Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study.

Background: Encephalitis has many causes, but for most patients the cause is unknown. We aimed to establish the cause and identify the clinical differences between causes in patients with encephalitis in England.

Methods: Patients of all ages and with symptoms suggestive of encephalitis were actively recruited for 2 years (staged start between October, 2005, and November, 2006) from 24 hospitals by clinical staff.

Large-scale immunohistochemical examination for lymphoreticular prion protein in tonsil specimens collected in Britain.

There have been 173 cases of variant Creutzfeldt-Jakob disease (vCJD) in the UK, as of 5 July 2010, as a result of the bovine spongiform encephalopathy epidemic. The number of individuals subclinically infected with vCJD, and thus the eventual number of cases, remains, however, uncertain. In an attempt to address this problem, 63,007 tonsil tissue specimens were previously tested by enzyme immunoassay (EIA) for the presence of disease-related prion protein (PrP(res)) and found to be negative.

Prevalence of disease related prion protein in anonymous tonsil specimens in Britain: cross sectional opportunistic survey.

Objective: To establish with improved accuracy the prevalence of disease related prion protein (PrP(CJD)) in the population of Britain and thereby guide a proportionate public health response to limit the threat of healthcare associated transmission of variant Creutzfeldt-Jakob disease (vCJD).

Design: Cross sectional opportunistic survey. Study samples Anonymised tonsil pairs removed at elective tonsillectomy throughout England and Scotland.

Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions.

Phylogenetic reconstructions of transmission events from individuals with acute human immunodeficiency virus (HIV) infection are conducted to illustrate this group's heightened infectivity. Varied definitions of acute infection and assumptions about observed phylogenetic clusters may produce misleading results. We conducted a phylogenetic analysis of HIV pol sequences from 165 European patients with estimated infection dates and calculated the difference between dates within clusters.

Virus discovery by sequence-independent genome amplification.

Genome sequences from several blood borne and respiratory viruses have recently been recovered directly from clinical specimens by variants of a technique known as sequence-independent single primer amplification. This and related methods are increasingly being used to search for the causes of diseases of presumed infectious aetiology, but for which no agent has yet been found. Other methods that do not require prior knowledge of the genome sequence of any virus that may be present in the patient specimen include whole genome amplification, random PCR and subtractive hybridisation and differential display.

Emergence of a three codon deletion in gag p17 in HIV type 1 subtype C long-term survivors, and general population spread.

In a population-based study in northern Malawi we investigated HIV-1 subtype C gag and env gene sequences associated with long-term survival. DNA samples were available from 31 individuals surviving between population surveys carried out in the 1980s and 1990s. Most survivors with paired sequences dating from the 1980s and the 1990s had a three codon deletion in the gag p17 region of the sequence retrieved from the sample collected in the 1990s that was not present in the sequence from the same individual dating from the 1980s.

An immunoassay for the pathological form of the prion protein based on denaturation and time resolved fluorometry.

Concern about the possible secondary spread of variant Creutzfeldt-Jakob disease (vCJD) through blood transfusion and blood products has increased the need for a sensitive and rapid test for the identification of PrP(Sc) in specimens collected non-invasively from living persons. Furthermore, an accurate estimate of the prevalence of pre-clinical vCJD in the British population would be possible if there were such a test that could be applied to specimens available readily (e.g.

Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups.

We explored the epidemic history of HIV-1 subtype B in the United Kingdom by using statistical methods that infer the population history of pathogens from sampled gene sequence data. Phylogenetic analysis of HIV-1 pol gene sequences from Britain showed at least six large transmission chains, indicating a genetically variable, but epidemiologically homogeneous, epidemic among men having sex with men. Through coalescent-based analysis, we showed that these chains arose through separate introductions of subtype B strains into the United Kingdom in the early to mid-1980s.

Prospects for the development of pre-mortem laboratory diagnostic tests for Creutzfeldt-Jakob disease.

At present the diagnosis of Creutzfeldt-Jakob disease (CJD) and related transmissible spongiform encephalopathies in humans is based on clinical criteria and (at post-mortem) the histopathological and immunological examination of brain tissue. The misfolded prion protein, PrPSc, is the single most significant marker, but its recognition by standard serological methods is complicated by its antigenic similarity to the normal prion protein, PrPC. Although there are commercial diagnostic assays available for bovine spongiform encephalopathy using brain specimens taken at slaughter, there are no suitable pre-mortem assays for cattle and none either for pre-mortem human disease.

Timing and reconstruction of the most recent common ancestor of the subtype C clade of human immunodeficiency virus type 1.

Human immunodeficiency virus type 1 (HIV-1) subtype C is responsible for more than 55% of HIV-1 infections worldwide. When this subtype first emerged is unknown. We have analyzed all available gag (p17 and p24) and env (C2-V3) subtype C sequences with known sampling dates, which ranged from 1983 to 2000.

Surveillance of HIV-1 subtypes among heterosexuals in England and Wales, 1997-2000.

The molecular diversity and demographic characteristics among 976 anti-HIV-1-positive heterosexuals attending 15 sexually transmitted infection (STI) clinics participating in an unlinked anonymous HIV prevalence serosurvey in England and Wales during 1997-2000 were investigated. Subtypes were assigned by heteroduplex mobility assay or sequencing of the p17/p24 region of gag and the V3/V4 region of env and by sequencing of the protease gene. Overall, there was no significant change in the subtype distribution, with subtype C accounting for the majority (32%) of subtyped infections.

New simian immunodeficiency virus infecting De Brazza's monkeys (Cercopithecus neglectus): evidence for a cercopithecus monkey virus clade.

Nearly complete sequences of simian immunodeficiency viruses (SIVs) infecting 18 different nonhuman primate species in sub-Saharan Africa have now been reported; yet, our understanding of the origins, evolutionary history, and geographic distribution of these viruses still remains fragmentary. Here, we report the molecular characterization of a lentivirus (SIVdeb) naturally infecting De Brazza's monkeys (Cercopithecus neglectus). Complete SIVdeb genomes (9,158 and 9227 bp in length) were amplified from uncultured blood mononuclear cell DNA of two wild-caught De Brazza's monkeys from Cameroon.

Enigmas and paradoxes: the genetic diversity and prevalence of the primate lentiviruses.

In a comparatively few years a previously unknown virus has spread from its animal host to infect more than 40 million people by the end of 2003, causing an estimated 3 million deaths in that year (World Health Organization figures). The size of this human immunodeficiency virus (HIV) epidemic and its associated health, social and economic problems make it imperative that we understand how its two types, HIV-1 and HIV-2, have evolved from their simian relatives, the primate lentiviruses (PLVs). There are several features of the PLVs that may be considered enigmatic or even paradoxical, and which are relevant to studies of their evolution.

HIV-1 pol gene variation is sufficient for reconstruction of transmissions in the era of antiretroviral therapy.

Objectives: We wished to assess the potential of using HIV-1 pol gene for the identification of transmissions events by phylogenetic means in the era of antiretroviral drug selective pressure.

Design: The relatedness of the viruses within a large database of pol sequences generated from HIV-1 infected individuals from the UK was reconstructed by phylogenetic analyses.

Methods: A total of 140 pol sequences were selected out of the 2500 database entries, on the basis of a pairwise genetic distance higher than 95%.

A role for arrays in clinical virology: fact or fiction?

Microarrays of DNA probes have at least three roles in clinical virology. These are: firstly, in diagnosis, to recognise the causative agent of an illness; secondly, for molecular typing for (i) patient management, (ii) epidemiological reasons (e.g.

Highly divergent HIV type 1 group M sequences evident in Karonga District, Malawi in early 1980s.

Six divergent HIV-1 partial env and gag genome sequences have been characterized in five subjects in Malawi, from whom blood spot samples were collected between 1982 and 1989, at the time that the AIDS epidemic there was starting. These sequences could not be classified with any of the recognized subtypes or circulating recombinant forms of HIV-1. They showed no consistent and/or supported associations with other subtypes by either env or gag gene phylogenetic analysis.

Coxsackievirus B3 sequences in the blood of a neonate with congenital myocarditis, plus serological evidence of maternal infection.

A fatal case of myocarditis in a neonate is described. The clinical features were evident at birth, and enteroviral RNA was detected in the blood of the baby on the day of birth and again 10 days later by a generic enterovirus nested reverse transcription-polymerase chain reaction (RT-PCR) assay. The enterovirus RNA was subsequently retested by a separate, newly developed nested RT-PCR assay yielding a PCR product within the VP1 coding region suitable for sequencing.

Characterization of a novel simian immunodeficiency virus (SIVmonNG1) genome sequence from a mona monkey (Cercopithecus mona).

A novel simian immunodeficiency virus (SIV) sequence has been recovered from RNA extracted from the serum of a mona monkey (Cercopithecus mona) wild born in Nigeria. The sequence was obtained by using novel generic (degenerate) PCR primers and spans from two-thirds into the gag gene to the 3' poly(A) tail of the SIVmonNG1 RNA genome. Analysis of the open reading frames revealed that the SIVmonNG1 genome codes for a Vpu protein, in addition to Gag, Pol, Vif, Vpr, Tat, Rev, Env, and Nef proteins.

Early evolution of the human immunodeficiency virus type 1 subtype C epidemic in rural Malawi.

We have tracked the early years of the evolution of the human immunodeficiency virus type 1 (HIV-1) epidemic in a rural district of central east Africa from the first documented introductions of subtypes A, D, and C to the present predominance of subtype C. The earliest subtype C sequences ever reported are described. Blood samples were collected on filter papers from 1981 to 1984 and from 1987 to 1989 from more than 44,000 individuals living in two areas of Karonga District, Malawi.

The application of molecular phylogenetics to the analysis of viral genome diversity and evolution.

DNA sequencing and molecular phylogenetics are increasingly being used in virology laboratories to study the transmission of viruses. By reconstructing the evolutionary history of viral genomes the behaviour of viral populations can be modelled, and the future of epidemics may be forecast. The manner in which such viral DNA sequences are analysed is the focus of this review.