Identification of Sensitive and Specific Avian Influenza Polymerase Chain Reaction Methods Through Blind Ring Trials Organized in the European Union

Many different polymerase chain reaction (PCR) protocols have been used for detection and characterization of avian influenza (AI) virus isolates, mainly in research settings. Blind ring trials were conducted to determine the most sensitive and specific AI PCR protocols from a group of six European Union (EU) laboratories. In part 1 of the ring trial the laboratories used their own methods to test a panel of 10 reconstituted anonymized clinical specimens, and the best methods were selected as recommended protocols for part 2, in which 16 RNA specimens were tested. Both panels contained H5, H7, other AI subtypes, and non-AI avian pathogens. Outcomes included verification of 1) generic AI identification by highly sensitive and specific M-gene real-time PCR, and 2) conventional PCRs that were effective for detection and identification of H5 and H7 viruses. The latter included virus pathotyping by amplicon sequencing. The use of recommended protocols resulted in improved results among all six laboratories in part 2, reflecting increased sensitivity and specificity. This included improved H5/H7 identification and pathotyping observed among all laboratories in part 2. Details of these PCR methods are provided. In summary, this study has contributed to the harmonization of AI PCR protocols in EU laboratories and influenced AI laboratory contingency planning following the first European reports of H5N1 highly pathogenic AI during autumn 2005.

Recent epidemiology and ecology of influenza A viruses in avian species in Europe and the Middle East

There have been at least ten distinct outbreaks of LPAI or HPAI in poultry caused by H5 or H7 viruses in the last eight years in Europe and the Middle East. There appears to be an increased occurrence of such episodes consistent with global trends. As a result, surveillance systems have been enhanced to facilitate early detection of infection in poultry, together with active surveillance of wild bird populations. These complementary activities have resulted in the detection of a number of viruses in wild bird populations, including some with high genetic similarity to newly detected viruses in poultry, for example, H7N3 in Italy and H7N7 in the Netherlands. Furthermore, there is evidence for continued circulation of H5 and H7 viruses in wild Anseriformes, thereby presenting a real and current threat for the introduction of viruses to domestic poultry, especially those reared in outdoor production systems. Viruses of H9N2 subtype continue to circulate widely in the Middle East and are associated with significant disease problems in poultry. The epidemiology has the potential to be complicated further by introduction of novel viruses through illegal importation of captive birds, such as was detected with H5N1 in Belgium in 2004. Continual genetic exchange in the avian virus gene pool and independent evolution of all gene segments either within an individual host species or among wild bird hosts suggests that these viruses are not in evolutionary stasis in the natural reservoir.

SERF: a new antigen in the Cromer blood group system

The Cromer blood group system consists of eight high incidence and three low incidence antigens carried on decay-accelerating factor (DAF). This report describes the identification and characterization of a new Cromer high incidence antigen, named SERF. Sequence analyses of DNA from a Thai female whose serum contained the alloantibody to a high incidence antigen in the Cromer blood group system (anti-SERF) and from her two children were performed. Reverse transcriptase-polymerase chain reaction (RT-PCR) and sequence analysis on cDNA from the proband and PCR-restriction fragment length polymorphism analysis on DNA from Thais were also performed. To map the epitope, DAF deletion mutants were tested by immunoblotting with anti-SERF. Sequence analysis revealed a substitution of 647C>T in exon 5 DAF in the proband. The proband's two children and two of 100 Thais were heterozygotes 647C/T. Analysis using DAF deletion mutants revealed the antigenic determinant to be within short consensus repeat 3 (SCR3), which is encoded by exon 5. This study describes a novel high incidence antigen (SERF) in the Cromer blood group system characterized by the amino acid proline at position 182 in SCR3 of DAF. The SERF-negative proband has a substitution mutation that predicts for leucine at this position. SERF has been provisionally assigned the International Society of Blood Transfusion number 021.012 (CROM 12).

LU21: a new high-frequency antigen in the Lutheran blood group system

BACKGROUND AND OBJECTIVES

The Lutheran blood group system comprises 18 antigens numbered LU1 to LU20, with two numbers obsolete. Thirteen antigens are of high frequency.

MATERIALS AND METHODS

Serological tests were performed by conventional methods. The monoclonal antibody-specific immobilization of erythrocyte antigens (MAIEA) assay was carried out with monoclonal antibodies to Lutheran glycoprotein. All exons of the LU gene were amplified by the polymerase chain reaction (PCR) and directly sequenced from genomic DNA.

RESULTS

A patient was found to have an antibody to a high-frequency red cell antigen during her second pregnancy. The antibody was shown to be Lutheran-related and was distinguished from all reported Lutheran antibodies. MAIEA suggested the antibody was defining a novel epitope in domain 1 of the Lu-glycoprotein. Sequencing of the LU gene revealed a new homozygous single-point mutation, C282G, in exon 3, encoding an Asp94Glu change in the first domain of the Lu-glycoprotein.

CONCLUSIONS

The antibody detected a new high-frequency Lutheran antigen, numbered LU21, that appears to result from an Asp94Glu substitution in the first, N-terminal domain of the Lu-glycoprotein.

Retrospective characterization of Newcastle Disease Virus Antrim '73 in relation to other epidemics, past and present

In November 1973 Newcastle disease suddenly appeared in Northern Ireland, where the viscerotropic disease had not been seen in 3 1/2 years and the two Irelands had been regarded as largely disease free for 30 years. It was successfully controlled with only 36 confirmed affected layer flocks, plus 10 more slaughtered as 'dangerous contacts'. Contemporary investigations failed to reveal the source of the Irish epidemic. Using archival virus samples from most of the affected flocks, RT PCR was conducted with primers selected for all six NDV genes. Phylogenetic analyses of three genes, HN, M and F, confirmed vaccine as the cause of one of the outbreaks. The other six samples were identical and closely related to previous outbreaks in the United States and western Europe initiated by infected imported Latin American parrots. The probable cause of the epidemic followed from the importation from The Netherlands of bulk feed grains contaminated with infected pigeon faeces.

White-tailed spider bites--arachnophobic fallout?

AIM

To investigate if public concern regarding the toxic effects of the bites from white-tailed spiders, Lampona cylindrata and L. murina, is reflected in the case histories of patients admitted to Christchurch Hospital with a diagnosis of spider bite.

METHODS

The case histories of patients admitted to Christchurch Hospital with a diagnosis of 'contact with venomous spiders' were examined for evidence that the patients developed necrotising arachnidism.

RESULTS

Ten patients were admitted to Christchurch Hospital between January 2001 and January 2003 with a diagnosis of 'contact with venomous spiders'. We found no evidence that patients developed necrotising arachnidism. No patients admitted to Christchurch Hospital required re-admission to treat sequelae of the putative spider bite. Support for a spider bite as the causative agent was not robust and alternative agents could have been the cause.

CONCLUSIONS

The public's fear of bites from white-tailed spiders is likely misplaced and, if the spider was not caught in the act of biting the patient, alternative diagnoses should be considered before assuming a white-tailed spider was responsible for the patient's symptoms.

Additional glycosylation at the receptor binding site of the hemagglutinin (HA) for H5 and H7 viruses may be an adaptation to poultry hosts, but does it influence pathogenicity?

Sequence analysis of the hemagglutinin (HA) gene of H5 and H7 viruses was used to determine phylogenetic relationships between high-pathogenicity avian influenza (HPAI) and low-pathogenicity avian influenza (LPAI) viruses from avian influenza (AI) outbreaks in Norfolk in 1979 and 1991 and Italy in 1999-2000. A common feature within these groups of viruses was the acquisition of additional glycosylation sites near the receptor binding site of the HA. Passage of H5 viruses through 14-day-old embryonated fowls' eggs readily selected viruses with additional glycosylation of HA1. Although additional glycosylation may not correlate with increased pathogenicity for fowl, it may predispose viruses to become highly pathogenic.

Genotypic and phenotypic characterization of the dynamics of the lactic acid bacterial population of adjunct-containing Cheddar cheese manufactured from raw and microfiltered pasteurised milk

AIMS

This study investigates the dynamics of the microflora, particularly the lactobacilli, in Cheddar cheese manufactured from raw and microfiltered milk containing different adjunct cultures.

METHODS AND RESULTS

Sixteen cheeses - raw milk, adjunct and control cheeses - were manufactured in four trials. Lactobacilli were identified by PCR methods in one trial, and by phenotypic typing for all trials. Numbers of lactobacilli were significantly different at day 1 and 3 months in the control and adjunct-containing cheeses. In the raw milk cheeses, Lactobacillus paracasei was detected throughout ripening, Lact. curvatus at the end, and Lact. plantarum at day 1 only. Lactobacillus strain diversity decreased from raw, control to adjunct cheeses. Enteroccoci and coliform numbers further differentiated raw cheeses from the others. Lactococcal starter numbers also differed in the three cheese types and differences were observed within adjunct cheeses. Although adjunct lactobacilli dominated in the cheese to which they were added, strains with similar phenotypic profiles were also detected on occasions in some of the control cheeses.

CONCLUSIONS

The addition of adjunct lactobacilli modified the growth kinetics of both adventitious lactobacilli and starter lactococci during ripening. Appropriate strain tracking is necessary to monitor changes in the population profiles of control and experimental cheeses in trials utilizing adjunct cultures.

SIGNIFICANCE AND IMPACT OF THE STUDY

Investigations of the role of adjunct strain(s) in cheeses may be complicated by the interactions between the adjunct and the other cheese strains, and effective strain monitoring by genotypic or phenotypic methods is essential if valid comparisons are to be made.

A molecular epidemiological study of avian paramyxovirus type 1 (Newcastle disease virus) isolates by phylogenetic analysis of a partial nucleotide sequence of the fusion protein gene

A sequence 375 nucleotides in length, which included the region encoding the cleavage activation site and signal peptide of the fusion protein gene, was determined for 174 isolates of Newcastle disease virus (avian paramyxovirus type 1). These were compared with the sequences of 164 isolates published on GenBank, and the resulting alignment was analysed phylogenetically using maximum likelihood. The results are presented as unrooted phylogenetic trees. Briefly, the isolates divided into six broadly distinct groups (lineages 1 to 6). Lineages 3 and 4 were further subdivided into four sublineages (a to d) and lineage 5 into five lineages (a to e). Considerable genetic heterogeneity was detected within avian paramyxoviruses type 1, which appears to be influenced by host, time and geographical origin. It is concluded that by using this dataset it will be possible to type future virus isolates rapidly on the basis of their nucleotide sequence and make inferences about their origins.

Long term variation in water colour from Yorkshire catchments

Water colour is a problem in the upland water-gathering grounds of the UK. It has shown considerable variation over recent years and this needs to be put into the longer-term context. In order to do this, factors to convert water colour measured in absorbance units per metre (Au/m) to Hazen units are presented for ten sites in the Yorkshire region using data from August 1997 to June 1998. The conversion factors are site-specific and there is some evidence that they may show seasonal variation. There is also a short-term upward trend in the conversion factor for a number of catchments, which may be related to their recovery following the 1995 drought. Time series of water colour in Hazen from 1980 to 1998 are shown for selected sites. The seasonal variation in colour levels is disrupted at all sites during and following drought periods, notably 1990-1992 and 1995-1998 and, in the case of two sites with long-term colour measurements, the 1975-1976 drought. These periods are followed by enhanced levels of colour and, since the end of the 1995 drought, unprecedented high values have been recorded at some catchments.

Changes in the haemagglutinin and the neuraminidase genes prior to the emergence of highly pathogenic H7N1 avian influenza viruses in Italy

Outbreaks of avian influenza due to an H7N1 virus of low pathogenicity occurred in domestic poultry in northern Italy from March 1999 until December 1999 when a highly pathogenic avian influenza (HPAI) virus emerged. Nucleotide sequences were determined for the HA1 and the stalk region of the neuraminidase (NA) for viruses from the outbreaks. The HPAI viruses have an unusual multibasic haemagglutinin (HA) cleavage site motif, PEIPKGSRVRRGLF. Phylogenetic analysis showed that the HPAI viruses arose from low pathogenicity viruses and that they are most closely related to a wild bird isolate, A/teal/Taiwan/98. Additional glycosylation sites were present at amino acid position 149 of the HA for two separate lineages, and at position 123 for all HPAI and some low pathogenicity viruses. Other viruses had no additional glycosylation sites. All viruses examined from the Italian outbreaks had a 22 amino acid deletion in the NA stalk that is not present in the N1 genes of the wild bird viruses examined. We conclude that the Italian HPAI viruses arose from low pathogenicity strains, and that a deletion in the NA stalk followed by the acquisition of additional glycosylation near the receptor binding site of HA1 may be an adaptation of H7 viruses to a new host species i.e. domestic poultry.

Analytical approaches to measuring cospeciation of host and parasites: through a glass, darkly

Studies of cophylogenetic associations between hosts and parasites have become increasingly common. Historically, congruence between host and parasite phylogenies has been seen as evidence for cospeciation. Analyses of such coevolutionary relationships, however, are made extremely difficult by the complex interplay of cospeciation, host switching, sorting (extinction), duplication (intrahost speciation) and inertia (lack of parasite speciation) events, all of which may produce incongruence between host and parasite phylogenies. Here we review several methods of analysing cospeciation. We illustrate these methods with an example from a Procellariiformes (seabird) and chewing louse (Halipeurus) association.

Membrane inlet mass spectrometric measurement of O2 and CO2 gradients in cultures of Lactobacillus paracasei and a developing Cheddar cheese ecosystem

Membrane inlet mass spectrometry was used to measure O2 and CO2 as depth profiles in stab cultures of 0.1% agar Man Rogosa Sharpe medium inoculated with Lactobacillus paracasei CI3. Diffusion of CO2 from the central column of growth into the medium was observed to show lower concentrations where bacteria were absent. CO2 profiles developed in a manner similar to those in Cheddar cheese and O2 was undetectable at similar depths. Gases were analysed in Cheddar cheese over a maturation period of 200 d. O2 was detectable to depths of 13, 6 and 2.5 mm on days 2, 9 and 15, respectively, but then became undetectable at depths of 2.5-3 mm. CO2 concentrations measured within the cheese increased 10-fold from day 2 to day 200 to reach a value of around 15 mM. The progress of measured CO2 concentration over time at a given depth in cheese shows a hyperbolic type increase. Coefficient of regression values increase with depth to a maximum value of R2 = 0.93. In both systems, reductions and increases in CO2 were due to the absence or presence of bacterial growth, respectively. Confocal scanning laser and scanning electron microscopy was used to show spatial heterogeneity of microcolonies within the cheese ecosystem. This information can potentially be used as a non-sensory evaluation of cheese maturity status. Measurement of gases in a cheese ecosystem provides the first description of mass spectrometry being used to monitor the processes of microbial gaseous exchange with respect to O2 and CO2 in a cheese ecosystem.

Doing things with illness. The micro politics of the CFS clinic

This paper focuses on lay and professional ideas about the nature of chronic fatigue syndrome (CFS), and in particular, the ways in which understandings of the disorder are developed in a clinical setting. Our data are drawn from observations of consultations between sufferers and physicians in a UK medical out-patients clinic. We treat the clinic as a political field. That is to say, as an arena in which 'problems' (about the management of illness) are constituted, and alternative approaches and solutions to such problems are pressed. We note that in the realms of symptoms, aetiology and treatment evaluation, lay people in the CFS clinic have quite distinct ideas about what their problems are and how they might be analysed and managed--ideas that are often in conflict with those of medical professionals. Thus, lay sufferers, for example, operate within a different conceptual terrain from that of many professional experts. They are more likely to refer to a disease (myalgic encephalomyelitis or ME), rather than a syndrome. They call upon different kinds of hypotheses to explain their symptoms. They hold to conflicting ideas about the order of causal sequences, and they give emphasis to different kinds of phenomena in their accounts of illness. As a consequence, clinical consultations can often take on the form of a political contest between physician and patient to define the true and real nature of the patient's disorder--a micro political struggle in which neurological symptoms can be re-framed as psychiatric symptoms, and psychiatric symptoms as neurological. In short, a contest in which the demarcation lines between mind and body are continually assessed and re-defined, and the tenets of 'biomedicine' are constantly challenged.

H9N2 subtype influenza A viruses in poultry in pakistan are closely related to the H9N2 viruses responsible for human infection in Hong Kong

Following the outbreak of H5N1 "bird flu" in Hong Kong in 1997, the isolation of H9N2 subtype viruses from patients in southern China and Hong Kong SAR once again raised the spectre of a possible influenza pandemic. H9N2 viruses have recently been responsible for disease in poultry in various parts of the world and preliminary studies of the H9 haemagglutinin (HA) genes of viruses isolated during 1998 and 1999 in Germany, Iran, Pakistan, and Saudi Arabia showed a close relationship to the HA genes of the viruses that infected two children in Hong Kong SAR. Analysis of the complete genome of a Pakistan isolate, A/chicken/Pakistan/2/99, showed that it is closely related in all eight genes (97-99% homology) to the human H9N2 isolates and furthermore that the six genes encoding internal components of the virus are similar to the corresponding genes of the H5N1 viruses that caused 6 (out of 18) fatal cases of human infection. Thus H9N2 viruses similar to those that caused human infections in Hong Kong are circulating more widely in other parts of the world. Whether or not these H9N2 viruses also have features that facilitate avian-to-human transmission is not known. Since avian H9N2 viruses are currently perceived to represent a significant threat to human health it is important to determine whether or not viruses of this subtype circulating in poultry in various parts of the world have the potential to infect people.

Endoscopic ultrasound guided biopsy of sub-carinal lymph nodes

AIM/METHODS

Endoscopic ultrasound (EUS) guided biopsy is not widely available in the U.K., and sub-carinal nodes can be difficult to biopsy percutaneously. Tissue obtained from these nodes can influence patient management. We describe our initial experience with EUS guided transoesophageal biopsy of sub-carinal nodes using a Pentax FG-34 EUS probe and a 22 G Hancke-Villman or Echotip needle in 20 patients.

RESULTS

Malignant cells were obtained from the nodes in 13 patients, and in another patient in whom the node biopsy was negative, small cell carcinoma cells were obtained from a lesion in the liver. There were no complications.

CONCLUSIONS

Mediastinoscopy to obtain tissue, or the blind treatment of presumed malignancy was avoided in all the patients in whom a positive biopsy was obtained. In many of these patients, more conventional methods to obtain a tissue diagnosis had already failed. The problem solving capability of this safe, well-tolerated technique is discussed.Roberts, S. A. Clinical Radiology55, 832-836.

Phylogenetic analysis of H7 haemagglutinin subtype influenza A viruses

A 945 nucleotide region (bases 76-1020) of the HA1 part of the HA gene was obtained for 31 influenza viruses of H7 subtype isolated primarily from Europe, Asia and Australia over the last 20 years. These were analysed phylogenetically and compared with sequences of the same region from 23 H7 subtype viruses available in Genbank. The overall results showed two geographically distinct lineages of North American and Eurasian viruses with major sublineages of Australian, historical European and equine viruses. Genetically related sublineages and clades within these major groups appeared to reflect geographical and temporal parameters rather than being defined by host avian species. Viruses of high and low virulence shared the same phylogenetic branches, supporting the theory that virulent viruses are not maintained as a separate entity in waterfowl.

A tale of two kidneys--how long can a kidney transplant wait?

This paper compares early graft function (EGF) of the first transplanted kidney (group 1) with the kidney transplanted second (group 2) in kidney pairs from the same cadaver donor. Thirty-one pairs of kidneys were harvested from cadaver donors between January 1997 and October 1998. Each pair was transplanted using a standard technique by the same team of surgeons, one after the other, as a result of limitations in theatre time and staff availability. Incidence of acute rejection (AR), acute tubular necrosis (ATN) and need for post-transplant dialysis was recorded for both groups, and was compared using the relevant statistical methods. Patients in both groups were well matched for age, gender and mode of dialysis pre-transplant. Human leucocyte antigen (HLA) matching and panel reactive antibody (PRA) status were similar in the two groups (p > 0.05). Cold ischaemia time (CIT) in the two groups was 14.1 +/- 5.7 and 19.2 +/- 6.9 h, respectively, the difference being statistically significant (p < 0.05). The incidence of AR was similar in the two groups. However, ATN (on renogram) was significantly more common in group 2 (p < 0.05; 12 patients versus 5 patients in group 1). All patients with ATN required post-transplant dialysis. Hospital stay was significantly prolonged in group 2 patients (p < 05; 20 +/- 10.6 versus 16.3 + 6.2 d for group 1). Even a relatively short increase in CIT can cause the second transplanted kidney of a pair to have a significantly higher incidence of ATN, resulting in need for dialysis and prolongation of hospital stay. Simultaneous transplantation, in areas lacking organ sharing networks, would not only improve EGF, but also improve long term graft survival. In addition, the reduced requirement for post-transplant dialysis and a shorter hospital stay would balance any increased demand on resources.