriptional factors within the LCR. Moreover, we performed a phylogenetic analysis with the Central Brazilian and worldwide sequences available at genomic databases.Results:Gathering LCR, E6, and L1 genomic regions, the highest genetic variability was found among HPV-53 isolates with 52 nucleotide variations, followed by HPVs 56 and 66 with 24 and 16 nucleotide substitutions, respectively. The genetic analysis revealed 11 new molecular variants of all HPV types analyzed, totalizing 31 new nucleotide and 3 new amino acid variations. Eight nonconservative amino acid substitutions were detected, which may indicate a biological and pathogenic diversity among HPV types. Furthermore, 8 nucleotide substitutions were localized at putative binding sites for transcription factors in the LCR with a potential implication on viral oncogene expression. The HPVs 53, 56, and 66 phylogenetic analysis confirmed a dichotomic division only described to HPV subtypes and different from the patterns described for HPVs 16 and 18 variants.Conclusions:The high genetic variability observed emphasizes the importance of investigating polymorphisms in types other than HPVs 16 or 18 to better understand the molecular genomic profile of viral infection by different HPV types.

scholarly journals Phylogenetic Analysis of New Isolates of Cucumber mosaic virus from Iran on the Basis of Different Genomic Regions

2012 ◽  
Vol 28 (4) ◽  
pp. 381-389 ◽  
Author(s):  
Sevil Nematollahi ◽  
Nemat Sokhandan-Bashir ◽  
Farshad Rakhshandehroo ◽  
Hamid Reza Zamanizadeh
Keyword(s):  
Phylogenetic Analysis ◽  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Genomic Regions

Su1003 RACIAL DISPARITY IN CHRONIC HEPATITIS C TREATMENT SUCCESS WITH DIRECT-ACTING ANTIVIRAL AGENTS.

2020 ◽  
Vol 158 (6) ◽  
pp. S-494
Author(s):  
Jahnavi Koppala ◽  
Mobashshir Alam ◽  
Ryan W. Walters ◽  
Sirish Rao ◽  
Elliott Baker ◽  
...  
Keyword(s):  
Chronic Hepatitis ◽  
Hepatitis C ◽  
Chronic Hepatitis C ◽  
Racial Disparity ◽  
Treatment Success ◽  
Antiviral Agents ◽  
Hepatitis C Treatment ◽  
Direct Acting Antiviral ◽  
Direct Acting ◽  
Direct Acting Antiviral Agents

scholarly journals Molecular Epidemiological Investigation of Human Parainfluenza 3 Virus Outbreak in a Pediatric Bone Marrow Transplantation Unit

2017 ◽  
Vol 4 (suppl_1) ◽  
pp. S358-S359
Author(s):  
Patrick Stapleton ◽  
Stephen Perusini ◽  
Angela Thomas ◽  
Michelle Science ◽  
Tal Schechter-Finkelstein ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Phylogenetic Analysis ◽  
Molecular Typing ◽  
Gene Sequence ◽  
Likelihood Method ◽  
Positive Pressure ◽  
Rt Pcr ◽  
Hematopoietic Stem ◽  
F Gene ◽  
Hn Gene

Abstract Background Human parainfluenza virus 3 (hPIV3), a common cause of respiratory infections in children, can cause nosocomial outbreaks in patients undergoing hematopoietic stem cell transplantation, resulting in significant morbidity and mortality. Between July and August 2016, an increased number of hPIV3 infections were noted in a pediatric bone marrow transplant unit (BMT). Two patients were identified in late July and 4 patients in August. We undertook molecular typing of hPIV3 to determine whether cases represented multiple introductions of community virus strains or patient to patient transmission of a single strain. Previous reports of molecular typing have targeted either the F (fusion protein) gene or HN (hemagglutinin-neuraminidase) gene. We compared results using both methods direct from clinical specimens. Methods Nasopharyngeal (NP) swabs from 6 patients in BMT ward and 6 patients hospitalized on other wards had hPIV3 detected by the Luminex NxTAG Respiratory Pathogen Panel over 2 months. For the F gene a single pair of primers were used to first amplify then sequence a 278 basepair (bp) region by reverse-transcriptase PCR (RT-PCR). For HN gene a 1719 bp region was amplified using nested RT-PCR, then sequenced with 6 sets of overlapping primers. The resulting contigs were assembled manually with ContigExpress. Phylogenetic analysis of assembled sequences was performed in MEGA7 using the maximum likelihood method. Results For the HN gene sequence of 1715 bp was obtained for 10 of 12 patients (5 in each group). Phylogenetic analysis of HN sequences indicated 2 distinct hPIV3 lineages (Figure 1). The 5 BMT patients differed by a maximum of 1bp, while 5 samples from other wards differed by 14 to 57 bp. For the F gene only 98 bp of common sequence was obtained for 7 patients, all of whom had HN gene sequences available. Phylogenetic analysis of F gene sequence also supported the presence of 2 distinct lineages. Conclusion Molecular typing of hPIV3 suggests there was transmission of a single hPIV3 strain within the BMT unit despite protective isolation of all BMT patients in positive pressure single rooms and the use of contact and droplet precautions for infected cases. We found sequencing the HN gene more informative than sequencing the F gene. Disclosures All authors: No reported disclosures.

scholarly journals Viral Determinants of Resistance to Treatment in Patients with Hepatitis C

2007 ◽  
Vol 20 (1) ◽  
pp. 23-38 ◽  
Author(s):  
Anette Wohnsland ◽  
Wolf Peter Hofmann ◽  
Christoph Sarrazin
Keyword(s):  
Hepatitis C ◽  
Antiviral Therapy ◽  
Phase 1 ◽  
Treatment Success ◽  
Antiviral Agents ◽  
Antiviral Drugs ◽  
Immune Defense ◽  
Phenotypic Resistance

SUMMARY Chronic hepatitis C virus (HCV) infection affects more than 170 million persons worldwide and is responsible for the development of liver cirrhosis in many cases. Standard treatment with pegylated alpha interferon (IFN-α) in combination with the nucleoside analogue ribavirin leads to a sustained virologic response in approximately half of the patients. IFN-α is classified as an indirect treatment, as it interacts with the host's immune response. The mechanism of action of ribavirin is still unknown. The benefit of triple therapy by adding other antiviral agents, e.g., amantadine, is controversial. Currently, new direct antiviral drugs (HCV protease/polymerase inhibitors) are being evaluated in phase 1/phase 2 trials. Phenotypic resistance to antiviral therapy has been attributed to amino acid variations within distinct regions of the HCV polyprotein. While sensitivity to IFN-α-based antiviral therapy in vivo is clearly correlated with the number of mutations within the HCV NS5A protein, the underlying functional mechanisms for this association are unknown. In turn, in vitro, several mechanisms to circumvent the host immune defense or to block treatment-induced antiviral activities have been described for different HCV proteins. By the introduction of direct antiviral drugs, hepatitis C therapy now is entering a new era in which the development of resistance may become the most important parameter for treatment success or failure.

scholarly journals Molecular barcode and morphological analysis of Smilax purhampuy Ruiz, Ecuador

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11028
Author(s):  
Pilar Soledispa ◽  
Efrén Santos-Ordóñez ◽  
Migdalia Miranda ◽  
Ricardo Pacheco ◽  
Yamilet Irene Gutiérrez Gaiten ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequence ◽  
Nuclear Dna ◽  
Vascular System ◽  
Sequence Similarity ◽  
Dna Barcode ◽  
Likelihood Method ◽  
Central Vein ◽  
Traditional Medicines ◽  
Molecular Barcode

Smilax plants are distributed in tropical, subtropical, and temperate regions in both hemispheres of the world. They are used extensively in traditional medicines in a number of countries. However, morphological and molecular barcodes analysis, which may assist in the taxonomic identification of species, are lacking in Ecuador. In order to evaluate the micromorphological characteristics of these plants, cross sections of Smilax purhampuy leaves were obtained manually. The rhizome powder, which is typically used in traditional medicines, was analyzed for micromorphological characteristics. All samples were clarified with 1% sodium hypochlorite. Tissues were colored with 1% safranin in water and were fixed with glycerinated gelatin. DNA was extracted from the leaves using a modified CTAB method for molecular barcode characterization and PCR was performed using primers to amplify the different loci including the plastid genome regions atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK–psbI spacer, and trnH–psbA spacer; and the nuclear DNA sequence ITS2. A DNA sequence similarity search was performed using BLAST in the GenBank nr database and phylogenetic analysis was performed using the maximum likelihood method according to the best model identified by MEGAX using a bootstrap test with 1,000 replicates. Results showed that the micromorphological evaluation of a leaf cross section depicted a concave arrangement of the central vein, which was more pronounced in the lower section and had a slight protuberance. The micromorphological analysis of the rhizome powder allowed the visualization of a group of cells with variable sizes in the parenchyma and revealed thickened xylematic vessels associated with other elements of the vascular system. Specific amplicons were detected in DNA barcoding for all the barcodes tested except for the trnH–psbA spacer. BLAST analysis revealed that the Smilax species was predominant in all the samples for each barcode; therefore, the genus Smilax was confirmed through DNA barcode analysis. The barcode sequences psbK-psbI, atpF-atpH, and ITS2 had a better resolution at the species level in phylogenetic analysis than the other barcodes we tested.

scholarly journals Multiple origin but single domestication led to Oryza sativa

2017 ◽  
Author(s):  
Jae Young Choi ◽  
Michael D. Purugganan
Keyword(s):  
Phylogenetic Analysis ◽  
Oryza Sativa ◽  
False Positive ◽  
Large Scale ◽  
Selective Sweep ◽  
De Novo ◽  
Wild Progenitor ◽  
Asian Rice ◽  
Genomic Regions ◽  
Domestication Alleles

AbstractThe domestication scenario that led to Asian rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated rice dataset, which were also analyzed by two studies but resulted in two contrasting domestication models. We suggest the analysis of false positive selective sweep regions and phylogenetic analysis of concatenated genomic regions may have been the sources that contributed to the different results. In the end, our result indicates Asian rice originated from multiple wild progenitor subpopulations; however, de novo domestication appears to have occurred only once and the domestication alleles were transferred between rice subpopulation through introgression.

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