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P Simmonds

Publications and source records attributed to P Simmonds.

At least 181 records · Page 10Linked to original sources
PubMed1994

In vivo distribution and cytopathology of variants of human immunodeficiency virus type 1 showing restricted sequence variability in the V3 loop.

The distribution, cell tropism, and cytopathology in vivo of human immunodeficiency virus (HIV) was investigated in postmortem tissue samples from a series of HIV-infected individuals who died either of complications associated with AIDS or for unrelated reasons while they were asymptomatic. Proviral sequences were detected at a high copy number in lymphoid tissue of both presymptomatic patients and patients with AIDS, whereas significant infection of nonlymphoid tissue such as that from brains, spinal cords, and lungs were confined to those with AIDS. V3 loop sequences from both groups showed highly restricted sequence variability and a low overall positive charge of the encoded amino acid sequence compared with those of standard laboratory isolates of HIV type 1 (HIV-1). The low charge and the restriction in sequence variability were comparable to those observed with isolates showing a non-syncytium-inducing (NSI) and macrophage-tropic phenotype in vitro. All patients were either exclusively infected (six of seven cases) or predominantly infected (one case) with variants with a predicted NSI/macrophage-tropic phenotype, irrespective of the degree of disease progression. p24 antigen was detected by immunocytochemical staining of paraffin-fixed sections in the germinal centers within lymphoid tissue, although little or no antigen was found in areas of lymph node or spleen containing T lymphocytes from either presymptomatic patients or patients with AIDS. The predominant p24 antigen-expressing cells in the lungs and brains of the patients with AIDS were macrophages and microglia (in brains), frequently forming multinucleated giant cells (syncytia) even though the V3 loop sequences of these variants resembled those of NSI isolates in vitro. These studies indicate that lack of syncytium-forming ability in established T-cell lines does not necessarily predict syncytium-forming ability in primary target cells in vivo. Furthermore, variants of HIV with V3 sequences characteristic of NSI/macrophage-tropic isolates form the predominant population in a range of lymphoid and nonlymphoid tissues in vivo, even in patients with AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1994

Hepatitis C virus genotypes among HCV-chronic liver disease patients in Egypt: a leading trial.

UNLABELLED: In this trial, we have checked 50 anti-HCV positive, HCV-RNA PCR positive chronic liver disease cases, 44 males, 6 females with a mean age of 51 years. HCV-RNA extraction and genotyping was carried out at the Department of Medical Microbiology, University of Edinburgh, U.K. results showed that 47 (94%) of patients were of genotype 4 and 3 (6%) were of genotype 1. Liver biopsies were performed in 22 only out of the 50 patients studied. The 3 genotype 1 patients were biopsied, 2 had cirrhotic profile and one had CAH. Of 47 genotype 4 patients, 19 were biopsied, 3 were CPH, 2 had CLH, 9 had CAH, 4 had cirrhosis and one patient had HCC. CONCLUSION: It appears that Egypt hosts predominantly HCV genotype 4 and less commonly genotype 1. This finding might have important implications concerning the epidemiological aspects, pathogenesis and response to antiviral therapy.

Chronic Disease↗
PubMed1994

Failure to detect hepatitis A virus RNA in factor VIII concentrates using the polymerase chain reaction. Results of a preliminary study.

The transmission of hepatitis A virus (HAV) infection to recipients of some batches of Factor VIII has recently been reported. The polymerase chain reaction (PCR) was used for the detection of HAV RNA in factor VIII concentrates. Primer sequences used were derived from a consensus of published sequences in the 5' non coding region; a nested PCR was used to increase sensitivity and specificity and the resulting fragment was 151 base pairs in length. The PCR was initially validated in clinical samples and only IgM anti-HAV positive patient samples and a sample of liver tissue from a patient who required liver transplantation for fulminant hepatitis A were HAV PCR positive. Other samples tested included those that were IgG anti-HAV positive; these were found to be PCR negative. In an investigation of coagulation factor VIII concentrates by HAV PCR, 40 batches of solvent/detergent-treated high-purity concentrate from four different manufacturers, including one batch of factor VIII possibly implicated in HAV transmission, and a further 3 batches of monoclonal antibody purified factor VIII were all HAV PCR negative. Gel chromatography material, before and after use in factor VIII purification, and eluates from this material were also negative for HAV RNA. Our preliminary results therefore suggest that either the contamination of factor VIII concentrates by HAV RNA is an extremely rare event or that the PCR is insufficiently sensitive to detect an infective HAV dose since each batch of factor VIII concentrate would have been derived from a plasma pool consisting of 10,000 donations, or more and the resulting concentration of virus may be 10(2) or less.

Base Sequence↗
PubMed1994

Hepatitis C virus genotypes: an investigation of type-specific differences in geographic origin and disease.

Because of the nucleotide sequence diversity of different isolates of hepatitis C virus, it has become important to clarify whether distinct genotypes of hepatitis C virus vary with respect to pathogenicity, infectivity, response to antiviral therapy and geographic clustering. We assessed nucleotide sequence variability in the 5' noncoding region of hepatitis C virus, using restriction enzymes to analyze the distribution of hepatitis C virus genotypes, in 80 patients with chronic hepatitis C virus infection. Genotypes were correlated with demographic, clinical and histological features. Thirty-seven patients were infected with type 1, 10 had type 2 and 8 had type 3, and another 23 were infected with a new distinct hepatitis C virus type now classified as type 4. Two were infected with variants whose classification are uncertain. Types 1, 2 and 3 were found in patients from the United Kingdom, southern Europe, Asia, Africa and South America. Nineteen of 23 type 4 genotype isolates were from Middle Eastern patients, compared with 0 of 37 type 1 isolates (p < 0.001). Of 21 Middle Eastern patients, 19 (90.4%) had type 4 hepatitis C virus (p = 0.001, odds ratio = 9). We found no significant difference between the mean ages or mean serum aminotransferase concentrations between the various types. Types 1, 2, 3 and 4 were found in patients with mild-to-moderate disease or severe disease. However, 21 of 29 (72.4%) patients with type 1 who underwent liver biopsy had severe chronic hepatitis, cirrhosis or hepatocellular carcinoma histologically; 8 had mild or moderate chronic hepatitis without cirrhosis (p = 0.03, odds ratio = 2.6).(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1993

Confirmation of hepatitis C virus antibody in blood donors.

Of 103,203 donations collected in Scotland and Northern Ireland over a 3-month period and screened for HCV antibody by Ortho or Abbott second-generation ELISAs, 340 were found repeatedly reactive. Supplementary testing with RIBA-2 resulted in 77 being classified as positive, 130 as indeterminate, and 133 as negative. PCR analysis of the positives and indeterminates indicated viraemia in 65 (84%) of the positives and 7 (5.5%) of the indeterminates. To determine if PCR analysis could be eliminated or reduced by further serological testing, all RIBA-2 positives and indeterminates were tested by UBI and Wellcozyme ELISAs and Innolia and RIBA-3 immunoblots. All RIBA-2 positives with bands to more than 1 gene product were detected in all 4 systems, but > 60% of RIBA-2 indeterminates were negative in those tests that contain either recombinant antigens or synthetic peptides derived independently from those used by Ortho/Abbott tests. A comparison of data from the 79 reactive with the core (c22) region revealed only 16 samples reactive in all 4 systems as well as Ortho and Abbott. These 16 included all 6 of the PCR positives in the 79 c22 indeterminate samples. ELISAs and immunoblots using independently derived antigens can offer a useful method of screening out nonspecific reactions in Ortho or Abbott ELISAs, hence reducing the need for PCR testing. Some caution is required as all such tests do not contain identical mixes of antigenic material.

Antigens, Viral↗
PubMed1993

A comparison of polymerase chain reaction and an infectivity assay for human immunodeficiency virus type 1 titration during virus inactivation of blood components.

Three examples of human plasma-derived concentrates, intermediate-purity factors VIII and IX, and fibrinogen were spiked with tissue culture-grown human immunodeficiency virus type 1 (HIV-1) strain RF. All examples were freeze-dried and heated at 80 degrees C for 72 hours by using validated production process models. HIV-1 infectivity was measured by a syncytial infectivity assay in C8166 cells and then compared with levels determined by nested HIV polymerase chain reaction (PCR). The infectivity assay demonstrated a reduction index of at least 4.5 log10, while PCR showed an average 1.7 log10. Large amounts of HIV-1 RNA (10(5)) were still detectable by PCR in samples in which infectivity assays failed to detect any HIV-1. These data suggest that HIV-1 PCR levels do not parallel HIV-1 infectivity levels during virus-inactivation procedures involved in coagulation factor concentrate production. PCR was able to detect the RNA associated with inactivated HIV-1 particles in the factor concentrates, which allows the conclusion that PCR is not a useful test with which to monitor virus-inactivation procedures such as heating at 80 degrees C for 72 hours. This judgment contrasts with the more definite and sensitive role of PCR in diagnosing HIV-1 infection in patients in whom a positive HIV-1 PCR result correlates with active HIV-1 infection and with PCR's usefulness in monitoring virus removal.

DNA, Viral↗
PubMed1993

Detection of three types of hepatitis C virus in blood donors: investigation of type-specific differences in serologic reactivity and rate of alanine aminotransferase abnormalities.

The serologic reactivity and epidemiology associated with different hepatitis C virus (HCV) variants were investigated in a cohort of 113 anti-HCV-positive donors. In Scotland, HCV type 1 accounted for one-half of all infections; 40 percent of subjects were infected with HCV type 3, and the remainder were infected with type 2. Reactivity with the NS-4-encoded antigens in the first-generation anti-c100 assay was absent in 68 percent of donors infected with types 2 and 3, as compared with 10 percent for those infected with type 1. Even when combined with surrogate marker testing, first-generation tests would have failed to detect 12 percent of HCV-infected blood donors. The age distribution, incidence of past infection with hepatitis B virus, and reported risk factors were similar in donors infected with types 1 and 3 (mean ages were 31.9 and 29.9; 18 and 17.5% were positive for antibody to hepatitis B core antigen; and 47 and 48% had past intravenous drug abuse). However, the distributions of alanine aminotransferase levels were significantly different in those infected with type 3 (abnormally raised in 83%) and those infected with type 1 (55% abnormal alanine aminotransferase; p < 0.05) or type 2 (60%; p < 0.01) and those who were nonviremic (8%; p < 0.0001). These data suggest that HCV type 1 is the most common HCV infection in blood donors and that infection with HCV type 3 may be associated with more severe liver disease, because of more recent infection or because of a greater inherent pathogenicity of type 3 variants.

Alanine Transaminase↗
PubMed1993

Infrequent vertical transmission of hepatitis C virus.

The rate of vertical transmission of hepatitis C virus (HCV) was determined by a combination of assays for anti-HCV antibody and the polymerase chain reaction (PCR) in 66 children born to infected mothers. Only 4 children showed evidence of infection with HCV, being positive for anti-HCV in all samples collected from 6 months to 5 years of age. All samples from the remaining 62 children were repeatedly anti-HCV-negative on screening by two second-generation antibody assays. Furthermore, samples collected at age 12 months from 30 antibody-negative children born of HCV-infected mothers were uniformly PCR-negative, showing that "seronegative" infection with HCV was rare or absent in this study group. Serologic reactivity to HCV-encoded antigens in samples from infected children was largely confined to the HCV core protein. Infection with human immunodeficiency virus in the mother was not a significant cofactor for mother-to-child transmission of HCV.

Child, Preschool↗
PubMed1993

Molecular investigation of human immunodeficiency virus (HIV) infection in a patient of an HIV-infected surgeon.

Recall of patients who had been treated by a human immunodeficiency virus (HIV)-infected surgeon uncovered 1 previously unknown HIV-seropositive person. Nucleotide sequencing of the gag gene and maximum likelihood phylogenetic analysis were used to investigate the relationships among sequences from the surgeon, the patient, and an anonymous blood donor from whom the patient had received blood products. The likelihoods of all possible pathways of transmission linking these persons were estimated. On these data, transmission from the surgeon to the patient was significantly less likely than from the blood donor to the patient. It is concluded that none of the recalled patients were infected by the surgeon.

Base Sequence↗
PubMed1993

Human immunodeficiency virus and the brain: investigation of virus load and neuropathologic changes in pre-AIDS subjects.

Brain tissue was examined for evidence of human immunodeficiency virus (HIV) infection in 23 intravenous drug users who died suddenly some years after seroconversion but while still in presymptomatic stages of infection. None showed giant cell encephalitis, but 14 showed T cell lymphocytic leptomeningitis and 3 showed other significant neuropathologic features. Quantitative polymerase chain reaction for HIV was applied to 13 of the 23 with negative results in 6 and very low positive results in the other 7, a finding consistent with contamination by residual infected blood in the brain tissue. This contrasted with findings in AIDS-infected tissue, in which substantial amounts of provirus were found. It is concluded that significant infection in brain tissue does not occur in presymptomatic stages of HIV infection and that invasion of the central nervous system may be delayed until the transition to symptomatic AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1993

Classification of hepatitis C virus into six major genotypes and a series of subtypes by phylogenetic analysis of the NS-5 region.

Hepatitis C virus (HCV) showed substantial nucleotide sequence diversity distributed throughout the viral genome, with many variants showing only 68 to 79% overall sequence similarity to one another. Phylogenetic analysis of nucleotide sequences derived from part of the gene encoding a non-structural protein (NS-5) has provided evidence for six major genotypes of HCV amongst a worldwide collection of 76 samples from HCV-infected blood donors and patients with chronic hepatitis. Many of these HCV types comprised a number of more closely related subtypes, leading to a current total of 11 genetically distinct viral populations. Phylogenetic analysis of other regions of the viral genome produced relationships between published sequences equivalent to those found in NS-5, apart from the more highly conserved 5' non-coding region in which only the six major HCV types, but not subtypes, could be differentiated. A new nomenclature for HCV variants is proposed in this communication that reflects the two-tiered nature of sequence differences between different viral isolates. The scheme classifies all known HCV variants to date, and describes criteria that would enable new variants to be assigned within the classification as they are discovered.

Base Sequence↗
PubMed1993

Sequence variability in the 5' non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity.

We have analysed the pattern of nucleotide sequence variability in the 5' non-coding region (5' NCR) of geographically dispersed variants of hepatitis C virus (HCV). Phylogenetic analysis of sequences in this region indicated the existence of a new virus type, provisionally termed type 4, the identity of which was confirmed by further analysis of the more variable part of the HCV core protein coding region. The geographical distribution of HCV type 4 was distinct from that of other HCV types, it being particularly widespread in Africa and absent or rare in Europe and the Far East. Much of the variability in the 5' NCR appears to be constrained by a requirement for specific secondary structures in the viral RNA. In one of the most variable regions of the 5' NCR (positions -169 to -114), most of the nucleotide changes that are characteristic of different HCV types were covariant, with complementary substitutions at other positions. According to the proposed secondary structure of the 5' NCR, such changes preserved base pairing within a stem-loop structure, whereas the nucleotide insertions found in a proportion of 5' NCR sequences, including those of type 4, localized exclusively to the non-base-paired terminal loop. The specific nucleotide substitutions in the 5' NCR that differentiate each of the four HCV types can be detected by restriction enzyme cleavage, providing a rapid and reliable method for virus typing.

Amino Acid Sequence↗
PubMed1993

Thymic hyperplasia in adults following chemotherapy for malignancy.

BACKGROUND: The accuracy of the assessment of patients with malignant disease and of their response to chemotherapy has been significantly improved with the routine availability of computerized tomography (CT) scanning. CT abnormalities, however, may be non-specific, especially after chemotherapy. Rebound enlargement of the thymus gland after chemotherapy induced atrophy is one cause of an abnormal thoracic CT scan on re-staging. AIMS: This phenomenon has previously been reported mainly in relation to the treatment of lymphoma and germ cell cancers. This paper highlights the occurrence of thymic hyperplasia after chemotherapy in these and other tumour types. METHODS: We discuss five cases including three patients with malignancies other than lymphoma in whom thymus enlargement occurred during or after intensive chemotherapy. RESULTS: Clear identification of the nature of CT abnormalities after chemotherapy, particularly in the mediastinum, is required prior to embarking on further anti-cancer treatments.

Adult↗
PubMed1993

Detection of parvovirus B19 in donated blood: a model system for screening by polymerase chain reaction.

A highly sensitive and rapid method for routinely screening large numbers of donated blood units for parvovirus B19 by the polymerase chain reaction (PCR) was developed. Over a 3-month trial period in Edinburgh, B19 DNA was detected in 6 of 20,000 consecutive units of blood (0.03%), in concentrations ranging from 2.4 x 10(4) to 5 x 10(10) copies of viral DNA per ml. Seroconversion for B19-specific immunoglobulin M and immunoglobulin G and disappearance of circulating B19 DNA occurred in the interval between donation and recall in four of the five implicated donors who could be recalled. B19 DNA was detected in 18 of 27 separate batches of non-heat-treated factor VIII and IX concentrate manufactured from donated plasma unscreened for B19 DNA. Dry-heat treatment at 80 degrees C for 72 h reduced but did not always eliminate detectable B19 from factor VIII concentrates, consistent with recent observations that current methods for virus inactivation during blood product manufacture are insufficient to entirely eliminate B19 infectivity. The methods developed in this study for PCR screening could be applied routinely to prevent transfusion of B19 in blood and blood products and could play an important role in the prevention of iatrogenic transmission of infection. PCR screening could also be used for detection and exclusion of a range of other transmission-associated viruses for which current serological detection methods are only partially effective.

Base Sequence↗