Optimizing congenital cytomegalovirus detection by pool testing in saliva by a rapid molecular test.

Universal congenital cytomegalovirus (cCMV) screening in saliva is increasingly recommended. The aim of our study was to correlate the performance of a point-of-care rapid molecular test with CMV real time PCR (CMV RT-PCR) detection, using saliva pool-testing in newborns under a universal screening strategy. Saliva swabs were prospectively collected from newborns < 21 days old and tested by Alethia-LAMP-CMV assay in pools of 5 samples. In positive pools, subjects were tested individually and by saliva and urine CMV RT-PCR. A subset of negative pools were studied with both techniques and viral loads in whole blood were determined in positive patients. From 1,642 newborns included in 328 pools, 8 were confirmed by urine CMV RT-PCR, (cCMV prevalence 0,49%). The PPA and NNA of the pooled saliva Alethia-LAMP-CMV testing were 87,5% and 99,8% with a negative and positive predictive value of 99,9% and 77,7%, respectively. Two false positives were detected (0,12%). A subset of 17 negative pools (85 samples), studied by saliva CMV RT-PCR, showed 100% concordance.  Conclusion: CMV pool-testing using a rapid molecular test in saliva proved feasible when compared to PCR gold standards. This strategy could improve cost-effectiveness for cCMV universal neonatal screening, based on the low prevalence of the infection and could be a more affordable approach in less developed regions with reduced detection capacity. What is Known: • cCMV is the most frequent congenital infection and a leading nongenetic cause of sensorineural hearing loss and brain disease. • Universal screening could allow early detection of congenitally infected infants, improving clinical outcome. • Saliva PCR is the preferred and non-invasive test for newborn cCMV screening. What is New: • The feasibility of a universal cCMV screening by pool-testing in saliva using a rapid test in pools of 5 samples. • PPA and NPA were 87,5 and 99,8% compared to CMV PCR in urine. • This strategy could be relevant specially in LMIC where detection capacity is reduced and could improve cost-effectiveness. • cCMV prevalence in our center was 0,49%.

Harmonization of forest disturbance datasets of the conterminous USA from 1986 to 2011.

Several spatial forest disturbance datasets exist for the conterminous USA. The major problem with forest disturbance mapping is that variability between map products leads to uncertainty regarding the actual rate of disturbance. In this article, harmonized maps were produced from multiple data sources (i.e., Global Forest Change, LANDFIRE Vegetation Disturbance, National Land Cover Database, Vegetation Change Tracker, and Web-Enabled Landsat Data). The harmonization process involved fitting common class ontologies and determining spatial congruency to produce forest disturbance maps for four time intervals (1986-1992, 1992-2001, 2001-2006, and 2006-2011). Pixels mapped as disturbed for two or more datasets were labeled as disturbed in the harmonized maps. The primary advantage gained by harmonization was improvement in commission error rates relative to the individual disturbance products. Disturbance omission errors were high for both harmonized and individual forest disturbance maps due to underlying limitations in mapping subtle disturbances with Landsat classification algorithms. To enhance the value of the harmonized disturbance products, we used fire perimeter maps to add information on the cause of disturbance.

[Prevalence of primary antiretroviral resistance among HIV infected patients in Chile]. / Prevalencia de resistencia primaria en pacientes con infección reciente por VIH-1 en Chile.

BACKGROUND: The main cause of virological failure during AIDS treatment is the resistance to antiretroviral medications (ARV). AIM: To search for mutations associated with ARV resistance in recently HIV-1 infected patients naïve to treatment, in Chile. MATERIAL AND METHODS: Patients over 18 years old with HIV-1 infection, naïve to anti-retroviral drugs before the study were included. Patients with CD4 cell counts less than 200 cells/mm3, viral load below 2000 copies/mL or any condition indicative of advanced AIDS were excluded. Criteria for diagnosis of recent infection (< 18 months) were a previous negative test for HIV antibodies or a history of an acute retroviral syndrome in the past 18 months. Resistance to drugs was analyzed using the TRUGENE HIV-1 assay from Bayer and the OpenGene DNA sequencing system. RESULTS: Ninety nine percent of patients had at least one mutation, 27% had 4 or more mutations, but high level resistance to ARV was found only in 2.7% of cases. Point mutations for non nucleoside reverse transcriptase inhibitors (NNRTI) were detected in 4.1% of cases (K103N in 1 patient, V179D in 2 patients), for nucleoside reverse transcriptase inhibitors (NRTI) in 8.1% of cases (T215S in 1 patient, V118I in 4 patients, M41L in 1 patient) and for protease inhibitors (PI) in 1.3% of cases. All mutations detected in the protease gene were secondary. Of these, the most common were L63P/T (38 patients), L10I/V (27 patients) and V77I (26 patients). Resistance to two or more antiretroviral classes was not detected. CONCLUSIONS: This study supports that, by now, primary resistance has a low prevalence in Chile. Therefore, a genotyping test before starting antiretroviral therapy is not necessary.

Detección de resistencia primaria en pacientes chilenos infectados por VIH / Detection of primary antiretroviral resistance in Chilean patients recently infected with human immunodeficiency virus (HIV)

Background: In countries with universal access to antiretroviral therapy a progressive increase in the number of patients that are infected with resistant virus, is observed. Aim To detect the presence of primary resistance to antiretroviral drugs among patients with a recent diagnosis of HIV infection. Material and methods: Twenty five male patients aged 25 to 45 years, with a diagnosis of a recent HIV infection, done between 2004 and 2005, were studied. Genotypic resistance to antiretroviral drugs was studied using the Genetic Resistance Test TRUGENE® from Bayer. Results: Resistance mutations were detected in 10 patients. All had an university title or had university studies. All lived in northeastern Santiago and had risky sexual behaviors while traveling abroad. Seven mutations were detected in reverse transcriptase. Of these, three were associated to a high resistance level and four, to an intermediate or low resistance, were also detected. Conclusions: A high frequency of genotypic resistance was detected in this group of Chilean patients recently infected with HIV. A higher socioeconomic status and lifestyle could have influenced these results.

[Detection of primary antiretroviral resistance in Chilean patients recently infected with human immunodeficiency virus (HIV)]. / Detección de resistencia primaria en pacientes chilenos infectados por VIH.

BACKGROUND: In countries with universal access to antiretroviral therapy a progressive increase in the number of patients that are infected with resistant virus, is observed. AIM: To detect the presence of primary resistance to antiretroviral drugs among patients with a recent diagnosis of HIV infection. MATERIAL AND METHODS: Twenty-five male patients aged 25 to 45 years, with a diagnosis of a recent HIV infection, done between 2004 and 2005, were studied. Genotypic resistance to antiretroviral drugs was studied using the Genetic Resistance Test TRUGENE from Bayer. RESULTS: Resistance mutations were detected in 10 patients. All had an university title or had university studies. All lived in northeastern Santiago and had risky sexual behaviors while traveling abroad. Seven mutations were detected in reverse transcriptase. Of these, three were associated to a high resistance level and four, to an intermediate or low resistance, were also detected. CONCLUSIONS: A high frequency of genotypic resistance was detected in this group of Chilean patients recently infected with HIV. A higher socioeconomic status and lifestyle could have influenced these results.

[Primary resistance to antiretroviral therapy in patients with HIV/AIDS in Chile]. / Resistencia primaria a terapia antirretroviral en pacientes con infección por VIH/SIDA en Chile.

BACKGROUND: Resistance to antiretroviral therapy is a determining factor for therapeutic failure in HIV/AIDS. The prevalence of primary resistance (i.e. in those patients that have not received treatment) varies in different parts of the world. AIM: To study the prevalence of primary resistance to antiretroviral drugs in patients living in Northern Santiago. PATIENTS AND METHODS: Viral load, lymphocyte subpopulations by flow cytometry and genotypic resistance testing were assessed in blood samples from 60 HIV-1 infected patients (mean age 37 years, 54 male). RESULTS: Mean CD4 cell count and viral load was 200 cells/ml and 142,840 RNA copies/ml respectively. Ten mutations were identified: V179D, L10I/V, M361, L63P, A71T/V, Y115F, V118I and K20R. None of these mutations is associated to a high degree of resistance to reverse transcriptase inhibitors, nucleoside analogs (NRTI), non nucleoside analogs (NNRTI) or viral protease inhibitors. CONCLUSIONS: This is a first approach to study antiretroviral resistance in Chilean patients. This study must be amplified, since the prevalence of resistance may experience changes with time.