Genomic Diversity of Human Immunodeficiency Viruses

Background

Globally circulating strains of human immunodeficiency virus type one (HIV-1) exhibit an extraordinary degree of genetic diversity. Sequences derived from HIV-1 strains have historically been classified on the basis of their phylogenetic relationships. The viruses have been classified into groups, subtypes or clades and circulating recombinant forms (CRFs). Groups were originally named M for main, O for outlier and N for Non-M-Non-O. The identification of subtypes and CRFs provides a means of tracking the dissemination of the pandemic.

Methods

Various methods to study the molecular epidemiology of HIV-1 are virus isolation, cloning, DNA sequencing, restricted fragment length polymorphism of the molecularly cloned and amplified genome (PCR-RFLP), RNase mismatch cleavage analyses of RNA, RNA heteroduplexes derived from culture amplified virus, primer mismatch sensitive PCR to identify specific mutations, single strand conformational polymorphism (SSCP) to localize mutations arising over short regions of env gene, denaturing gradient gel electrophoresis and serological assays based on V3 peptide. Except for PCR-RFLP and denaturing gradient gel electrophoresis, these techniques do not easily allow simultaneous analyses of multiple sequence variants and include the laborious and selective process of virus co-cultivation or molecular cloning prior to analyses. The extensive DNA sequence analyses remain the gold standard for epidemiological investigations.

Conclusions

Both HIV-1 and HIV-2 are present in India. The Indian strains of HIV1 also show diverse subtypes with HIV1 subtype C predominance. Tracking the genetic diversity has implications towards understanding the evolution of the epidemic, immunopathogenesis, natural course of infection, response to therapy and most importantly vaccine design.Key Words: Genetic diversity, Human immunodeficiency virus type one (HIV-1), Subtypes     

Substrate reduction therapy with miglustat for type 1 Gaucher disease: A retrospective analysis from a single institution

Introduction.

Gaucher disease (GD) is an infrequent progressive multisystem lysosomal storage disorder caused by the deficient activity of the lysosomal enzyme, glucocerebrosidase. A retrospective, single-center analysis of the clinical experience concerning the use of miglustat (N-butyldeoxynojirimycin), an oral inhibitor of glucosylceramide synthase, in type 1 Gaucher disease (GD1) was conducted to evaluate the efficacy, adverse events (AE), and outcome of miglustat therapy.

Patients and methods.

Six adult Caucasian patients with GD1 (two women and four men), aged 21–81 years (median age 59 years), were treated with miglustat between October 2005 and April 2011. All but one patient (83%) carried at least one allele with c.1226A>G (N370S) mutation in the GBA1 gene.

Results.

Weight loss, diarrhea, poor appetite, and tremor were frequently reported AE by the patients. All of them experienced at least 2 AE, and three patients (50%) experienced at least 4 AE. Only two out of six patients (33%) have used miglustat longer than 12 months, of which only one used it longer than 15 months.

Conclusions.

The major obstacle to successful miglustat therapy in GD1 was the high proportion of patients discontinuing their treatment due to the AE and the worsened quality of life. Further efforts are needed to improve tolerability of miglustat and, in consequence, compliance of patients treated with this orphan drug.     

Named entity recognition of follow-up and time information in 20 000 radiology reports

Objective

To develop a system to extract follow-up information from radiology reports. The method may be used as a component in a system which automatically generates follow-up information in a timely fashion.

Methods

A novel method of combining an LSP (labeled sequential pattern) classifier with a CRF (conditional random field) recognizer was devised. The LSP classifier filters out irrelevant sentences, while the CRF recognizer extracts follow-up and time phrases from candidate sentences presented by the LSP classifier.

Measurements

The standard performance metrics of precision (P), recall (R), and F measure (F) in the exact and inexact matching settings were used for evaluation.

Results

Four experiments conducted using 20 000 radiology reports showed that the CRF recognizer achieved high performance without time-consuming feature engineering and that the LSP classifier further improved the performance of the CRF recognizer. The performance of the current system is P=0.90, R=0.86, F=0.88 in the exact matching setting and P=0.98, R=0.93, F=0.95 in the inexact matching setting.

Conclusion

The experiments demonstrate that the system performs far better than a baseline rule-based system and is worth considering for deployment trials in an alert generation system. The LSP classifier successfully compensated for the inherent weakness of CRF, that is, its inability to use global information.     

深圳部分吸毒人群HIV感染者HIV-1分子流行病学调查

目的对深圳市2008年吸毒人群进行HIV-1分子流行病学调查研究,了解本地区吸毒人群HIV-1流行情况、亚型种类、毒株来源、变异情况等,为预防和控制HIV在吸毒人群中的流行提供有价值的资料。方法收集深圳市2008年份吸毒人群HIV-1抗体阳性样本21例,应用巢式聚合酶链式反应（nested—PCR）技术,对该样本膜蛋白基因（env基因）和核心蛋白（gag基因）进行扩增,并对其各基因区核苷酸序列进行测定和分析。结果21例HIV-1阳性样本中共存在CRF01-AE 1种重组毒株以及A11种亚型,其在所有分析样本中的比例分别为90．5％和9．5％;其中12份Env基因样本中,10份为CRF01-AE重组亚型,与国际参考株01AE．TH．90．CM240最近,基因离散率为（9．910±2．432）％,组内离散率为（12．747±3．066）％;2份为A1亚型,与国际参考株a1．gu.92．92ug037最近,基因离散率为（17．15±0．354）％,组内基因离散率0．900％。21份Gag基因样本中,19份为CRF01-AE重组亚型,与国际参考株01AE．TH．90．CM240最近,基因离散率为（5．083±1．341）％,组内离散率为（6．072±1．968）％;2份A1亚型,与国际参考株01ae．en．97．97cngx2f最近,基因离散率为（11．550±0．636）％,组内离散率为2．200％。结论2008年深圳地区HIV-1抗体阳性吸毒人群中HIV-1流行株以CRF01-AE重组亚型为主,并首次在深圳地区吸毒人群中发现A1亚型。     

Usefulness of enzyme immunoassay (EIA) for screening of anti HIV antibodies in urinary specimens: A comparative analysis

Background

Standard HIV testing is done using serum or plasma. FDA approved ELISA to screen urine for IgG antibodies to HIV-1 in 1996. It is a simple, noninvasive test and is appropriate for developing countries where health care personnel may not be professionally trained or where clean needles for drawing blood may not always be available.

Methods

436 individuals with high-risk behavior and strong clinical suspicion of HIV infection were screened for IgG antibodies to HIV-1 in urine by ELISA. Urine HIV testing was performed by enzyme immunoassay, at the ongoing Voluntary Confidential Counseling and Testing Center (VCCTC) at a large tertiary care microbiology lab. The individuals enrolled for the study had high-risk exposure to the virus and majorities were from a state with a high incidence of HIV infection. In all individuals, both serum and urine were tested for IgG antibodies to HIV-1.

Results

Overall, 135 individuals (30.96%) were HIV-positive, of whom 96 (71%) had never previously tested positive; 87% of those who tested positive received their results, and most were referred for medical care. Sensitivity, specificity and predictive values of HIV-1 urine ELISA test kit were determined. Sensitivity was found to be 89.6%; 95% CI [82.9–94.0], specificity 97.3%; 95% CI [94.6–98.8], positive predictive value 93.8%; 95% CI [87.8–97.1] and negative predictive value 95.4%; 95% CI [92.3–97.4].

Conclusion

Efficiency, sensitivity, and specificity of the urine-based screening for HIV-1 test kits were excellent as compared to the reference test.     

Research and applications: Phenotyping for patient safety: algorithm development for electronic health record based automated adverse event and medical error detection in neonatal intensive care

Background

Although electronic health records (EHRs) have the potential to provide a foundation for quality and safety algorithms, few studies have measured their impact on automated adverse event (AE) and medical error (ME) detection within the neonatal intensive care unit (NICU) environment.

Objective

This paper presents two phenotyping AE and ME detection algorithms (ie, IV infiltrations, narcotic medication oversedation and dosing errors) and describes manual annotation of airway management and medication/fluid AEs from NICU EHRs.

Methods

From 753 NICU patient EHRs from 2011, we developed two automatic AE/ME detection algorithms, and manually annotated 11 classes of AEs in 3263 clinical notes. Performance of the automatic AE/ME detection algorithms was compared to trigger tool and voluntary incident reporting results. AEs in clinical notes were double annotated and consensus achieved under neonatologist supervision. Sensitivity, positive predictive value (PPV), and specificity are reported.

Results

Twelve severe IV infiltrates were detected. The algorithm identified one more infiltrate than the trigger tool and eight more than incident reporting. One narcotic oversedation was detected demonstrating 100% agreement with the trigger tool. Additionally, 17 narcotic medication MEs were detected, an increase of 16 cases over voluntary incident reporting.

Conclusions

Automated AE/ME detection algorithms provide higher sensitivity and PPV than currently used trigger tools or voluntary incident-reporting systems, including identification of potential dosing and frequency errors that current methods are unequipped to detect.     

A sequence labeling approach to link medications and their attributes in clinical notes and clinical trial announcements for information extraction

Objective

The goal of this work was to evaluate machine learning methods, binary classification and sequence labeling, for medication–attribute linkage detection in two clinical corpora.

Data and methods

We double annotated 3000 clinical trial announcements (CTA) and 1655 clinical notes (CN) for medication named entities and their attributes. A binary support vector machine (SVM) classification method with parsimonious feature sets, and a conditional random fields (CRF)-based multi-layered sequence labeling (MLSL) model were proposed to identify the linkages between the entities and their corresponding attributes. We evaluated the system''s performance against the human-generated gold standard.

Results

The experiments showed that the two machine learning approaches performed statistically significantly better than the baseline rule-based approach. The binary SVM classification achieved 0.94 F-measure with individual tokens as features. The SVM model trained on a parsimonious feature set achieved 0.81 F-measure for CN and 0.87 for CTA. The CRF MLSL method achieved 0.80 F-measure on both corpora.

Discussion and conclusions

We compared the novel MLSL method with a binary classification and a rule-based method. The MLSL method performed statistically significantly better than the rule-based method. However, the SVM-based binary classification method was statistically significantly better than the MLSL method for both the CTA and CN corpora. Using parsimonious feature sets both the SVM-based binary classification and CRF-based MLSL methods achieved high performance in detecting medication name and attribute linkages in CTA and CN.     

北京市部分男男同性恋人群中HIV-1分子流行病学研究

目的了解北京市部分男男同性恋(men who have sex with men,MSM)人群HIV-1的分子流行情况,监测该地区人群HIV毒株的最新流行情况。方法提取17例男男同性恋者HIV-1抗体阳性样本全血基因组DNA,直接进行巢式PCR扩增HIVenv基因C2-V5区及gag基因P17-P24区,对PCR产物进行核苷酸序列测定和分析,确定基因亚型。结果17例患者中,共存在CRF01-AE、B亚型和CRF07-BC3种亚型,其中CRF01-AE9例(52.94%),B亚型5例(29.41%),CRF07-BC3例(17.65%)。结论小样本量的流行病学调查显示,北京地区部分男男同性恋人群中主要存在CRF01-AE、B和CRF07-BC3种亚型;CRF01-AE已取代B亚型而成为北京市MSM人群中HIV主要流行亚型,CRF07-BC重组亚型在北京市MSM人群中增长迅速。     

Banding pattern indicative of echinococcosis in a commercial cysticercosis western blot

Objective

A commercial cysticercosis Western blot was evaluated for serological cross-reactivity of sera from patients with alveolar (AE) and cystic echinococcosis (CE).

Methods

A total of 161 sera were examined, including 31 sera from AE-patients, 11 sera from CE-patients, 9 sera from patients with other parasitic diseases and 109 sera from patients with unrelated medical conditions. All AE-and CE-sera were also examined by the echinococcosis Western blot.

Results

More sera from patients with AE than with CE showed cross-reactivity in the form of ladder-like patterns ("Mikado aspect") and untypical bands at 6-8 kDa (71% and 77.4% versus 27.3% and 45.5%, respectively). In contrast, triplets of bands in the area above 50 kDa and between 24 and 39-42 kDa were more frequent in CE than in AE sera. The fuzzy band at 50-55 kDa typical for cysticercosis was absent in all AE and CE sera.

Conclusions

Atypical banding patterns in the cysticercosis Western blot should raise the suspicion of a metacestode infection different from Taenia solium, i.e. Echinococcus multilocularis or E. granulosus, especially when the Mikado aspect and an altered 6-8 kDa band is visible in the absence of a fuzzy 50-55 kDa band.     

Biomedical negation scope detection with conditional random fields

Objective

Negation is a linguistic phenomenon that marks the absence of an entity or event. Negated events are frequently reported in both biological literature and clinical notes. Text mining applications benefit from the detection of negation and its scope. However, due to the complexity of language, identifying the scope of negation in a sentence is not a trivial task.

Design

Conditional random fields (CRF), a supervised machine-learning algorithm, were used to train models to detect negation cue phrases and their scope in both biological literature and clinical notes. The models were trained on the publicly available BioScope corpus.

Measurement

The performance of the CRF models was evaluated on identifying the negation cue phrases and their scope by calculating recall, precision and F1-score. The models were compared with four competitive baseline systems.

Results

The best CRF-based model performed statistically better than all baseline systems and NegEx, achieving an F1-score of 98% and 95% on detecting negation cue phrases and their scope in clinical notes, and an F1-score of 97% and 85% on detecting negation cue phrases and their scope in biological literature.

Conclusions

This approach is robust, as it can identify negation scope in both biological and clinical text. To benefit text mining applications, the system is publicly available as a Java API and as an online application at http://negscope.askhermes.org.     

Switch from a ZDV/3TC-based regimen to a completely once daily (QD) regimen of emtricitabine/tenofovir DF fixed dose combination plus a third QD agent (SONETT)

Objectives

To assess the efficacy and safety of a treatment switch from a twice-daily (BID) regimen containing zidovudine (ZDV) and lamivudine (3TC) plus a third agent to a once daily (QD) regimen containing the fixed-dose combination of tenofovir DF/emtricitabine (TDF/FTC, Truvada^®) plus a divergent third QD agent in HIV-1 infected patients.

Methods

Prospective, 48-week, non-randomised, single-group, open-label, study. Fifty-one patients on stable ZDV/3TC-containing HAART, with HIV-1 RNA < 50 copies/ml and CD4+ T-cell count > 50 cells/μl, were switched to TDF/FTC plus a third agent. Plasma HIV-1 RNA, CD4+ and CD8+ T-cell counts were assessed at baseline and weeks 4, 12, 24, 36 and 48 post-switch.

Results

During the 48-week study, 10 patients discontinued prematurely, including three due to adverse events (AEs). At week 48, plasma HIV-1 RNA was < 50 copies/ml in 40 patients (78.4%). No patient experienced virological failure (defined as HIV-1 RNA ≥50 copies/ml at two consecutive post-baseline measurements) during the study. Immunologic control was maintained, with no significant changes in CD4+ or CD8+ T-cell counts. A statistically significant improvement from baseline in haemoglobin level was observed at week 48 (median change 0.8 g/dl; p < 0.001). There was also a statistically significant decrease in total cholesterol concentration at week 48 (-26.0 mg/dl; p = 0.001) in a subset of patients (n = 22) entering the study with elevated total cholesterol. Treatment was well tolerated and no treatment-related grade 3 or 4 AEs were seen.

Conclusions

Results from this study support switching from a ZDV/3TC-containing HAART regimen to a completely QD regimen of TDF/FTC plus a third agent. Virologic and immunologic control are maintained, with apparent benefits in haemoglobin.     

Outbreak of Influenza (H1N1) amongst children in a residential school

Background

An outbreak of pandemic Influenza H1N1 occurred from 13 Feb to 20 Feb 2010 in a residential school at Belgaum, India.

Methods

On report of sudden increase in number of students reporting sick with symptoms suggestive of flu like illness, an investigation was launched to detect the source of infection and to control the spread of infection amongst those not affected. Six random samples of throat from the initial cluster were collected and RT-PCR was done to confirm the diagnosis. The outbreak in this institution was effectively controlled by standard preventive & control measures in the absence of vaccine.

Result

In a school of 335 children, 96 cases of Influenza like illness possibly resulting from pH1N1 (2009) were reported with an attack rate of 28.6%. Out of a total of 96 cases reported, 73 (76%) were hospitalized and 23 treated as outdoor patients. Serogroup A of Influenza H1N1 pandemic was identified to be the agent responsible for this outbreak as 06 random samples drawn from initial cluster tested positive on RT-PCR. A visit to an exhibition in the city was possibly the source of exposure amongst the children.

Conclusion

An outbreak of Influenza H1N1 infection amongst students in a residential public School was found to be linked to a visit to an exhibition following which the secondary transmission led to further occurrence of cases.     

Twenty-seven years follow-up of a patient with congenital retinocephalofacial vascular malformation syndrome and additional congenital malformations (Bonnet-Dechaume-Blanc syndrome or Wyburn-Mason syndrome)

Purpose

Follow-up of vascular changes in a patient with congenital retinocephalofacial vascular malformation syndrome.

Methods

MRI and cerebral angiography.

Results

In a 36-year-old man, magnetic resonance im aging of the skull and cerebral angiography revealed left intracranial arteriovenous malformations. Follow-up observation of 27 years revealed no essential change of retinal and cerebral arteriovenous malformations. Additional congenital deficits in this patient were described.

Conclusion

Patients with retinal arteriovenous malformations should be early examined with neuroradiological methods.     

中国HIV-1 B/C重组病毒的gag-pol区基因序列特征分析

目的对6株中国人类免疫缺陷病毒1型(HIV-1)B／c重组病毒的完整gag基因和部分pol基因进行序列分析,从基因水平上分析是否存在新模式的B／C重组病毒并与其母本毒株进行比较研究,尝试对其不同的生物学表型进行解释。方法从确诊的HIV感染者的全血样本中,提取样本基因组DNA,经套式聚合酶链反应(PCR)扩增后,将扩增产物进行纯化和测序。然后将所得序列进行系统进化树和氨基酸变异分析。用Simplot软件进行序列重组分析并确定重组断点区域;用MEGA软件按断点分段做基因进化树分析以验证该断点的正确性;用GCG软件包的Distance程序计算基因距离。并分析所研究的HIV-1B／C重组毒株长2550bp基因区段的分区段的基因离散率及基因重组对其功能可能造成的影响。结果新疆5份样本均未发现重组断点的变化,而重庆1份样本的逆转录酶区内的B／C断点发生了160个核苷酸的移动。氨基酸序列分析显示,我国流行的B／C重组株与其母本B、C毒株之间发生第286位(R—K／N)和第799位(A—T)的变化。结论我国现在流行的HIV-1 B／C重组病毒仍以CRF07-BC和CRF08-BC两种模式为主,在本研究涉及的基因区内尚未发现新模式重组毒株的流行。初步分析表明我国B／C重组毒株286位和799位氨基酸的变异可能为B／C重组株在我国流行中获得传播优势的原因。     

Genetic analysis of polymerase complex (PA,PB1 and PB2) genes of H9N2 avian influenza viruses from Iran (1999 to 2009)

Objective

To determine the molecular characterization of Polymerase complex (PA, PB1 and PB2) genes of H9N2 avian influenza viruses and the genetic relationship of Iranian H9N2 viruses and other Asian viruses.

Methods

The Polymerase complex (PA, PB1 and PB2) genes from seven isolates of H9N2 viruses isolated from commercial chickens in Iran during 2008-2009 were amplified (by RT-PCR method) and sequenced. Nucleotide sequences (Open Reading Frame: orf) of the PA, PB1 and PB2 genes were used for phylogenetic tree construction.

Results

Most PB2 and PA genes of the H9N2 viruses isolated in 2008-2009 belonged to the unknown avian sublineage which grouped with the 2004 Pakistani H7N3 viruses. The PB1 genes of Iranian viruses indicated greater genetic diversity and shared a high level of similarity to PB1 genes from either H5 or H7 subtypes with compared to established H9N2 Eurasian sublineages.

Conclusions

Our findings demonstrated that the H9N2 viruses in Iran exhibit striking reassortment which has led to the generation of new genotypes.