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Results for “Genomic subtypes”

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At least 307 records · Page 17Linked to original sources

PubMed2000

Genetic characterization of adenovirus strains isolated from patients with acute conjunctivitis in the city of São Paulo, Brazil.

Genome analysis was carried out on adenovirus strains isolated from patients with acute follicular conjunctivitis in the city of São Paulo, Brazil. Eighteen conjunctival scrapings, collected between December 1993 and March 1994, were analyzed by two methods: a combination of polymerase chain reaction with restriction fragment length polymorphism and viral DNA restriction analysis, carried out using 10 restriction endonucleases: BamHI, BglI, BglII, HindIII, KpnI, SacI, SalI, SmaI, XbaI, and XhoI. Among 11 adenovirus detected by cell culture isolation, nine were Ad8, and two were Ad7. By restriction analysis the Ad8 isolates were typed as two new variants-Ad8/D11 (seven of nine samples) and Ad8/D12 (two of nine samples). Ad7 isolates were identified as a subtype of the widespread genome type Ad7b and the virulent type Ad7h, a predominant genome type circulating in Argentina, Chile, and Uruguay but absent in Brazil until 1991.

Acute Disease↗

PubMed2026

Genomic detection of highly pathogenic avian influenza H5N1 in Antarctic seabirds reveals connectivity with South American viral lineages.

Emerging avian viruses increasingly threaten Antarctic wildlife, raising concerns about ecosystem health and biodiversity. In this study, we conducted a comprehensive investigation of avian influenza virus (influenza A virus, IAV) in both resident and migratory birds inhabiting the South Shetland Islands, Antarctica. During the 2024-2025 austral summer, 278 samples were collected and screened using real-time RT-PCR targeting the IAV M gene. IAV RNA was detected in 30 samples, and eight of these were found to be positive for H5. Complete genome sequencing was performed on samples from a gentoo penguin (Pygoscelis papua) and a southern giant petrel (Macronectes giganteus), revealing the presence of highly pathogenic avian influenza virus H5N1, clade 2.3.4.4b. Phylogenetic analysis demonstrated that these viral genomes closely cluster with contemporary South American strains, indicating a direct connectivity between Antarctic seabirds and the broader H5N1 transmission network. Our findings highlight the heightened vulnerability of Antarctic ecosystems to emerging infectious diseases and emphasize the critical need for sustained genomic surveillance. These efforts are essential to monitor wildlife health, inform conservation strategies, and implement effective biosecurity measures to safeguard Antarctic biodiversity.

Animals↗

PubMed2005

Unusual genomic structure: melanocortin receptors in Fugu.

The melanocortin (MC) receptors are found in five subtypes in mammals and chicken, while recent studies have shown that the Fugu (Takifugu rubripes) genome has only four MC receptors and the zebrafish genome has six subtypes. The MC3 receptor seems to be missing from the two closely related pufferfishes, Fugu and Tetraodon (Tetraodon nigroviridis). The MC2 and MC5 receptors in the pufferfish have introns. Moreover, these two receptors are found in a tandem that is remarkably conserved in several vertebrate species. Here, we speculate about the genomic origin of the MC receptors.

Animals↗

PubMed2026

Dissemination of blaKPC-3-harbouring Klebsiella pneumoniae across ST48 and ST628 in multiple healthcare facilities in the Republic of Korea.

Klebsiella pneumoniae carbapenemase-3 (KPC-3) remains rare in South Korea, where KPC-2 is the dominant carbapenemase, making the repeated detection of a concentrated blaKPC-3 signal over five years notable. We performed genomic analyses of blaKPC-3-harbouring K. pneumoniae from a regional healthcare network. Two chromosomally distinct lineages with concordant capsule loci (ST628/KL15 and ST48/KL62) presented multidrug-resistant phenotypes, and the virulence-associated loci were confined to ST48. Single-nucleotide polymorphism (SNP) analyses revealed near-clonal relatedness within lineages, with 0-38 pairwise SNPs among ST628 isolates and 8 SNPs between the two ST48 isolates. Core-genome multilocus sequence typing (cgMLST) supported this structure, as ST628 isolates were assigned to complex type 19149 with 0-7 allelic differences, and ST48 isolates were assigned to complex type 19150 with 5 allelic differences. These patterns support vertical spread via clonal expansion across multiple facilities. Despite substantial chromosomal separation, most isolates carried the same IncFII(K) plasmid backbone and blaKPC-3, and they were nearly indistinguishable from a plasmid previously reported in South Korea. One isolate carried blaKPC-3 on a distinct multireplicon IncFIB(K)/IncFII(K) plasmid, indicating that the signal was not confined to a single plasmid backbone. In both plasmids, blaKPC-3 was embedded within Tn4401b. These findings indicate that a rare blaKPC-3 genotype can persist regionally through sustained clonal dissemination and that cross-lineage linkage is compatible with past horizontal transfer involving a conserved plasmid. These findings underscore the need for subtype-resolved, regionally coordinated genomic surveillance in connected healthcare networks to detect uncommon carbapenemase variants early.

Klebsiella pneumoniae↗

PubMed2026

Core genome and whole genome multi-locus sequence typing of Cronobacter isolates.

UNLABELLED: Cronobacter species, especially C. sakazakii and C. malonaticus, are opportunistic pathogens that are linked to severe infections in infants with high case fatality rates. In this study, we investigated whole genome sequencing (WGS) analysis approaches, specifically 7-gene multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) to subtype Cronobacter isolates. We analyzed a comprehensive set of 743 Cronobacter isolates derived from clinical, food, and environmental sources. We also evaluated high-quality single nucleotide polymorphism (hqSNP), cgMLST, and wgMLST to cluster epidemiologically related and differentiate sporadic C. sakazakii isolates. Our results indicate that both cgMLST and wgMLST accurately identify closely related isolates and are consistent with epidemiological findings. The allele-based analyses were also comparable with hqSNP analyses, the current gold standard. Our workflow also outputs 7-gene MLST allele calls, Cronobacter sequence types, and clonal complexes, which may be useful for historic comparisons during outbreak investigations. Following the recent classification of Cronobacter infections as nationally notifiable in the United States, our findings demonstrate the efficacy of WGS-based approaches within the PulseNet framework to improve outbreak detection and response strategies for Cronobacter. IMPORTANCE: Cronobacter species, specifically C. sakazakii and C. malonaticus, are opportunistic pathogens linked to severe infections in infants with high case fatality rates. This study highlights the critical importance of advanced molecular techniques in public health surveillance, using whole genome sequencing (WGS) methodologies such as multi-locus sequence typing (7-gene MLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST). The validation of these WGS-based approaches within the PulseNet framework is timely, especially following the recent classification of Cronobacter infections as nationally notifiable in the United States. WGS methods not only enhance outbreak detection but can also inform public health guidance aimed at preventing infections and reducing mortality in vulnerable populations, especially infants. Our research supports implementation of cgMLST as a standardized approach for routine PulseNet surveillance of Cronobacter, with wgMLST and hqSNP analyses providing additional discriminatory power for outbreak investigations and high resolution phylogenetic analysis.

Multilocus Sequence Typing↗

PubMed2006

Risk of HIV-1 transmission by breastfeeding among mothers infected with recombinant and non-recombinant HIV-1 genotypes.

BACKGROUND: Viral genotype and intersubtype recombination may influence the rate and/or timing of mother-to-child HIV-1 transmission. METHODS: We determined the HIV-1 subtype of the C2-C5 env and 5'LTR regions from milk and blood samples of 61 Tanzanian mothers who transmitted the virus through breastfeeding and their HIV-1 positive non-transmitting controls. Cases and controls were matched on infant's age at sample collection. All mothers resided in Dar es Salaam, Tanzania. RESULTS: Most infections among cases were due to recombinant viruses (41.0%), followed by HIV-1 subtype A (26.2%), subtype D (19.7%), and subtype C (13.1%). In multivariate analysis including maternal CD4+ cell counts, HIV disease stage, and proviral load in breast milk, the odds of breast milk transmission were 7.2 times higher if the mother carried an intersubtype recombinant genome in comparison to a subtype C virus (p=0.02). Viruses with recombinant LTRs were 4.9 times more likely to be transmitted through breastfeeding than viruses with non-recombinant LTRs of subtype A, C or D combined (p=0.01). CONCLUSIONS: This suggested that intersubtype recombinant genomes, and especially recombination within the LTR, might render HIV-1 more fit for transmission via breast milk in comparison with non-recombinant subtypes A, C, and D.

Adult↗

PubMed2000

Application of a fluorogenic PCR assay for typing and subtyping of influenza viruses in respiratory samples.

A fluorogenic PCR-based method (TaqMan-PCR) was developed for typing and subtyping of influenza virus genomes in clinical specimens. The TaqMan-PCR employs a probe technology that exploits the endogenous 5'-3' nuclease activity of the Taq DNA polymerase to allow direct detection of the amplicon by release of a fluorescent reporter during the PCR. Therefore, post-PCR analysis is avoided since hybridization with the fluorogenic probe and quantification of the amplified product is performed simultaneously during PCR cycling. The specificity of the method was evaluated on 86 influenza A (25 H1N1 and 61 H3N2) and 49 influenza B virus reference strains and isolates. The sensitivity of the technique was found to be at the level of 0.1 50% tissue culture infective dose. This TaqMan-PCR was applied prospectively to surveillance work by community-based sampling in Germany during the last two influenza seasons. Seven hundred five throat swabs were analyzed during the winter of 1997-1998. A total of 195 of 705 samples (28%) were positive by PCR. Influenza viruses could be isolated from 125 specimens (18%). During the 1998-1999 season, 1,840 respiratory samples were received. Influenza viruses were isolated from 281 specimens (15%) out of 525 throat swabs (29%) which were positive for influenza A or B virus by TaqMan-PCR. Further differentiation of influenza A virus-positive swabs revealed an intensive circulation of the subtype H3N2 during both seasons, 1997-1998 and 1998-1999. The TaqMan-PCR was much more sensitive than culture and revealed an excellent correlation for typing and subtyping of influenza viruses when samples were positive by both methods.

DNA Primers↗

PubMed2005

Subtyping of Clostridium difficile polymerase chain reaction (PCR) ribotype 001 by repetitive extragenic palindromic PCR genomic fingerprinting.

Fifty isolates of the most common UK strain of Clostridium difficile [polymerase chain reaction (PCR) ribotype 001] were analysed by three PCR-based typing methods in order to determine genomic diversity within this strain that may form the basis of a subtyping method. The three methods used were repetitive extragenic palindromic elements (REP), conserved repetitive DNA elements (BOX), and enterobacterial repetitive PCR intergenic consensus sequences (ERIC). The performance of each typing method was assessed by comparing powers of discrimination, typeability and reproducibility. All methods had satisfactory levels of typeability and reproducibility as determined by blind-coded repeats, but REP-PCR typing proved to be the most discriminatory method, yielding seven distinct amplicon profiles consisting of up to eight major bands. BOX-PCR generated between two and five major amplicons with four distinct BOX profiles. ERIC-PCR primers, however, could not discriminate between isolates. These results suggest that PCR ribotype 001 is not clonal in nature at present, and that REP-PCR subtyping methods offer promise to further our understanding of the epidemiology of C. difficile PCR ribotype 001 disease in UK hospitals.

Belgium↗

PubMed2006

First report of an HIV-1 triple recombinant of subtypes B, C and F in Buenos Aires, Argentina.

We describe the genetic diversity of currently transmitted strains of HIV-1 in men who have sex with men (MSM) in Buenos Aires, Argentina between 2000 and 2004. Nearly full-length sequence analysis of 10 samples showed that 6 were subtype B, 3 were BF recombinant and 1 was a triple recombinant of subtypes B, C and F. The 3 BF recombinants were 3 different unique recombinant forms. Full genome analysis of one strain that was subtype F when sequenced in pol was found to be a triple recombinant. Gag and pol were predominantly subtype F, while gp120 was subtype B; there were regions of subtype C interspersed throughout. The young man infected with this strain reported multiple sexual partners and sero-converted between May and November of 2004. This study reported for the first time the full genome analysis of a triple recombinant between subtypes B, C and F, that combines in one virus the three most common subtypes in South America.

Adult↗

PubMed1989

Epidemiology of boutonneuse fever in western Sicily: demonstration of multiple spotted fever group-Rickettsiae subtypes.

Electrophoretic analysis of the proteins and genomic DNA of spotted fever-group Rickettsiae isolated from ticks and a human in Western Sicily show that at least two distinct subtypes other than R. conorii are present in this region. All of the spotted fever-group isolates share common features with other, well-defined spotted fever-group rickettsial species, e.g. R. sibirica, Thai Tick Typhus, and R. rickettsii. Based on these data, caution is recommended when identifying species by the more traditional and less specific tests. Studies of the ecology and epidemiology of spotted fever-group Rickettsiae in regions where R. conorii infections occur would benefit and be challenged by intensive antigenic analyses of the proteins and genomic DNA of the various strains of the spotted fever-group Rickettsiae present in those areas.

Animals↗

PubMed1984

Association of human papillomavirus subtype and clinical course in respiratory papillomatosis.

The relationship of human papillomavirus type 6 (HPV-6) subtypes to the clinical manifestations of respiratory papillomatosis was investigated. DNA was isolated from biopsy specimens of 21 patients and the viral genome analyzed by molecular hybridization. Four subtypes, designated HPV-6c through HPV-6f, were distinguishable by restriction endonuclease cleavage patterns of the viral genome. Patient records were reviewed to identify associations between viral subtype and sex, race, age at onset of papilloma, duration of disease, frequency of operations, history of tracheotomy and anatomical extension of papilloma. HPV-6c was present in 13 cases which were characterized by extensive anatomical spread of disease, higher frequency of operations, and a need for tracheotomy. HPV-6d occurred in 4 black patients with juvenile onset papilloma. HPV-6c was found in 2 white patients--1 with juvenile onset and 1 with adult onset papilloma. HPV-6f was identified in 2 white patients with adult onset disease.

Adolescent↗

PubMed1993

Molecular cloning and sequencing of a human somatostatin receptor, hSSTR4.

We recently reported the cloning of a somatostatin receptor (SSTR) subtype from a rat genomic library designated rSSTR4. In the present study, we report the cloning of the human SSTR4 gene. A human genomic library was screened with a 1.2 kb fragment of rSSTR4 containing the full open reading frame and a genomic clone, hSSTR4, was isolated. The deduced amino acid sequence of this clone encoded a protein of 388 amino acids and is a member of the G-protein coupled receptor superfamily. Comparison of rat and human SSTR4 sequences demonstrated 89% identity. In addition, the sequence of hSSTR4 shows 61%, 46%, and 47% sequence identity with previously identified isoforms hSSTR1, hSSTR2, and hSSTR3, respectively.

Amino Acid Sequence↗

PubMed1988

Comparison by restriction fragment pattern analysis and molecular characterization of some European isolates of Suid herpesvirus 1: a contribution to strain differentiation of European isolates.

Eleven European isolates of Suid herpesvirus type 1 (SHV-1) were compared by restriction fragment pattern analyses and Southern blot hybridization using different genomic probes. The presence of strain discriminative 4 major genome types and several subtypes as well as the molecular distinctions between these were demonstrated. Evolutionary relationships between the different types are suggested on the basis of homologous restriction fragment length polymorphisms.

Blotting, Southern↗

PubMed2004

Hormonal suppressive therapy for endometriosis may not improve patient health.

OBJECTIVE: To critically examine the possible association between hormonal treatment of endometriosis and ovarian cancer. RESULT(S): The malignant potential of endometriosis has been suggested by several clinical studies. Although controversial, ovarian carcinoma of the endometrioid and clear cell subtypes has been associated with endometriosis, particularly among subjects with a longstanding disease. Furthermore, a significantly higher frequency of endometriosis has been found in patients undergoing surgery for endometrioid, clear cell, and mixed subtypes of ovarian carcinoma, as compared with the other subtypes. Changes in the genomic material in endometriotic implants were observed by many investigators in chromosomes 1, 5, 6, 7, 16, and 22 by several methods (fluorescent in situ hybridization, comparative genomic hybridization, and others). Because hormonal ablative treatments may suppress the normal, eukaryotic cells more than the aneuploid cells bearing chromosomal aberrations, it may increase the rate of dyskaryotic cells in the endometriotic implants, possibly augmenting the risk of malignant transformation. A recent published association between Danazol and ovarian cancer suggests that such a theoretical risk may occur. CONCLUSION(S): The hormonal ablative treatment of endometriosis may increase the risk of malignant transformation in the endometriotic implants by causing a negative selection and increasing the rate of dyskaryosis and loss of heterozygosity.

Danazol↗

PubMed1997

At least three hepatitis C virus strains implicated in Swedish and Danish patients with intravenous immunoglobulin-associated hepatitis C.

BACKGROUND: Three reported Swedish cases of hepatitis C in patients receiving an intravenous immunoglobulin (Gammagard, Baxter Healthcare, Deerfield, IL) were among the first to bring to light a worldwide outbreak of hepatitis C associated with non-solvent/detergent (SD)-treated Gammagard. In February 1994, all implicated batches of Gammagard were recalled and exposed patients traced. STUDY DESIGN AND METHODS: Sera from all identified and hepatitis C-viremic Swedish and Danish patients (n = 14) exposed to the implicated batches underwent hepatitis C virus genotyping and sequencing of the core region and hypervariable region 1 of E2. Genomic amplification was also done on 15 non-SD-treated batches of Gammagard. RESULTS: Twelve patients were infected with subtype 1a and surprisingly, two with subtype 2b. Analysis of the core region showed identical sequences in four patients and the only consistently positive batch. Five patients shared another sequence, whereas three other subtype 1a patients each manifested unique sequences. The two subtype 2b isolates were identical. Genomic fingerprinting of the hypervariable region confirmed identity within each group with great stringency. Amplification with isolate-specific primers showed mixed infection in one patient whose exposure was confined to a single batch. CONCLUSION: The few batches implicated presumably were contaminated with several strains.

Adolescent↗

PubMed2002

HIV-1 subtype J recombinant viruses in Spain.

Genetic characterization of HIV-1 was carried out in two women who originated in Cameroon and Equatorial Guinea, respectively, and who were diagnosed more recently as HIV-1 seropositive in Madrid, Spain. Phylogenetic studies showed that the protease-encoding gene from both individuals clustered with subtype J sequences with a high bootstrap. However, env sequences clustered with subtypes A and C, respectively. This work represents the first characterization of HIV-1 containing subtype J-like genomic regions in Spain.

Base Sequence↗

PubMed1996

Molecular cloning and functional expression of the alpha1A-adrenoceptor of Medaka fish, Oryzias latipes.

A genomic DNA encoding a subtype adrenoceptor (AR) was cloned from Medaka fish, Oryzias latipes, using an oligonucleotide probe corresponding to the consensus sequence of mammalian alpha-AR and beta-AR. The gene spans at least 9kbp, and the coding region consists of two exons split by an intron of 7.2 kbp located at the same position as those of mammalian alpha1B-AR genes. The gene encodes 470 amino acid residues, the sequence of which shows the highest similarity to that of mammalian alpha1A-AR (61%) and significant but lower similarities to other alpha-AR and beta-AR proteins (31-45%), indicating that the gene encodes a Medaka homolog of alpha1A-AR. To characterize the encoded protein, the mRNA was synthesized in vitro and injected into Xenopus oocytes. As a result, the oocytes responded to 100 nM epinephrine evoking a Ca2 + -dependent C1- current in the order of microamperes, which was not observed for oocytes injected with water alone. The response was reversibly inhibited by an alpha1-selective antagonist, WB4101 (2-[2,6-dimethoxphenoxyethyl]aminomethyl)-1,4-benzodioxane). Similar experiments using several adrenergic agonists revealed that Medaka alpha1A-AR responds to the following agonists in the order: epinephrine > or = (-)norepinephrine > oxymetazoline > or = methoxamine, which is similar to the responses of rat alpha1A receptor expressed in COS cells. The results indicate that fish contains adrenoceptor systems similar to those of mammals in terms of primary structure and pharmacological properties.

Amino Acid Sequence↗

PubMed2006

Genotyping of human and porcine Yersinia enterocolitica, Yersinia intermedia, and Yersinia bercovieri strains from Switzerland by amplified fragment length polymorphism analysis.

In this study, 231 strains of Yersinia enterocolitica, 25 strains of Y. intermedia, and 10 strains of Y. bercovieri from human and porcine sources (including reference strains) were analyzed using amplified fragment length polymorphism (AFLP), a whole-genome fingerprinting method for subtyping bacterial isolates. AFLP typing distinguished the different Yersinia species examined. Representatives of Y. enterocolitica biotypes 1A, 1B, 2, 3, and 4 belonged to biotype-related AFLP clusters and were clearly distinguished from each other. Y. enterocolitica biotypes 2, 3, and 4 appeared to be more closely related to each other (83% similarity) than to biotypes 1A (11%) and 1B (47%). Biotype 1A strains exhibited the greatest genetic heterogeneity of the biotypes studied. The biotype 1A genotypes were distributed among four major clusters, each containing strains from both human and porcine sources, confirming the zoonotic potential of this organism. The AFLP technique is a valuable genotypic method for identification and typing of Y. enterocolitica and other Yersinia spp.

Animals↗