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Biomedical subjects

Neil Renwick

Publications and source records attributed to Neil Renwick.

10 recordsLinked to original sources

Greene SCPrimer: a rapid comprehensive tool for designing degenerate primers from multiple sequence alignments.

Polymerase chain reaction (PCR) is widely applied in clinical and environmental microbiology. Primer design is key to the development of successful assays and is often performed manually by using multiple nucleic acid alignments. Few public software tools exist that allow comprehensive design of degenerate primers for large groups of related targets based on complex multiple sequence alignments. Here we present a method for designing such primers based on tree building followed by application of a set covering algorithm, and demonstrate its utility in compiling Multiplex PCR primer panels for detection and differentiation of viral pathogens.

Algorithms↗

MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004-2005.

In New York State during winter 2004, there was a high incidence of influenza-like illness that tested negative both for influenza virus, by molecular methods, and for other respiratory viruses, by virus culture. Concern that a novel pathogen might be implicated led us to implement a new multiplex diagnostic tool. MassTag polymerase chain reaction resolved 26 of 79 previously negative samples, revealing the presence of rhinoviruses in a large proportion of samples, half of which belonged to a previously uncharacterized genetic clade. In some instances, knowledge of the detected viral and/or bacterial (co)infection could have altered clinical management.

Adolescent↗

MassTag polymerase chain reaction for differential diagnosis of viral hemorrhagic fever.

Viral hemorrhagic fevers are associated with high rates of illness and death. Although therapeutic options are limited, early differential diagnosis has implications for containment and may aid in clinical management. We describe a diagnostic system for rapid, multiplex polymerase chain reaction identification of 10 different causes of viral hemorrhagic fevers.

Diagnosis, Differential↗

Severe acute respiratory syndrome coronavirus persistence in Vero cells.

BACKGROUND: Several coronaviruses establish persistent infections in vitro and in vivo, however it is unknown whether persistence is a feature of the severe acute respiratory syndrome coronavirus (SARS-CoV) life cycle. This study was conducted to investigate viral persistence. METHODS: We inoculated confluent monolayers of Vero cells with SARS-CoV at a multiplicity of infection of 0.1 TCID50 and passaged the remaining cells every 4 to 8 days for a total of 11 passages. Virus was titrated at each passage by limited dilution assay and nucleocapsid antigen was detected by Western blot and immunofluoresence assays. The presence of viral particles in passage 11 cells was assessed by electron microscopy. Changes in viral genomic sequences during persistent infection were examined by DNA sequencing. RESULTS: Cytopathic effect was extensive after initial inoculation but diminished with serial passages. Infectious virus was detected after each passage and viral growth curves were identical for parental virus stock and virus obtained from passage 11 cells. Nucleocapsid antigen was detected in the majority of cells after initial inoculation but in only 10%-40% of cells at passages 2-11. Electron microscopy confirmed the presence of viral particles in passage 11 cells. Sequence analysis at passage 11 revealed fixed mutations in the spike (S) gene and ORFs 7a-8b but not in the nucleocapsid (N) gene. CONCLUSIONS: SARS-CoV can establish a persistent infection in vitro. The mechanism for viral persistence is consistent with the formation of a carrier culture whereby a limited number of cells are infected with each round of virus replication and release. Persistence is associated with selected mutations in the SARS-CoV genome. This model may provide insight into SARS-related lung pathology and mechanisms by which humans and animals can serve as reservoirs for infection.

Animals↗

Diagnostic system for rapid and sensitive differential detection of pathogens.

Naturally emerging and deliberately released pathogens demand new detection strategies to allow early recognition and containment. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples.

Bacterial Infections↗

Genetic similarities between Spitz nevus and Spitzoid melanoma in children.

BACKGROUND: Melanoma in children is rare. Diagnosis of the subtype of melanoma known as Spitzoid melanoma can be extremely challenging in this age group. Spitzoid melanoma clinically and histopathologically resembles a benign melanocytic proliferation referred to as Spitz nevus. In some cases, distinction between the two is impossible. Initial misdiagnoses of Spitzoid melanomas as Spitz nevi, thus leading to fatal outcomes, have occurred. The genetic basis and biologic behavior of Spitzoid melanoma is unknown. Although melanoma specimens exhibit high rates of mutation in the B-RAF and N-RAS genes, the Spitzoid melanoma subtype has not been evaluated. Spitz nevi have been found to be associated with a low percentage of mutations in the H-RAS gene; however, the mutational profile of H-RAS in Spitzoid melanoma is unknown. METHODS: The authors evaluated a unique series of melanomas occurring in prepubescent children that showed Spitz nevus-like histopathology (Spitzoid melanoma). All of the melanomas in the current series have metastasized to lymph nodes, confirming the diagnosis of melanoma. The authors examined these tumors, as well as age-matched Spitz nevi, for mutations in the B-RAF, N-RAS, and H-RAS genes. RESULTS: Activating hotspot mutations in the B-RAF, N-RAS, and H-RAS genes were not identified in Spitzoid melanoma or Spitz nevus specimens. CONCLUSIONS: There are genetic similarities with respect to the B-RAF, N-RAS, and H-RAS genes between Spitzoid melanoma and Spitz nevi. Such similarities further differentiate these two tumor types from other melanoma subtypes and from melanocytic nevi, respectively. However, mutation analysis of B-RAF, N-RAS, and H-RAS was not useful in differentiating between Spitzoid melanoma and Spitz nevus in children.

Age Factors↗

Foamy podocytes.

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Diagnosis, Differential↗

Vascular endothelial growth factor levels in serum do not increase following HIV type 1 and HHV8 seroconversion and lack correlation with AIDS-related Kaposi's sarcoma.

The utility of vascular endothelial growth factor (VEGF) concentrations in serum as a predictive marker for AIDS-KS was studied. Sera were obtained from 40 homosexual men who seroconverted for HIV-1 and HHV8 prior to or during their participation in the Amsterdam Cohort Studies (1984-2000). We designed an ELISA to detect VEGF and measured VEGF prior to either infection, at HIV-1 and HHV8 seroconversion, after both infections, at AIDS-KS diagnosis (n = 11), and in the most recently available serum sample. The geometric mean serum VEGF concentration was 81.5 pg/ml in those with AIDS-KS and 80.4 pg/ml in those with AIDS but without KS. Median serum VEGF concentrations did not differ between the time points described above. Higher VEGF concentrations in serum were observed at higher CD4(+) cell counts. Serum concentrations of VEGF were not influenced by HIV-1 or HHV8 infection or by the conditions leading to AIDS-KS. Sequential measurement of VEGF in serum is not expected to contribute to the prediction or therapeutic monitoring of AIDS-KS.

Acquired Immunodeficiency Syndrome↗

Risk factors for human herpesvirus 8 infection in a cohort of drug users in the Netherlands, 1985-1996.

To elucidate the mode of human herpesvirus 8 (HHV-8) transmission in a population of Amsterdam drug users, HHV-8 seroprevalence and seroincidence were determined in 1179 drug users in the Amsterdam Cohort Studies (1985-1996). Risk factors for HHV-8 infection were examined. Serum samples were screened with an enzyme immunoassay by using HHV-8 lytic capsid (open-reading frame [ORF] 65) and latent nuclear (ORF73) antigens; positive results were confirmed by Western blot and immunofluorescence assay. Seroprevalence (men, 3.4%; women, 1.4%) and seroincidence (men, 0.08; women, 0.05/100 person-years) were low in this study. Infections with human immunodeficiency virus (HIV) type 1, hepatitis B virus (HBV), and hepatitis C virus (HCV), but not HHV-8, were associated with injection drug use (IDU). Independent risk factors for HHV-8 seropositivity were homosexual contacts and Mediterranean nationality for men and sexual contact with bisexual men, absence of a steady partner, and unprotected commercial sex for women. Unlike HIV-1, HBV, or HCV infection, HHV-8 infection is uncommon in Amsterdam drug users, as is HHV-8 transmission through IDU.

Adult↗