High-Throughput CRISPR-Cas13 SARS-CoV-2 Test

BACKGROUND

The ability to control the spread of COVID-19 continues to be hampered by a lack of rapid, scalable, and easily deployable diagnostic solutions.

METHODS

: We developed a diagnostic method based on CRISPR that can deliver sensitive, specific, and high-throughput detection of Sudden Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The assay utilizes SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the qualitative detection of SARS-CoV-2 RNA and may be performed directly on a swab or saliva sample without nucleic acid extraction. The assay uses a 384-well format and provides results in less than one hour.

RESULTS

Assay performance was evaluated with 105 (55 negative, 50 positive) remnant SARS-CoV-2 specimens previously identified as positive using Food and Drug Administration emergency use authorized assays and re-tested with a modified version of the Centers for Disease Control and Prevention (CDC) RT-qPCR assay. When combined with magnetic bead-based extraction, the high throughput SHERLOCK SARS-CoV-2 assay was 100% concordant (n = 60) with the CDC RT-qPCR. When used with direct sample addition the high throughput assay was also 100% concordant with the CDC RT-qPCR direct method (n = 45). With direct saliva sample addition, the negative and positive percent agreements were 100% (15/15, 95% CI : 81.8-100%) and 88% (15/17, 95% CI : 63.6-98.5%), respectively, compared with results from a collaborating clinical laboratory.

CONCLUSIONS

This high throughput assay identifies SARS-CoV-2 from patient samples with or without nucleic acid extraction with high concordance to RT-qPCR methods. This test enables high complexity laboratories to rapidly increase their testing capacities with simple equipment.

Control of a programmed cell death pathway in Pseudomonas aeruginosa by an antiterminator

In Pseudomonas aeruginosa the alp system encodes a programmed cell death pathway that is switched on in a subset of cells in response to DNA damage and is linked to the virulence of the organism. Here we show that the central regulator of this pathway, AlpA, exerts its effects by acting as an antiterminator rather than a transcription activator. In particular, we present evidence that AlpA positively regulates the alpBCDE cell lysis genes, as well as genes in a second newly identified target locus, by recognizing specific DNA sites within the promoter, then binding RNA polymerase directly and allowing it to bypass intrinsic terminators positioned downstream. AlpA thus functions in a mechanistically unusual manner to control the expression of virulence genes in this opportunistic pathogen.

Sequential conformational rearrangements in flavivirus membrane fusion

The West Nile Virus (WNV) envelope protein, E, promotes membrane fusion during viral cell entry by undergoing a low-pH triggered conformational reorganization. We have examined the mechanism of WNV fusion and sought evidence for potential intermediates during the conformational transition by following hemifusion of WNV virus-like particles (VLPs) in a single particle format. We have introduced specific mutations into E, to relate their influence on fusion kinetics to structural features of the protein. At the level of individual E subunits, trimer formation and membrane engagement of the threefold clustered fusion loops are rate-limiting. Hemifusion requires at least two adjacent trimers. Simulation of the kinetics indicates that availability of competent monomers within the contact zone between virus and target membrane makes trimerization a bottleneck in hemifusion. We discuss the implications of the model we have derived for mechanisms of membrane fusion in other contexts.

DOI:http://dx.doi.org/10.7554/eLife.04389.001

Flaviviruses are a group of viruses that cause serious diseases in humans, including yellow fever, West Nile fever and dengue fever. Like all viruses, flaviviruses protect their genetic material with a protein shell and, like many other viruses, that shell also has a lipid membrane.

Flaviruses use one of their surface membrane proteins, known as ‘envelope protein’ or simply ‘E’, to bind to the surface of host cells. Once the virus has attached to the host cell membrane, it becomes engulfed within a bubble-like structure called an endosome, which also has a surrounding membrane. The interior of an endosome is acidic. Under these conditions the E protein undergoes a series of changes that bring the two membranes into close contact, so that the membrane of the virus can fuse with the membrane of the endosome. This membrane fusion allows the genome of the virus to escape the endosome and hijack the cell to make new copies of the virus.

The E proteins on a mature flavivirus particle are found in pairs, but previous work showed that these proteins must work together in groups of three (called ‘trimers’) for the viral and endosomal membranes to fuse. Chao et al. have now asked: what are the rate-limiting steps that lead to the formation of trimers? And how many trimers are necessary to cause the membranes to fuse?

Chao et al. have investigated these questions using virus-like particles containing the E protein of West Nile Virus. They used techniques that can track individual particles, which their laboratory had previously used to investigate the influenza virus, to model changes in the E protein before, during and after membrane fusion. Chao et al. then made mutant versions of the envelope protein and used virus-like particles containing them to test the model.

The data that Chao et al. obtained and computer simulations they carried out suggest that exposure to acidic conditions encourages the pairs of E proteins to separate and extend towards the endosome membrane. Individual E proteins then group together into trimers, and at least two trimers are needed to exert enough force to allow the membranes to fuse. The experimental design used by Chao et al. will now allow them to study the action of molecules that inhibit membrane fusion by West Nile Virus and other viruses.

DOI:http://dx.doi.org/10.7554/eLife.04389.002

[Imported malaria and HIV infection in Madrid. Clinical and epidemiological features]

INTRODUCTION

Few data are available in Spain data on human immunodeficiency virus (HIV) patients coinfected with malaria. This study has aimed to determine the epidemiological and clinical characteristics of imported malaria in patients coinfected with HIV.

PATIENTS AND METHODS

A case-series retrospective study was performed using the patient's medical records. The study population consisted on patients diagnosed with malaria attended in our center from january 1, 2002 to december 31, 2007.

RESULTS

A total of 484 episodes of malaria, 398 of which were included in this study, were identified. Co-infection with HIV was described in 32 cases. All of them occurred in individuals presumably with some degree of semi-immunity. In the coinfected group, there were 13 cases (40.6%) asymptomatic, whereas this event occurred in 99 cases of patients not coinfected (37.2%) (P=0.707). The greater presence of anemia in co-infected patients (62.5% vs 32.3% in non-coinfected [P=0.001]) stands out.

CONCLUSIONS

In present study, the clinical presentation forms were similar, regardless of the presence or absence of HIV infection. Although the study population does not reflect all possible scenarios of malaria and HIV coinfection, our results indicate the reality of patients attended in the Autonomous Community of Madrid.

[Imported malaria in adults. Clinical, epidemiological and analytical features]

INTRODUCTION

Up to now, the epidemiological and clinical features of imported malaria in Spain have been described in small series from general hospitals. Almost all diagnosis had been made based on symptomatic patients. The aim of this study has been to determine the epidemiological, clinical and laboratorial characteristics of imported malaria in a Reference Unit for Tropical Diseases.

PATIENTS AND METHODS

We performed a cross-sectional, observational and retrospective study. The series consisted of patients diagnosed of malaria who had been attended at the Hospital Carlos III from January 1, 2002 to December 31, 2007.

RESULTS

We identified 484 episodes of malaria, of which 398 cases were included in the analysis. Almost 50% of the patients were natives of endemic areas, while the rest were native-travelers or travelers. Most cases (88-98% according to the group) had not taken malaria chemoprophylaxis correctly when indicated. At the time of diagnosis, 30.4% of patients were asymptomatic and 28.1% of asymptomatic patients had anemia, 19.8% thrombocytopenia, 14% leukopenia, 5% hypocholesterolemia, 5% renal failure and 4.1% hypoglycemia. Low parasitemia was present in 97.5% of asymptomatic individuals compared to 80.5% of the symptomatic patients (P<0.001).

DISCUSSION

Absence of chemoprophylaxis (or poor compliance) is the main reason for malaria in individuals traveling to endemic areas. Malaria must be ruled out in individuals coming from tropical countries with compatible symptoms, and it also should be suspected in certain groups of asymptomatic individuals with abnormal laboratorial parameters.

A randomized trial comparing the efficacy and tolerability of two HAART strategies at two years in antiretroviral naive patients

BACKGROUND

The use of HAART combining 2 nucleoside analogues reverse transcriptase inhibitors (NRTIs) plus one protease inhibitor (PI) or 2 NRTIs + 1 non-nucleoside reverse transcriptase inhibitor (NNRTI) has shown comparable efficacy. The study was designed to compare long term (2 years) effectiveness of two antiretroviral (ARV) treatment strategies in patients not previously treated: starting with a nelfinavir based HAART switching to nevirapine in case of failure or side effects or the reverse sequence.

METHODS

This multicenter, randomized, open label clinical trial enrolled ARV-naïve HIV patients with CD4 counts below 500 cells/mm3. They were randomly assigned to start ddI + d4T + nelfinavir (switching to ZDV + 3TC + NEV in case of failure or toxicity) (PI-NEV arm) or ddI + d4T + nevirapine, switching to ZDV + 3TC + NFV in case of failure or toxicity (NEV-PI arm). The primary study endpoint was the Kaplan-Meier estimates of the time to failure after switching to second regimen if necessary (considering failure as two consecutive plasma HIV-1 RNA determinations above 200 copies/mL, death, a new category C event or toxicity leading to treatment discontinuation of the second regimen) after a minimum follow-up of two years.

RESULTS

A total of 137 patients were evaluable (67 and 70 in the PI-NEV and NEV-PI arms respectively). Baseline characteristics did not differ among groups. Kaplan-Meier estimates of time to failure did not show differences between the two arms neither in the on-treatment (OT) analysis (log rank test, p = 0.81) nor in the intent-to-treat (ITT) analysis (p = 0.58). At 24 months, the estimated proportion of patients free of failure were 72% and 66% respectively in the PI-NEV and NEV-PI arms OT analysis (p = 0.54) and 73% and 64% in the PI-NEV and NEV-PI arms in the ITT analysis (p = 0.49). The difference in the median in CD4+ lymphocyte count at 24 months was not significantly different in the two groups: 393 and 307 CD4 cells/mm3 in the PI-NEV and NEV-PI arms respectively (p = 0.167). The incidence of adverse events (AEs) in the two arms was very similar: 50 (75%) in the PI-NEV and 54 (70%) in the NEV-PI group, as it was for grade 3-4 AEs leading to drug switching.

CONCLUSION

At two years both treatments strategies (PI-NEV vs NEV-PI) had a high and comparable efficacy and were generally well tolerated.

Growing Bayesian network models of gene networks from seed genes

MOTIVATION

For the last few years, Bayesian networks (BNs) have received increasing attention from the computational biology community as models of gene networks, though learning them from gene-expression data is problematic. Most gene-expression databases contain measurements for thousands of genes, but the existing algorithms for learning BNs from data do not scale to such high-dimensional databases. This means that the user has to decide in advance which genes are included in the learning process, typically no more than a few hundreds, and which genes are excluded from it. This is not a trivial decision. We propose an alternative approach to overcome this problem.

RESULTS

We propose a new algorithm for learning BN models of gene networks from gene-expression data. Our algorithm receives a seed gene S and a positive integer R from the user, and returns a BN for the genes that depend on S such that less than R other genes mediate the dependency. Our algorithm grows the BN, which initially only contains S, by repeating the following step R + 1 times and, then, pruning some genes; find the parents and children of all the genes in the BN and add them to it. Intuitively, our algorithm provides the user with a window of radius R around S to look at the BN model of a gene network without having to exclude any gene in advance. We prove that our algorithm is correct under the faithfulness assumption. We evaluate our algorithm on simulated and biological data (Rosetta compendium) with satisfactory results.

Bayesian analysis using continuous likelihood ratios for identifying pleural exudates

STUDY OBJECTIVES

To ascertain if equations that calculate continuous likelihood ratios (CLRs) for pleural exudates improve pleural fluid categorization, especially when false positive or false negative test results are obtained by using Light's criteria.

DESIGN AND SETTING

Retrospective review of the clinical and pleural fluid data from a consecutive series of patients with pleural effusion who underwent thoracentesis at the University Hospital Arnau de Vilanova (Lleida, Spain) over an 11-year period.

PATIENTS AND METHODS

A total of 1490 patients with pleural effusion (298 transudates and 1192 exudates) were recruited into the study. The presence of a transudate or exudate was established by clinical judgment. We examined the comparative diagnostic accuracy of 4 tests (i.e. pleural fluid protein and lactate dehydrogenase (LDH), and pleural fluid to serum protein and LDH ratios) for discriminating between transudates and exudates. Decision thresholds were determined by receiver operating characteristics (ROC) analysis. Equations for calculating CLRs derived from a logistic regression analysis based on a previously described method.

RESULTS

Individual pleural fluid tests did not differ in their diagnostic accuracies according to ROC analysis. We calculated CLRs for the elements of Light's criteria and pleural fluid protein, and also illustrated the sequential use of CLRs for determining posttest probabilities. Overall, CLR formulas had marginal performance for the correct categorization of pleural fluid.

CONCLUSIONS

CLRs provide a probabilistic statement as to the likelihood an effusion is a transudate or exudate. However, clinical judgment is little changed by the application of CLRs, and in doubtful cases a great amount of uncertainty remains. This Bayesian approach is likely to have no major impact on the clinical practice.

[Immunophenotype of progression to AIDS: deficiency, activation and dysfunction of CD4 and CD8 T-cells]

INTRODUCTION

One key piece of information required when deciding whether to initiate antiretroviral therapy is the risk of AIDS. The aim of this study was to better characterize the baseline immunophenotypic profile of patients with progression to AIDS.

MATERIAL AND METHODS

A cross-sectional analysis of the distribution of functional subpopulations of CD4+ and CD8+ T-lymphocytes in 85 intravenous drug addicts with HIV infection. The values observed on patient enrolment in a prospective study were analyzed. Those patients who progressed and did not progress were compared to the HIV-negative controls. Lymphocyte subpopulations were studied by flow cytometry, including the markers: CD3, CD4, CD7, CD8, CD45RO, CD38, HLA-DR and CD25.

RESULTS

The immunophenotypic profile that precedes progression to AIDS was mainly characterized by an increase in memory (CD45RO) activated cells and total activated CD4+ and CD8+ cells, and by an increase of T CD4+ cells that have loss expression of markers as receptor or the differentiation marker CD7 (CD7-). Patients not meeting laboratory criteria to initiate antiretroviral therapy (> 350 CD4+ T-cells and < 30,000 HIV-ARN-copies/ml) also showed increased levels of CD4+ and CD8+ activation subsets (CD4+CD38+DR+, CD8+CD38+).

DISCUSSION

The fact that immunological activation may contribute to immunological and clinical deterioration of HIV-positive patients might be an additional factor which should be taken into account when deciding whether to initiate antiretroviral therapy.

Multidrug-resistant tuberculosis without HIV infection: success with individualised therapy

OBJECTIVE

To evaluate the results of the treatment of non-HIV-infected multidrug-resistant tuberculosis (MDR-TB) patients admitted to a tuberculosis unit in a reference centre between June 1998 and December 2000.

RESULTS

Twenty-five patients were studied (23 men). Empirical treatment was selected according to drugs previously used and adjusted according to in vitro test results. Patients had previously received an average of 5.5 drugs and were resistant to an average of 4.7 drugs. They were treated with a median number of four drugs (an injectable drug plus three oral drugs) for a median of 18 months. Ofloxacin and cycloserine was used in 17 cases (68%), ethionamide/prothionamide in 18 (72%) and para-aminosalicylic acid in 12 patients (48%). Psychological support and counselling was provided. Two patients required surgery. Globally, 21 patients (84%) met cure criteria. After a 24-month follow-up, none of the 21 patients who successfully completed treatment presented relapse or death.

CONCLUSION

MDR-TB is a curable disease in non-HIV-infected patients. Individualised treatment regimens should be based on treatment history and the study of in vitro susceptibility and by promoting a relationship with the patient that makes adherence to treatment easier and minimises side effects.

[Late nephrology referral influences on morbidity and mortality of hemodialysis patients. A provincial study]

OBJECTIVE

To evaluate the influence of late referral to nephrology of the patients with chronic renal failure in the morbimortality of the patients who start hemodialysis. SUBJETS AND METHODS: There were included in the study the patients who started hemodialysis (HD) as first form of treatment, and that survived at least three months in both hospitals of reference of the province of Huesca from january 1990 to december 2001. Patients who started HD after acute renal failure were excluded. Clinical and analytical data were determined for each patient at the start of HD and during the follow-up. Early (ER) and late referral (LR) were defined by the time of first nephrology encounter greather than or less than 4 months respectively, before HD initiation. Morbidity analysis (using multiple linear regression with rate of days of hospitalization as dependent variable) and global and anual during the first three years of follow-up survival analysis (using Cox proportional hazards regression) were carried out.

RESULTS

A total of 139 patients (78%) started HD in the ER group and 39 (22%) in LR group. Mean follow-up was similar in both (ER = 34.43 +/- 25.5 months; LR = 34.42 +/- 28.37 months). At the start of dialysis LR was associated to higher proportion of temporary catheters, lower level of hematocrit and albumin, higher comorbidity and higher levels of urea and creatinine. Risk factors selected by the model in the morbidity analysis were index of comorbidity (CI), late referral, serum albumin, urea reduction ratio (URR) and hematocrit (R2 = 0.334, F = 16.97, p < 0.005). The final equation of regression was: Rate of hospitalization's days = 101.12 + (2.45 x CI) - (12. 11 x LR) - (11.57 x Alb.) - (0.43 x PRU) - (0.83 x Hto). Variables selected by Cox's regression model that were associated with survival throughout complete follow-up were hematocrit (RR = -0,207, CI 95% 0.726-0.910, p < 0.0005), index of comorbidity (RR = 0,265, CI 95% 1.066-1.594, p = 0.007), PRU (RR = - 0,059, CI 95% 0.893-0.996, p = 0.038) and type of dialysis membrane (RR = 0,771, Cl 95% 0.260-0.822, p = 0.007). Nevertheless, in successive models fitting after 12, 24 and 36 months of follow-up the variable LR influenced in an independent way survival first two years, losing his significance later.

CONCLUSION

In our study patients of the group LR presented a worse clinical and metabolic situation at the beginning of the HD. Later there was demonstrated in this group a higher long-term morbidity and a lower survival the first two years.

Abnormalities in the bone mineral metabolism in HIV-infected patients

OBJECTIVE

To evaluate bone mineral metabolism in HIV infected and asymptomatic patients receiving highly active antiretroviral therapy (HAART) containing protease inhibitors (PI) and naïve patients.

METHODS

We studied 30 asymptomatic HIV infected male patients, 13 in the naive group and 17 in the IP group, both without differences in demographics characteristics. We excluded women and patients with any known factor associated to osteopenia. We did a nutritional questionnaire, a DEXA scan in lumbar spine and femur, a study of CD4 lymphocytes, viral load and an analysis of bone formation and resorption markers in all patients. We compared vitamin D and PTH levels with a control group of healthy male volunteers age-pareated. For the statistical analysis we used the SPSS program.

RESULTS

Osteopenia was present in 17/30 (57%), 8/13 (61.5%) in the naïve group and 9/17 (53%) in the PI group (not significant differences). We found a vitamin D deficiency in 86% of patients, with mean serum levels that was found to be significantly lower than those from a healthy control group (p=0.04). Testosterone level was significantly related to bone mineral density in lumbar spine (p</=0.05).

CONCLUSIONS

HIV may be an individual risk factor in bone disorders, requiring calcium and vitamin D supplementation.

Single (B or C), dual (BC or BD) and triple (BCD) viral hepatitis in HIV-infected patients in Madrid, Spain

INTRODUCTION

There are very limited data about the prevalence of multiple hepatitis virus infections in HIV infected individuals. In HIV uninfected individuals with triple BCD hepatitis, hepatitis D virus (HDV) appears to be the dominant virus. However, in HIV infected patients with triple hepatitis it is not known if HDV replication inhibits hepatitis B virus (HBV) and/or hepatitis C virus (HCV) replication.

METHODS

We calculated the prevalence of single (B or C), dual (BC) and triple (BCD) hepatitis in 423 HIV-infected patients with positive HCV serum antibodies and/or positive serum HBsAg. In patients with multiple infections we performed an evaluation of serum markers of HBV, HCV and HDV replication.

RESULTS

The prevalence of multiple hepatitis was 4.7% (95% confidence interval, 2.7-6.7%). Multiple hepatitis occurred only among patients who acquired HIV through injection drug use. The most common multiple hepatitis was triple BCD. Patients with hepatitis BC and past or chronic hepatitis D were significantly more likely to have cirrhosis and a negative serum HBeAg and HCV PCR than patients with single hepatitis B or hepatitis C. Patients with chronic hepatitis D showed uniform suppression of HBV and HCV replication markers.

CONCLUSIONS

In our geographic area approximately 5% of HIV infected patients with hepatitis suffer multiple hepatitis virus infection. In patients with triple hepatitis BCD virus infection, HDV appears to be the dominant virus causing inhibition of both HBV and HCV replication.

Globally multimodal problem optimization via an estimation of distribution algorithm based on unsupervised learning of Bayesian networks

Many optimization problems are what can be called globally multimodal, i.e., they present several global optima. Unfortunately, this is a major source of difficulties for most estimation of distribution algorithms, making their effectiveness and efficiency degrade, due to genetic drift. With the aim of overcoming these drawbacks for discrete globally multimodal problem optimization, this paper introduces and evaluates a new estimation of distribution algorithm based on unsupervised learning of Bayesian networks. We report the satisfactory results of our experiments with symmetrical binary optimization problems.

Therapeutic immunization with an inactivated HIV-1 Immunogen plus antiretrovirals versus antiretroviral therapy alone in asymptomatic HIV-infected subjects

To determine whether the addition of an inactivated-gp120-depleted HIV-1 Immunogen to antiretrovirals (ARTs) conferred a beneficial effect on delaying time to virologic failure relative to that obtained by ARTs alone, a phase II clinical trial was performed in 243 asymptomatic, ART naïve, HIV-1 seropositive adults. The Cox model showed that HIV-1 Immunogen treatment was associated with a 34% decrease in the risk of virologic failure (P = 0.056). When the analysis incorporated baseline HIV-RNA stratification the risk of virologic failure in the HIV-1 Immunogen Arm was significantly reduced a 37% compared to the IFA placebo Arm (P = 0.034). The data suggest that therapeutic immunization plus ARTs could influence virologic control.

Impact of tuberculosis on the course of HIV-infected patients with a high initial CD4 lymphocyte count

OBJECTIVE

To assess the influence of tuberculosis (TB) on the progression of human immunodeficiency virus (HIV) infection in patients without immunological impairment.

MATERIAL AND METHODS

In an observational study of retrospective cohorts, the evolution of 28 HIV-infected patients with TB and a CD4 lymphocyte count >500 x 10(6) cells/l was compared with 56 HIV-infected patients without TB. Each case was paired with two controls by CD4 lymphocyte count (+/-50 x 10(6)/l) and date of starting follow-up (+/-6 months). The progression of HIV infection was evaluated as: 1) immunological progression: time to CD4 lymphocyte count <200 x 10(6)/l; 2) clinical progression: time to development of acquired immune-deficiency syndrome (AIDS), excluding TB; 3) survival; and 4) global disease progression: time to the first defined event in 1, 2 and/or 3. The times to these events were estimated using Kaplan Meier curves.

RESULTS

There were no significant differences between the cohorts for age, sex and risk group. Faster immunological impairment (RR 2.94; 95%CI 1.46-8.6; P < 0.01), greater progression to AIDS (RR 4.01; 95%CI 1.66-9.69; P < 0.01), lower survival (RR 3.89; 95%CI 1.53-9.87; P < 0.05) and higher global disease progression (RR 2.82; 95%CI 1.57-5.09; P < 0.01) were found in the cohort of TB patients. These associations were still significant after adjustment for CD4 lymphocyte counts.

CONCLUSION

The diagnosis of TB in HIV-infected patients with a high initial CD4 lymphocyte count (>500 x 10(6)/l) was related to greater progression to AIDS and shorter survival.

Quantitation of Human Immunodeficiency Virus Type 1 RNA Loads in Cervicovaginal Secretions in Pregnant Women and Relationship Between Viral Loads in the Genital Tract and Blood

The purpose of this study was to analyze the quantitation of the human immunodeficiency virus type 1 RNA (HIV-1 RNA) in the genital tract of HIV-1-infected pregnant women and to evaluate a possible correlation with the viral load in blood plasma (Spearman's rank correlation coefficient). A total of 38 each of cervical, vaginal, and blood samples from 38 women were obtained during the third trimester of pregnancy for quantitation of the HIV-1 RNA load. Viral loads were determined by reverse transcription-polymerase chain reaction. The HIV-1 RNA viral load was detectable in 29 of the 38 (76.3%) blood samples, in 6 of the 38 (15.7%) cervical secretion samples, and in 8 of the 38 (21%) vaginal secretion samples. Overall, the correlation between the HIV-1 RNA viral load in the blood plasma and in cervical secretion samples was 0.51 ( P<0.001). However, the correlation disappeared ( r=0.27) when three patients with high blood plasma viral loads were eliminated from the statistical study. The viral load in the vaginal secretions did not correlate with that in the blood samples ( r=0.26). There were two cases in which HIV-1 RNA was undetectable in the blood and cervix but was detectable in vaginal secretions: one woman had 220 copies/ml and the other 68 copies/ml. These results suggest that pregnant women with undetectable viral loads in blood plasma are still at risk of transmitting the virus vertically during vaginal delivery. Because of this, antiretroviral prophylaxis during vaginal delivery must be administered to HIV-1-infected women and their newborns, regardless of the mother's viral load in plasma. In conclusion, quantification of cervicovaginal levels of HIV-1 may represent a useful tool for assessing the individual risk associated with a vaginal delivery and for guiding decisions about whether a scheduled caesarean should be recommended.

Fever of unknown origin: classic and associated with human immunodeficiency virus infection. a comparative study

Fever of unknown origin (FUO) associated with HIV infection is different from classic FUO. Relevant etiologies, procedures and time to diagnosis were analyzed. Patients admitted with FUO from 1991 to 1996 were prospectively followed. Thirty with classic FUO (group I) and 46 with FUO and HIV (group II) were included. Data on diagnosis, time to achieve it, and procedures were registered. Diagnosis was obtained in 87% and 93% of cases in groups I and II. Infections were the most frequent cause in group II. Collagen diseases were found in group I and absent in group II. Prevalence of neoplasia was similar. Mean time to diagnosis was near 5 weeks. In HIV the predominant diagnostic method was the Lowenstein culture. Invasive methods were similarly employed. It is concluded that predominance of Mycobacteria and absence of collagen diseases make FUO associated with HIV a different form of FUO. No differences were found in approach and time to diagnosis.

A randomized trial of the discontinuation of primary and secondary prophylaxis against Pneumocystis carinii pneumonia after highly active antiretroviral therapy in patients with HIV infection. Grupo de Estudio del SIDA 04/98

BACKGROUND

Prophylaxis against Pneumocystis carinii pneumonia is indicated in patients with human immunodeficiency virus (HIV) infection who have less than 200 CD4 cells per cubic millimeter and in those with a history of P. carinii pneumonia. However, it is not clear whether prophylaxis can be safely discontinued after CD4 cell counts increase in response to highly active antiretroviral therapy.

METHODS

We conducted a randomized trial of the discontinuation of primary or secondary prophylaxis against P. carinii pneumonia in HIV-infected patients with a sustained response to antiviral therapy, defined by a CD4 cell count of 200 or more per cubic millimeter and plasma HIV type 1 (HIV-1) RNA level of less than 5000 copies per milliliter for at least three months. Prophylactic treatment was restarted if the CD4 cell count declined to less than 200 per cubic millimeter.

RESULTS

The 474 patients receiving primary prophylaxis had a median CD4 cell count at entry of 342 per cubic millimeter, and 38 percent had detectable HIV-1 RNA. After a median follow-up period of 20 months (758 person-years), there had been no episodes of P. carinii pneumonia in the 240 patients who discontinued prophylaxis (95 percent confidence interval, 0 to 0.85 episode per 100 person-years). For the 113 patients receiving secondary prophylaxis, the median CD4 cell count at entry was 355 per cubic millimeter, and 24 percent had detectable HIV-1 RNA. After a median follow-up period of 12 months (123 person-years), there had been no episodes of P. carinii pneumonia in the 60 patients who discontinued prophylaxis (95 percent confidence interval, 0 to 4.5 episodes per 100 person-years).

CONCLUSIONS

In HIV-infected patients receiving highly active antiretroviral therapy, primary and secondary prophylaxis against P. carinii pneumonia can be safely discontinued after the CD4 cell count has increased to 200 or more per cubic millimeter for more than three months.

Enhanced acute-phase response and oxidative stress in older adults with type II diabetes

OBJECTIVE

To test whether oxidative stress could promote a systemic acute-phase response in elderly patients with type II diabetes.

DESIGN AND METHODS

In a group of 30 older diabetic patients with poor glycemic control, serum levels of lipid peroxides, measured as thiobarbituric acid-reacting substances (TBARS); C-reactive protein (CRP); interleukin (IL)-6 and the soluble form of its receptor (slL-6R), were evaluated at baseline and after 2 and 3 months of therapeutic intervention. Thirty asymptomatic, untreated individuals with abnormal fasting glycemia, but otherwise healthy status, of similar age, sex, and weight served as control group.

RESULTS

At baseline, glycemia (8.83 +/- 0.67mmol/l), HbA1C (8.66 +/- 0.59%), TBARS (8.68 +/- 1.21 micromol/l), CRP (16.05 +/- 3.81 mg/l) IL-6 (5.39 +/- 1.25 pg/ml) and sIL-6R (1425 +/- 492 pg/ml) were significantly higher in diabetic patients than in asymptomatic hyperglycemic individuals (p<0.001). After treatment, glycemia significantly decreased with respect to baseline values (- 9.82% after 60 days and -13.74% after 90 days), as did serum levels of TBARS (-14.05% and -21.89%, respectively), CRP (-32.71% and -43.86%), IL-6 (-23.75% and -40.63%) and sIL-6R (-34.53% and -48.49%, respectively). In diabetic patients, multiple regression showed, at each time, that TBARS and IL-6 were independently correlated with CRP, considering CRP as the dependent variable. Similar correlations were found in asymptomatic hyperglycemic subjects.

CONCLUSION

These results suggest that oxidative stress might be implicated in promoting a state of low-grade systemic inflammation in elderly patients with type II diabetes.

Cervical squamous intraepithelial lesions in HIV-infected women: prevalence, incidence and regression. European Study Group on Natural History of HIV Infection in Women

OBJECTIVES

To assess the impact of HIV-related immunodeficiency and antiretroviral treatment on the occurrence and evolution of abnormal Papanicolaou tests.

STUDY DESIGN

Cohort of 485 HIV-infected women with a known date of infection, enrolled during May 1993-April 1998 in 23 centres (gynaecology, infectious disease or STD clinics, or drug treatment centres) in 12 European countries; in 21 centres, follow-up was performed every 6 months (median follow-up: 2 years).

METHODS

Human papillomavirus (HPV) was detected at inclusion by Southern blot and PCR. The prevalence of squamous intraepithelial lesions (SIL), the incidence of SIL and regression from low-grade SIL were studied according to CD4 count after controlling for HPV detection results.

RESULTS

Compared with women with CD4 cell counts > 500 x 10(6)/l, women with CD4 cell counts < 200 x 10(6)/l had a twofold increase in both prevalence and incidence of SIL and in non-regression from untreated low-grade SIL; in addition, these women had a lower response rate to treatment of high-grade cervical intraepithelial neoplasia. The increase in SIL incidence associated with a low CD4 cell count was significant in women not receiving antiretroviral treatment (relative risk, CD4 cell count 200-499 x 10(6)/l, 1.9; CD4 cell count < 200 x 10(6)/l, 2.9; CD4 cell count > 500 x 10(6)/l, reference), whereas it was less marked and not statistically significant in treated women.

CONCLUSIONS

Severe HIV-related immunodeficiency strongly increases the risk of occurrence of SIL; antiretroviral treatment may reduce this risk, probably by restoring or at least preserving immune function.

Tuberculous radiculomyelitis complicating tuberculous meningitis: case report and review

Tuberculous radiculomyelitis (TBRM) is a complication of tuberculous meningitis (TBM), which has been reported rarely in the modern medical literature. We describe a case of TBRM that developed in an human immunodeficiency virus (HIV)-infected patient, despite prompt antituberculous treatment. To our knowledge, this is the second case of TBRM reported in an HIV-infected patient. We also review 74 previously reported cases of TBRM. TBRM develops at various periods after TBM, even in adequately treated patients after sterilization of the cerebrospinal fluid (CSF). The most common symptoms are subacute paraparesis, radicular pain, bladder disturbance, and subsequent paralysis. CSF evaluation usually shows an active inflammatory response with a very high protein level. MRI and CT scan are critical for diagnosis, revealing loculation and obliteration of the subarachnoid space along with linear intradural enhancement. As in other forms of paradoxical reactions to antituberculous treatment, there is evidence that steroid treatment might have a beneficial effect.

Impact of protease inhibitor therapy on HIV-related oropharyngeal candidiasis

OBJECTIVE

To determine the relationship between antiretroviral therapy and changes in prevalence and amount of oropharyngeal candidiasis (OPC) and skin test reactivity for delayed type hypersensitivity.

DESIGN

Observational cohort.

SETTING

University-based public hospital AIDS clinic.

PATIENTS

Adults with advanced HIV infection who had been taking nucleoside transcriptase inhibitor drugs but had not taken a protease inhibitor and who started antiretroviral treatment with ritonavir.

MAIN OUTCOME MEASURES

OPC lesions score, oral candidal colonization, oral candidal quantification, skin test reactivity for delayed type hypersensitivity (purified protein derivative, candidal and streptokinase antigens), plasma HIV RNA and CD4 cell count at weeks 8, 16 and 48 weeks.

RESULTS

In the 99 patients who entered the study, there was a significant reduction in the HIV plasma RNA (mean log decrease from baseline at 48 weeks 0.88) and a significant increase in CD4 cell counts (mean CD4 cell increase from baseline at 48 weeks 128 x 10(6) cells/l). Only 17% of patients had < 200 copies/ml HIV RNA at 48 weeks. There were significant decreases in the prevalence of OPC lesions (31% at baseline to 1% at 48 weeks; P < 0.001), and in oral candidal loads [2226 to 811 colony-forming units (CFU)/ml; P = 0.0171]. The percentage of patients with at least one positive skin test increased significantly (6 to 28%; P < 0.05). Patients whose CD4 lymphocyte count was > 200 x 10(6) cells/l at 48 weeks had significantly lower oral candidal loads and were more likely to have a positive skin test than patients whose CD4 cell count was < 200 x 10(6) cells/l.

CONCLUSION

In patients with advanced HIV infection, antiretroviral treatment including a protease inhibitor has a positive impact in the natural history of OPC. This positive impact appears to be correlated with a better immunological function and occurs despite continuous HIV replication.

[Influence of a day care hospital on the incidence of hospital admission of AIDS patients]

BACKGROUND

Day care units have become an usual way of medical care for AIDS patients. However, their influence on the incidence of hospital admissions has not been evaluated.

METHODS

Observational and longitudinal study of a cohort of 308 patients with aids diagnosed between 1990 and 1994 and followed-up to June 1996. The incidence of hospital admissions according to the hospital of follow-up (with or without day care unit) was analyzed. A multivariate analysis of the number of hospital admissions was performed using regression model adjusted to a distribution of Poisson.

RESULTS

After AIDS diagnosis, the incidence of hospital admissions was 108 per 100 patient-years of follow up (21 days as inpatient per patient-year). Those patients controlled in the hospital with day care unit have less hospital admissions (relative risk after adjusting by CD4+ cells count and type of diagnostic disease: 0.64; CI95% 0.55-0.76), and less days as inpatient through their follow-up (11 to 31 days less). There was no difference in survival among patients followed in both hospitals.

CONCLUSIONS

A day care unit decrease the incidence of hospital admissions in aids patients. This positive impact is more evident in patients with lesser CD4+ cell counts.

Racial identity and its assessment in a sample of African-American men in treatment for cocaine dependence

Substance abuse treatment studies frequently include subjects from different ethnic and racial groups, but many investigations limit the examination of race and ethnicity to the use of nominal labels. This approach reveals little about the social or psychological significance of racial and ethnic group membership to the subjects of study or about the potential effects of these factors on substance-involved behaviors. In this study, a principal components analysis (PCA) with varimax rotation was conducted on the 50-item long form of the Racial Identity Attitude Scale (RIAS) (1) in a sample of 294 African-American men in treatment for cocaine dependence. The RIAS was developed to measure attitudes about race and racial status among blacks, but it has not been utilized widely in substance abuse research. Our findings provide evidence for the structural validity of this instrument in this sample of substance abusers. We discuss how recent advances in racial identity theory and its measurement may provide an important avenue for understanding the psychological consequences of racial group membership and for examining the potential effects of these factors on treatment response in studies of substance misuse.

Successful treatment of aphthous ulcerations in AIDS patients using topical granulocyte-macrophage colony-stimulating factor

Oral recurrent aphthous ulceration (RAU) is a well-recognized complication in patients infected with human immunodeficiency virus. RAU can be progressive and destructive, causing dysphagia and secondary malnutrition. The aetiology of RAU remains unknown, and its response to available treatments is often unsatisfactory. We describe three patients with advanced AIDS who suffered from extensive RAU which failed to respond to several treatments, including topical viscous lidocaine and topical and systemic glucocorticoids. Owing to difficulties in using thalidomide (two patients had neurological conditions which precluded thalidomide use), all three patients were treated with an oral solution containing recombinant human granulocyte-macrophage colony-stimulating factor (GM-CSF, 400 microg in 5% glucose 200 mL). From the first application, all three patients showed significant improvement of their lesions and amelioration of pain, and they were completely cured in a few days. No adverse effects were recorded. The patients did not show relapses of RAU over a prolonged follow-up. Controlled trials are warranted in order to establish the role of GM-CSF as a valid, alternative option for aphthous ulcerations of the mouth in AIDS patients in whom corticosteroids or thalidomide are not suitable.

A two-rate hypothesis for patterns of retention in psychosocial treatments of cocaine dependence: findings from a study of African-American men and a review of the published data

In this article, we examine patterns of retention in psychosocial treatment programs for cocaine dependence. We present new data from a comparison trial of Drug Counseling and Supportive-Expressive Psychotherapy and review published data from all studies utilizing psychosocial interventions alone. We compared Drug Counseling and Psychotherapy on rates of pretreatment and during-treatment attrition in a sample of 294 African-American men seeking treatment for cocaine dependence (mean age, 37.6). Survival analyses were utilized to identify significant differences in during-treatment attrition between the two treatments and to identify significant changes in the rate of attrition during the course of each treatment. We then compared the patterns of retention in this study with those from other available published reports of psychosocial treatments for cocaine abuse. The weekly during-treatment attrition rate was not constant in either treatment condition, and the change in rate of attrition occurred at week six for both Drug Counseling and Psychotherapy. Comparison with other studies suggested that the during-treatment pattern of attrition among most psychosocial treatments for cocaine abuse is typified by two rates, with the rate of subject attrition early in treatment being greater than the rate of later attrition and also exhibiting greater variance. Future studies of treatment retention should identify significant shifts in the rate of during-treatment attrition, examine if the pattern of attrition is typified by two rates, and, if so, determine where the shift occurs. Future studies should also assess if changes in the rate of during-treatment attrition signal the timeframes within which strategies that enhance retention can be implemented in the treatment program.

Time course and prognostic significance of hemostatic changes in sepsis: relation to tumor necrosis factor-alpha

OBJECTIVES

To describe the time course and prognostic significance of tumor necrosis factor-alpha (TNF-alpha) levels and hemostatic abnormalities in clinical sepsis.

DESIGN

Prospective, observational study with sequential measurements in an inception cohort.

SETTING

An emergency department in a university teaching hospital. Patients were followed up until they either left the hospital or died.

PATIENTS

During a 1-yr period, 43 adult patients were selected from all emergency department patients who met the established criteria for sepsis. Excluded were patients with either organ dysfunction or septic shock at the time of admission.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Blood samples were collected serially (day of admission and on days 3, 5, and 7) to determine TNF-alpha, platelet count, fibrinogen, factor VII, antithrombin III, tissue-type plasminogen activator activity, plasminogen activator inhibitor activity, plasminogen, and alpha2-antiplasmin. Fibrinopeptide A was measured only on the day of admission. Data were analyzed to determine whether admission values or serially obtained values within 7 days were useful in predicting outcome. Thirteen patients died and 30 survived. On admission, assay values indicated that platelet count and antithrombin III were significantly lower than normal (as observed in 50 healthy adults). Fibrinogen, plasminogen activator inhibitor type 1, tissue-type plasminogen activator, fibrinopeptide A, and TNF-alpha were higher than normal, whereas concentrations of factor VII, plasminogen, and alpha2-antiplasmin were in the normal range. No differences were detected in the admission values between survivors and nonsurvivors, except for antithrombin III. However, subsequent values of some variables demonstrated a difference between survivors and nonsurvivors. Survivors showed increasing platelet count and antithrombin III values compared with nonsurvivors, in whom the values remained low, with no significant changes during the study period. High TNF-alpha levels were found in both groups, but only survivors experienced progressive decrease during the observation period.

CONCLUSIONS

Early clinical sepsis is characterized by high plasma levels of TNF-alpha and by activation of the coagulation and fibrinolysis systems. Longitudinal analysis of some variables (antithrombin III, platelet count, and TNF-ea) showed some differences with time between the survivor and nonsurvivor groups, but we feel that such differences were not large enough to be predictive in individual patients.

Evaluation of autofocus functions in molecular cytogenetic analysis

This work describes a systematic evaluation of several autofocus functions used for analytical fluorescent image cytometry studies of counterstained nuclei. Focusing is the first step in the automatic fluorescence in situ hybridization analysis of cells. Thirteen functions have been evaluated using qualitative and quantitative procedures. For the last of these procedures a figure-of-merit (FOM) is defined and proposed. This new FOM takes into account five important features of the focusing function. Our results show that functions based on correlation measures have the best performance for this type of image.