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PubMed2026

Development and evaluation of an ARTIC-based amplicon sequencing assay for whole-genome characterization of respiratory syncytial virus.

Respiratory syncytial virus (RSV), a ~15.2 kb negative-sense RNA virus, causes acute respiratory infections in infants and older adults. Its two subtypes, RSV-A and RSV-B, evolve rapidly, making ongoing monitoring of circulating strains essential. The Georgia Public Health Laboratory (GPHL) developed and evaluated an amplicon-based whole-genome sequencing (WGS) assay for RSV surveillance. A total of 214 de-identified remnant clinical specimens (102 RSV-A and 112 RSV-B) with RT-PCR Cq values <31 were included. RSV genomes were amplified using ARTIC-style and custom primer sets, with the ARTIC set showing superior performance. Libraries were prepared using a modified Illumina COVIDSeq protocol, sequenced on NextSeq 1000/2000 instruments, and analyzed using the GPHL-RSV-PIPE bioinformatics pipeline. Among genomes meeting validation criteria, sequencing depth was slightly higher for RSV-A (median 53,433&#xd7;; mean 51,076&#xd7;) than RSV-B (median 49,699&#xd7;; mean 46,945&#xd7;), whereas genomic coverage was slightly lower for RSV-A (median 97.5%; mean 96.6%) than RSV-B (median 98.3%; mean 97.6%). Predominant lineages were A.D.3.1 and A.D.5.2 for RSV-A and B.D.E.1 for RSV-B. For RSV-A, the assay showed 92.8% accuracy, 96.2% sensitivity, 87.2% specificity, 92.6% positive predictive value, and 93.2% negative predictive value. Intra- and inter-run precision assessed using 16 and 53-57 genomes, respectively, showed nearly 100% consensus genome identity with 0-5 nucleotide differences. Specificity testing of 31 non-RSV specimens produced no false-positive detections. Limits of detection were 4.4 TCID50/mL for RSV-A and 18.6 TCID50/mL for RSV-B. These results demonstrate that the ARTIC-based RSV WGS assay enables near real-time surveillance and strengthens data-driven public health responses to future outbreaks.IMPORTANCERSV, with two major subtypes, RSV-A and RSV-B, causes acute respiratory infections that can be severe in infants under 6 months and older adults. Current RSV surveillance at the GPHL relies on the Thermo Fisher TaqMan Gene Expression Capillary assay, which detects and subtypes RSV but lacks resolution for lineage classification and identification of emerging variants. To address this critical gap, GPHL developed and evaluated an amplicon-based WGS assay using 214 de-identified RSV clinical specimens. Genomes were amplified using ARTIC-style and custom-primer sets, with ARTIC primers showing superior performance. The assay demonstrated strong sequencing depth, genomic coverage, specificity, repeatability, reproducibility, and low limits of detection. RSV lineages were accurately determined based on genetic variation. These results establish that the ARTIC-based WGS assay enables near real-time genomic surveillance, supporting monitoring of circulating RSV strains and informing data-driven public health responses.

bioinformatics pipeline↗
PubMed2004

Coexistence of multiple genotypes, including newly identified genotypes, in outbreaks of gastroenteritis due to Norovirus in Japan.

Norovirus (NV) (formerly called Norwalk-like virus) is the most common cause of acute nonbacterial gastroenteritis in humans. Recently, we reported an NV genotyping scheme based on variability in the capsid N-terminal/shell (N/S) domain gene (Katayama et al., Virology 299:225-239, 2002). We found 19 genotypes, including nine of genogroup I and 10 of genogroup II. In the present study, we investigated the molecular epidemiology of NV from 66 outbreaks that occurred in Saitama Prefecture, Japan, from 1997 to 2002. We screened 416 stool specimens by a real-time reverse transcription (RT)-PCR method (Kageyama et al., J. Clin. Microbiol. 41:1548-1557, 2003) and detected 156 NV-positive specimens, from which we amplified the capsid N/S domain gene by RT-PCR and then cloned the PCR products. After sequencing these clones, we obtained 368 sequence variants (strains). By applying our classification scheme to the strains from Saitama and other published strains, we identified a total of 31 genotypes, including an additional five genotypes for genogroup I and seven for genogroup II. Of the 31 genotypes, 26 were present in the Saitama area during that time period. These results provide additional evidence for the great diversity of human NV genotypes. Specimens from all shellfish-related infections contained multiple genotypes, including several new genotypes. On the other hand, single genotypes were observed mostly in outbreaks that originated in semiclosed communities. Thus, the number of NV genotypes in each outbreak depended on the route of transmission.

Caliciviridae Infections↗
PubMed1980

Role of intestinal metaplasia in the histogenesis of gastric carcinoma.

Recent evidence suggests that intestinal metaplasia (IM) cannot be regarded as a single entity. A simple classification of IM and its variants based on histological and mucin histochemical criteria was devised, and the incidence of IM subtypes in cancerous and benign gastrectomy specimens was recorded. A particular subtype was associated with 'intestinal' cancers but not with tumours considered to arise in normal gastric epithelium (P < 0.01) or with benign lesions (P < 0.01). This subtype appeared to lack absorptive cells at light microscopic level and secreted both neutral and acid mucins, including marked amounts of sulphomucin but no O-acetyl sialomucin.

Gastric Mucosa↗
PubMed1999

Clinical range and MRI in Creutzfeldt-Jakob disease with heterozygosity at codon 129 and prion protein type 2.

A 68 year old woman with sporadic Creutzfeldt-Jakob disease is described, who neither showed characteristic EEG abnormalities nor a positive test of the neuronal protein 14-3-3 or neuron specific enolase (NSE) in CSF, despite a clinical presentation with ataxia of cerebellar type, rapidly progressive dementia, myoclonus, and marked hyperintense signal abnormalities in the deep cortical layers and the basal ganglia on T2 and diffusion weighted MRI. Moreover she showed atypical clinical features with a syndrome of inappropriate antidiuretic hormone (ADH) secretion (SIADH) and a peripheral sensorimotor polyneuropathy. Whether these disturbances are independent of Creutzfeldt-Jakob disease or a feature of it is discussed. It has recently been shown that in Creutzfeldt-Jakob disease different clinical and pathological phenotypes correlate with the polymorphism at codon 129 of the prion protein gene (PRNP) and the type of the protease resistant fragment that accumulates in the brain. According to the new classification at least six sporadic variants of Creutzfeldt-Jakob disease exist. The molecular genetic analysis showed heterozygosity of PRNP at codon 129 for methionine and valine and the presence of PrP(CJD) type 2 in the brain of this patient. As a new feature of changes on MRI, striking cortical changes of hyperintense signals are described in diffusion weighted as well as T2 weighted MRI that directly correlate with the histomorphological spongy degeneration of the brain in this region. In cases of rapidly progressive dementia, Creutzfeldt-Jakob disease always needs to be considered even if unusual features are present and current diagnostic criteria are not in favour of this disease.

Aged↗
PubMed2002

Chronic pelvic pain in men.

Chronic pelvic pain is a condition which receives less attention in men than in women. It is often difficult to diagnose and more difficult to treat. The new classification of prostatis and its variants has introduced the term 'chronic pelvic pain syndrome' which underlines the difficulties in dealing with this disorder which may represent a variety of chronically painful conditions with a large functional component.

Analgesics↗
PubMed1991

Five cases of DeMyer sequence: an interophthalmic dysplasia.

Five cases with vomero-septal-prolabium agenesis, four with premaxillary agenesis, and one with hemipremaxillary agenesis are presented. All five patients had complete clefts of the secondary palate. No known family history for craniofacial dysmorphia was reported. Height and weight ranged from 2nd to 10th centile. Psychological testing showed intelligent quotients of 121, 93, 72 for three patients; two were microcephalic with undetermined IQ, but severe generalized developmental delay. CT scans for the patient with the IQ of 72 and for one of the two microcephalic subjects showed normal brain structures. The other microcephalic patients had midline prosencephalic dysgenesis. Cephalometric analysis of the cranial base and interorbital dimension using normal standards and self indexing showed hypotelorism and small anterior cranial bases to be apparently related to reduced size of the sphenoid. An intact ethmoid, nasal bone, and crista galli appear to represent key anatomic differences in these patients as compared to classical holoprosencephaly sequence subjects. It was suggested that this pattern of midline facial agenesis may range from a solitary central incisor to the most severe variant presented. Using the embryologic classification, these subjects fall best under the heading of craniofacial dysplasia rather than cerebral craniofacial dysplasia, as a different type of interophthalmic dysplasia or DeMyer sequence.

Cephalometry↗
PubMed1991

Genetic comparison of human immunodeficiency virus (HIV-1) isolates by polymerase chain reaction.

Amplification of DNA by polymerase chain reaction (PCR) is influenced by the homology of oligonucleotide primers with the DNA template. We have developed a procedure, termed anchored PCR, whereby nucleotide sequence alterations in the template can be directly related to the quantity of amplified product. Genetic variation in the human immunodeficiency virus HIV-1 has been studied using anchored PCR. In four field isolates of the virus, the 3'LTR was compared both by PCR analysis of DNA from virus cultures and DNA sequencing. DNA templates that matched the primers varied less than threefold in PCR product yield, whereas significant 3' end primer-template mispairing decreased PCR product 10- to 100-fold. Using these guidelines for genetic variability manifested through PCR, 40 PCR primers encompassing the GAG, ENV, and 3' LTR segments of the genome were used to compare sequential HIV-1 isolates form six patients. Some primers were apparently located in genomic regions without significant interisolate variability, as they yielded equivalent amounts of amplified DNA from all the isolates. The quantity of amplified DNA obtained with other primers varied 10- to 100-fold among patients, but was consistent for sequential isolates from an individual patient. Two African HIV-1 isolates were readily distinguished from a panel of North American isolates by the same method. Systematic classification of HIV-1 genetic variants may be possible by anchored PCR.

Acquired Immunodeficiency Syndrome↗
PubMed1991

Spinocerebellar degeneration.

Forty cases with several forms of spinocerebellar degenerations were studied. The diagnosis was based on an appropriate clinical picture, radiological investigation and family history. There are multiple variants of spinocerebellar degeneration and classification of these diseases remains unsatisfactory and therefore controversial. We classified cases into three main groups. The numbers of cases in each of these groups were as follows: cerebellar group = 16 cases, cerebellar plus group = 9 cases, spinal group = 15 cases. The age, age of onset, mode of inheritance, clinical pictures and cerebrospinal fluid analysis of these cases were discussed. Results of various radiological investigations of these cases were reviewed. From our observations we can conclude that the morphologic changes seen in radiological investigations in our cases were more varied than the observed clinical syndromes. The cause of these syndromes remains unknown and there is no established treatment for spinocerebellar degeneration. We can only offer symptomatic treatment, physiotherapy and genetic counselling for this group of patients.

Adult↗
PubMed1990

Improved method for identifying alpha 1-antitrypsin Pi M subtypes by isoelectric focusing in agarose.

We describe an improved method for the classification of alpha 1-antitrypsin variants by isoelectric focusing in agarose. Identification of the three Pi M subtypes can now be made by using a narrow-range carrier ampholyte (pH 4.2-4.9) and pretreating serum with dithioerythritol-iodoacetic acid to enhance band resolution. Phenotype results for two groups of Pi M homo- and heterozygotes are compared to illustrate the improved accuracy of the new method.

Isoelectric Focusing↗
PubMed1990

An improved method for complement subcomponent C1R typing.

An improved method has been developed for the reliable classification of different C1R genetic variant forms from human serum or plasma. The method combines the use of neuraminidase-digested samples followed by monodimensional isoelectric focusing in the pH range 5 to 8 followed by immunoblotting. The method yields a simple pattern, with one major band in homozygote and two major bands in heterozygote cases.

Blood Grouping and Crossmatching↗
PubMedDate not supplied

Pathogenetic interrelations between cholesterolosis and cholesterol gallstone disease.

In order to define the relationship between cholesterolosis (COL) and cholesterol gallstone disease (CGD), risk factors were comparatively investigated in a great number of patients. Sex, age and metabolic risk factors were the same for both diseases, but gallbladder anomalies and neuroendocrine disturbances were more often associated with COL. The lipid composition of the gallbladder bile was determined in patients with COL. The bile acid decrease and the increase of cholesterol molar concentration (moles %) were found, similar to those known in CGD. The similarity of risk factors and of bile lithogenicity, as well as the frequent association of COL and CGD suggest a pathogenic relationship of both diseases. Local morphological changes in conditions of high biliary cholesterol levels may be responsible for the intraparietal precipitation of cholesterol in COL. Thus, COL seem to be a peculiar variant of CGD and its classification into the heterogeneous group of cholecystoses is at present questionable.

Adult↗
PubMedDate not supplied

Antigenic variability of Shigella flexneri serovars 1-5.

Data on the genetic basis of the classification of Shigella flexneri serological variants 1-5 are presented. Subserovars "a" are related to monolysogenic variants of the basic lipopolysaccharide (LPS) structure 0 antigen 3,4, "b" to bilysogenic ones. A scheme of their antigenic variability, with regard to loss of one or both prophages is presented. This scheme helps differentiate between antigenic variability and mixed or superinfections. Recent reports confirming our previously published suggestion to exclude serovar 6 (Shigella newcastle) from Shigella flexneri are analyzed. We propose that antigenic variability of S. flexneri 1-5 results from lysogenization of naturally occurring strains. The possibility of consecutive lysogenization of S. flexneri y (-:3,4) by bacteriophages 6 and 7 has been shown, as exemplified by the circulation of a previously unknown subserovar IV:7,8.

Antigens, Bacterial↗
PubMed1991

Surface osteosarcoma.

Osteosarcoma arising on the periosteal aspect of bone comprises a biologically heterogeneous group of neoplasms. The group as a whole may be referred to by a single descriptive term that emphasizes their common site of origin and underscores their malignant osteogenic potential: surface osteosarcoma. Its biologic heterogeneity may be approached via a number of avenues. Detailed description of individual tumors and grading are frequently employed. However, implementation of a classification system based upon reproducible clinical, roentgenographic, macroscopic, and histologic parameters is advantageous. The suggested classification system serves to clearly define parosteal and periosteal osteosarcoma, as well as recognize unusual variants. Most important, it defines therapeutic strategy. The classification system identifies low-grade, biologically indolent forms (i.e., parosteal osteosarcoma and periosteal osteosarcoma) that are best treated by surgery alone. At the same time, it recognizes high-grade forms with significant potential for life-threatening behavior (i.e., 'dedifferentiated' parosteal osteosarcoma and high-grade surface osteosarcoma) that are best managed by multimodality therapy incorporating chemotherapy and surgery.

Bone Neoplasms↗
PubMed1980

Three aortic arch anomalies: a review of the literature and proposal of a new classification.

Four patients with three rare aortic arch anomalies, all of which can be classified as variants of Edwards' hypothetical double aortic arch system, were studied. The diagnosis was based on angiographic findings in all cases and, in addition, on operative findings in all cases and, in addition, on operative findings in three and operative and autopsy findings in one case. All normal and anomalous variants of aortic arches may be incorporated into a new classification based upon Edwards' hypothetical double aortic arch system. In the new classification the term double aortic arch with types A, B, C, or D atresia or interruption of the left or the right arch covers all known arch anomalies. The types A, B, C, and D refer to the site of atresia or interruption of the hypothetical double aortic arch model in relationship to the ductus arteriosus and brachiocephalic vessels.

Adult↗
PubMed2006

A working group classification of focal prostate atrophy lesions.

Focal atrophy is extremely common in prostate specimens. Although there are distinct histologic variants, the terminology is currently nonstandardized and no formal classification has been tested for interobserver reliability. This lack of standardization hampers the ability to study the biologic and clinical significance of these lesions. After informal and formal meetings by a number of the authors, focal atrophy lesions were categorized into 4 distinct subtypes as follows: (i) simple atrophy, (ii) simple atrophy with cyst formation, (iii) postatrophic hyperplasia, and (iv) partial atrophy. In phase 1 of the study, pathologists with varying levels of experience in prostate pathology were invited to view via the Internet a set of "training" images with associated descriptions of lesions considered typical of each subtype. In phase 2 of the study, each participant provided diagnoses on a series of 140 distinct "test" images that were viewed over the Internet. These test images consisted of the 4 subtypes of atrophy and images of normal epithelium, high grade prostatic intraepithelial neoplasia, and carcinoma. The diagnoses for each image from each pathologist were compared with a set of "standard" diagnoses and the kappa statistic was computed. Thirty-four pathologists completed both phases of the study. The interobserver reliability (median kappa) for classification of lesions as normal, cancer, prostatic intraepithelial neoplasia, or focal atrophy was 0.97. The median kappa for the classification of atrophy lesions into the 4 subtypes was 0.80. The median percent agreement with the standard diagnosis for the atrophy subtypes were: simple 60.6%, simple with cyst formation 100%; postatrophic hyperplasia 87.5%; partial atrophy 93.9%. The lower percentage for simple atrophy reflected a propensity to diagnose some of these as simple atrophy with cyst formation. Seven pathologists completed the phase 2 analysis a second time, and their intraobserver reproducibility was excellent. Three of 4 pathologists with low agreement with the standard diagnosis for simple atrophy improved their scores after repeating the analysis after re-examination of the "training set" of images. In conclusion, these criteria for variants of focal prostate atrophy may facilitate studies to examine the relation between various patterns of prostate atrophy and prostate cancer.

Atrophy↗