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1.  The Spectrum of Undiagnosed Hepatitis C Virus Infection in a US HIV Clinic 
AIDS Patient Care and STDs  2014;28(1):4-9.
United States guidelines endorse one-time HCV antibody screening at HIV diagnosis. Rescreening HCV-seronegative patients on a regular basis is still not policy, although HIV-infected persons have reasonably substantial HCV incidence. We evaluated routine risk factor-independent HCV antibody re-testing in a Rhode Island HIV clinic. We instituted annual HCV antibody testing for HCV-seronegative patients who had not been rescreened in a year or more. Testing based on clinical suspicion continued. We conducted a chart review of new antibody-positive cases in the first year of rescreening, July 2006 to June 2007. Of 245 rescreened patients, 11 (4.5%) seroconverted. Five (45%) were female. Median time between last negative and first positive result was 32 months (range 8–98 months). Six (55%) had documented risk factors and 6 (55%) elevated ALT (>45 IU/L) between antibody tests; none prompted re-testing. One seroconverter died of hepatocellular carcinoma 3.7 years after HCV diagnosis. A twelfth was rescreened for suspected acute HCV based on ALT of 515 IU/L. He had newly detectable HCV RNA then seroconversion, and achieved SVR following 6 months of treatment in the acute phase for genotype 1 infection. Incident HCV is not uncommon among HIV-infected patients in care. Rescreening identified undiagnosed HCV in this population. HCV RNA should be checked promptly in HCV-seronegative persons with ALT elevation. We observed consequences of late diagnosis (hepatocellular carcinoma) and benefits of early diagnosis (cure with treatment of acute HCV). Adding annual rescreening to the Ryan White Program would facilitate earlier identification of undiagnosed HCV and create an instant widespread surveillance system, providing HCV incidence data.
PMCID: PMC3894677  PMID: 24428794
2.  HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya 
Antiretroviral resistance leads to treatment failure and resistance transmission. Resistance data in western Kenya are limited. Collection of non-plasma analytes may provide additional resistance information.
We assessed HIV diversity using the REGA tool, transmitted resistance by the WHO mutation list and acquired resistance upon first-line failure by the IAS–USA mutation list, at the Academic Model Providing Access to Healthcare (AMPATH), a major treatment programme in western Kenya. Plasma and four non-plasma analytes, dried blood-spots (DBS), dried plasma-spots (DPS), ViveSTTM-plasma (STP) and ViveST-blood (STB), were compared to identify diversity and evaluate sequence concordance.
Among 122 patients, 62 were treatment-naïve and 60 treatment-experienced; 61% were female, median age 35 years, median CD4 182 cells/µL, median viral-load 4.6 log10 copies/mL. One hundred and ninety-six sequences were available for 107/122 (88%) patients, 58/62 (94%) treatment-naïve and 49/60 (82%) treated; 100/122 (82%) plasma, 37/78 (47%) attempted DBS, 16/45 (36%) attempted DPS, 14/44 (32%) attempted STP from fresh plasma and 23/34 (68%) from frozen plasma, and 5/42 (12%) attempted STB. Plasma and DBS genotyping success increased at higher VL and shorter shipment-to-genotyping time. Main subtypes were A (62%), D (15%) and C (6%). Transmitted resistance was found in 1.8% of plasma sequences, and 7% combining analytes. Plasma resistance mutations were identified in 91% of treated patients, 76% NRTI, 91% NNRTI; 76% dual-class; 60% with intermediate-high predicted resistance to future treatment options; with novel mutation co-occurrence patterns. Nearly 88% of plasma mutations were identified in DBS, 89% in DPS and 94% in STP. Of 23 discordant mutations, 92% in plasma and 60% in non-plasma analytes were mixtures. Mean whole-sequence discordance from frozen plasma reference was 1.1% for plasma-DBS, 1.2% plasma-DPS, 2.0% plasma-STP and 2.3% plasma-STB. Of 23 plasma-STP discordances, one mutation was identified in plasma and 22 in STP (p<0.05). Discordance was inversely significantly related to VL for DBS.
In a large treatment programme in western Kenya, we report high HIV-1 subtype diversity; low plasma transmitted resistance, increasing when multiple analytes were combined; and high-acquired resistance with unique mutation patterns. Resistance surveillance may be augmented by using non-plasma analytes for lower-cost genotyping in resource-limited settings.
PMCID: PMC4238965  PMID: 25413893
HIV; drug resistance; subtype; diversity; Kenya; analyte; AMPATH
3.  Extensive Drug Resistance in HIV-Infected Cambodian Children Who Are Undetected as Failing First-Line Antiretroviral Therapy by WHO 2010 Guidelines 
Antiretroviral therapy in resource-limited settings is monitored clinically and immunologically according to WHO guidelines. Frequent misclassification of virologic failure is reported, mostly in adults, leading to early therapy switch or late failure diagnosis. Pediatric treatment monitoring and resistance data upon first-line failure are limited, particularly when the 2010-WHO pediatric guidelines are used without routine viral load monitoring. We previously reported high treatment failure misclassification rates by pediatric 2010 guidelines in Cambodian children on first-line therapy. Here we determine the extent and patterns of resistance, with yearly viral load and 6-monthly CD4. Drug resistance mutations were determined using the IAS-USA 2011 list. Predicted resistance interpretation was determined with Stanford Database tools. Fifty-one children with available genotypes met inclusion criteria. All but one (subtype B) were CRF01_AE. The most common regimen was stavudine, lamivudine, and nevirapine (96%), taken for a median of 2.2 years. Resistance was seen in 98%; 96% to nucleoside and nonnucleoside reverse transcriptase inhibitors (NRTIs and NNRTIs); 51% with ≥4 mutations. The most common NRTI mutations were 184V/I and 67N and the most common NNRTI mutations were 181C/Y/I/V and 190A/S. A total of 22% had multiresistant mutations and 18% had predicted high-level resistance to subsequent therapy options didanosine, abacavir, etravirine, and tenofovir. In 98% of Cambodian children misclassified as nonfailing first-line therapy by 2010 guidelines, 51% had extensive drug resistance to current and 18% to subsequent antiretroviral therapy. Affordable routine viral load monitoring allowing for early and more accurate treatment failure diagnosis is desperately needed in resource-limited settings.
PMCID: PMC3685690  PMID: 23506238
4.  Optimizing linkage and retention to hypertension care in rural Kenya (LARK hypertension study): study protocol for a randomized controlled trial 
Trials  2014;15:143.
Hypertension is the leading global risk factor for mortality. Hypertension treatment and control rates are low worldwide, and delays in seeking care are associated with increased mortality. Thus, a critical component of hypertension management is to optimize linkage and retention to care.
This study investigates whether community health workers, equipped with a tailored behavioral communication strategy and smartphone technology, can increase linkage and retention of hypertensive individuals to a hypertension care program and significantly reduce blood pressure among them. The study will be conducted in the Kosirai and Turbo Divisions of western Kenya. An initial phase of qualitative inquiry will assess facilitators and barriers of linkage and retention to care using a modified Health Belief Model as a conceptual framework. Subsequently, we will conduct a cluster randomized controlled trial with three arms: 1) usual care (community health workers with the standard level of hypertension care training); 2) community health workers with an additional tailored behavioral communication strategy; and 3) community health workers with a tailored behavioral communication strategy who are also equipped with smartphone technology. The co-primary outcome measures are: 1) linkage to hypertension care, and 2) one-year change in systolic blood pressure among hypertensive individuals. Cost-effectiveness analysis will be conducted in terms of costs per unit decrease in blood pressure and costs per disability-adjusted life year gained.
This study will provide evidence regarding the effectiveness and cost-effectiveness of strategies to optimize linkage and retention to hypertension care that can be applicable to non-communicable disease management in low- and middle-income countries.
Trial registration
This trial is registered with (NCT01844596) on 30 April 2013.
PMCID: PMC4113229  PMID: 24767476
Hypertension; Linkage to care; Retention in care; Community health workers; Tailored behavioral communication; Smartphone technology; Cost-effectiveness
5.  Persistent Genital Tract HIV-1 RNA Shedding After Change in Treatment Regimens in Antiretroviral-Experienced Women with Detectable Plasma Viral Load 
Journal of Women's Health  2013;22(4):330-338.
To longitudinally assess the association between plasma viral load (PVL) and genital tract human immunodeficiency virus (GT HIV) RNA among HIV-1 infected women changing highly active antiretroviral therapy (HAART) because of detectable PVL on current treatment.
Women were eligible for the study if they had detectable PVL (defined as two consecutive samples with PVL>1000 copies/mL) and intended to change their current HAART regimen at the time of enrollment. Paired plasma and GT HIV-1 RNA were measured prospectively over 3 years. Longitudinal analyses examined rates of GT HIV-1 RNA shedding and the association with PVL.
Sixteen women were followed for a median of 11 visits contributing a total of 205 study visits. At study enrollment, all had detectable PVL and 69% had detectable GT HIV-1 RNA. Half of the women changed to a new HAART regimen with ≥3 active antiretroviral drugs. The probability of having detectable PVL ≥30 days after changing HAART was 0.56 (95% CI: 0.37 to 0.74). Fourteen women (88%) had detectable PVL on a follow-up visit ≥30 or 60 days after changing HAART; and 12 women (75%) had detectable GT HIV-1 RNA on a follow-up visit ≥30 or 60 days after changing HAART. When PVL was undetectable, GT shedding occurred at 11% of visits, and when PVL was detectable, GT shedding occurred at 47% of visits.
Some treatment-experienced HIV-infected women continue to have detectable virus in both the plasma and GT following a change in HAART, highlighting the difficulty of viral suppression in this patient population.
PMCID: PMC3627435  PMID: 23531097
6.  Evaluation of Longitudinal Clinical Outcomes and Adherence to Care among HIV-Infected Refugees 
HIV-infected refugees resettled in the United States face many challenges. Longitudinal data regarding HIV-specific outcomes in this population are limited.
We reviewed charts of 51 HIV-infected sub-Saharan African refugees matched to 102 nonrefugees. Outcomes analyzed included CD4 counts, viral loads (VLs), antiretroviral treatment (ART) use, appointment adherence, opportunistic infections, and resistance mutations.
The ART initiation was similar. Appointment adherence was similar in year 1, but refugees were significantly less adherent beyond year 3. Refugees and nonrefugees spent similar amounts of time in care suppressed (83% vs 80%, P = .93). Refugees had higher odds of viremia following undetectable VL (OR 2.3, P < .05).
Initially, sub-Saharan African HIV-infected refugees have comparable appointment adherence, ART use, and VL suppression to nonrefugees. Overtime refugees were less adherent to appointments and more likely to have postsuppression viremia. The support services provided to refugees early in care may be important for retention in care and treatment success.
PMCID: PMC3966284  PMID: 23024042
refugee; sub-Saharan Africa; HIV; clinic adherence; postsuppression viremia
7.  Antiretroviral Treatment Interruptions Induced by the Kenyan Postelection Crisis Are Associated With Virological Failure 
Antiretroviral treatment interruptions (TIs) cause suboptimal clinical outcomes. Data on TIs during social disruption are limited.
We determined effects of unplanned TIs after the 2007–2008 Kenyan postelection violence on virological failure, comparing viral load (VL) outcomes in HIV-infected adults with and without conflict-induced TI.
Two hundred and one patients were enrolled, median 2.2 years after conflict and 4.3 years on treatment. Eighty-eight patients experienced conflict-related TIs and 113 received continuous treatment. After adjusting for preconflict CD4, patients with TIs were more likely to have detectable VL, VL >5,000 and VL >10,000.
Unplanned conflict-related TIs are associated with increased likelihood of virological failure.
PMCID: PMC3920989  PMID: 24047971
HIV; treatment interruption; political crisis Kenya; virological failure; drug resistance
8.  Sequence Quality Analysis Tool for HIV Type 1 Protease and Reverse Transcriptase 
Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1–2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or <0.5% or >15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.
PMCID: PMC3399557  PMID: 21916749
9.  Prediction of Treatment Failure Using 2010 World Health Organization Guidelines Is Associated With High Misclassification Rates and Drug Resistance Among HIV-Infected Cambodian Children 
The 2010 World Health Organization pediatric guidelines for nonvirological treatment monitoring have high misclassification rates and limited accuracy, even among children with extensive drug resistance. Affordable virological monitoring suitable for resource-limited settings is desperately needed.
Background. Antiretroviral therapy (ART) in resource-limited settings (RLSs) is monitored clinically and immunologically, according to World Health Organization (WHO) or national guidelines. Revised WHO pediatric guidelines were published in 2010, but their ability to accurately identify virological failure is unclear.
Methods. We evaluated performance of WHO 2010 guidelines and compared them with WHO 2006 and Cambodia 2011 guidelines among children on ≥6 months of first-line ART at Angkor Hospital for Children between January 2005 and September 2010. We determined sensitivity, specificity, positive and negative predictive values, and accuracy using bootstrap resampling to account for multiple tests per child. Human immunodeficiency virus (HIV) resistance was compared between those correctly and incorrectly identified by each guideline.
Results. Among 457 children with 1079 viral loads (VLs), 20% had >400 copies/mL. For children with WHO stage 1/2 HIV, misclassification as failure (met CD4 failure criteria, but VL undetectable) was 64% for WHO 2006 guidelines, 33% for WHO 2010 guidelines, and 81% for Cambodia 2011 guidelines; misclassification as success (did not meet CD4 failure, but VL detectable) was 11%, 12%, and 12%, respectively. For children with WHO stage 3/4 HIV, misclassification as failure was 35% for WHO 2006 guidelines, 40% for WHO 2010 guidelines, and 43% for Cambodia 2011 guidelines; misclassification as success was 13%, 24%, and 21%, respectively. Compared with WHO 2006 guidelines, WHO 2010 guidelines significantly increased the risk of misclassification as success in stage 3/4 HIV (P < .05). The WHO 2010 guidelines failed to identify 98% of children with extensive reverse-transcriptase resistance.
Conclusions. In our cohort, lack of virological monitoring would result in unacceptable treatment failure misclassification, leading to premature ART switch and resistance accumulation. Affordable virological monitoring suitable for use in RLSs is desperately needed.
PMCID: PMC3491779  PMID: 22539664
10.  Global analysis of sequence diversity within HIV-1 subtypes across geographic regions 
Future virology  2012;7(5):505-517.
HIV-1 sequence diversity can affect host immune responses and phenotypic characteristics such as antiretroviral drug resistance. Current HIV-1 sequence diversity classification uses phylogeny-based methods to identify subtypes and recombinants, which may overlook distinct subpopulations within subtypes. While local epidemic studies have characterized sequence-level clustering within subtypes using phylogeny, identification of new genotype – phenotype associations are based on mutational correlations at individual sequence positions. We perform a systematic, global analysis of position-specific pol gene sequence variation across geographic regions within HIV-1 subtypes to characterize subpopulation differences that may be missed by standard subtyping methods and sequence-level phylogenetic clustering analyses.
Materials & methods
Analysis was performed on a large, globally diverse, cross-sectional pol sequence dataset. Sequences were partitioned into subtypes and geographic subpopulations within subtypes. For each subtype, we identified positions that varied according to geography using VESPA (viral epidemiology signature pattern analysis) to identify sequence signature differences and a likelihood ratio test adjusted for multiple comparisons to characterize differences in amino acid (AA) frequencies, including minority mutations. Synonymous nonsynonymous analysis program (SNAP) was used to explore the role of evolutionary selection witihin subtype C.
In 7693 protease (PR) and reverse transcriptase (RT) sequences from untreated patients in multiple geographic regions, 11 PR and 11 RT positions exhibited sequence signature differences within subtypes. Thirty six PR and 80 RT positions exhibited within-subtype geography-dependent differences in AA distributions, including minority mutations, at both conserved and variable loci. Among subtype C samples from India and South Africa, nine PR and nine RT positions had significantly different AA distributions, including one PR and five RT positions that differed in consensus AA between regions. A selection analysis of subtype C using SNAP demonstrated that estimated rates of nonsynonymous and synonymous mutations are consistent with the possibility of positive selection across geographic subpopulations within subtypes.
We characterized systematic genotypic pol differences across geographic regions within subtypes that are not captured by the subtyping nomenclature. Awareness of such differences may improve the interpretation of future studies determining the phenotypic consequences of genetic backgrounds.
PMCID: PMC3400699  PMID: 22822410
geography; HIV-1; pol gene sequences; protease; reverse transcriptase; subtyping
11.  Recent Clinical History and Cognitive Dysfunction for Attention and Executive Function among Human Immunodeficiency Virus-Infected Patients 
This study examined the association between recent trends in CD4 and viral loads and cognitive test performance with the expectation that recent history could predict cognitive performance. Eighty-three human immunodeficiency virus (HIV)-infected patients with a mean CD4 count of 428 copies/ml were examined in this study (62% with undetectable plasma viral load [PVL]). We investigated the relationships between nadir CD4 cell count, 1-year trends in immunologic function/PVLs, and cognitive performance across several domains using linear regression models. Nadir CD4 cell count was predictive of current executive function (p = .004). One year clinical history for CD4 cell counts and/or PVLs were predictive of executive function, attention/working memory, and learning/memory measures (p < .05). Models that combined recent clinical history trends and nadir CD4 cell counts suggested that recent clinical trends were more important in predicting current cognitive performance for all domains except executive function. This research suggests that recent CD4 and viral load history is an important predictor of current cognitive function across several cognitive domains. If validated, clinical variables and cognitive dysfunction models may improve our understanding of the dynamic relationships between disease evolution and progression and CNS involvement.
PMCID: PMC3243921  PMID: 21873325
HIV; Cognition; Neuropsychology; Executive function; Recent clinical history
12.  Predictors of the Initiation of HIV Postexposure Prophylaxis in Rhode Island Emergency Departments 
AIDS patient care and STDs  2008;22(1):41-52.
The objective of this study was to elucidate factors that predicted the initiation of HIV postexposure prophylaxis (PEP) for blood or body fluid exposures evaluated at Rhode Island emergency departments (EDs). The study involved a retrospective review of patient visits to all civilian Rhode Island EDs for these exposures from 1995 to mid-2001. Multivariate logistic regression models were created to evaluate predictors of the offering and the acceptance and receipt of HIV PEP from 1996 to 2001. The search identified 3622 patients who sustained a blood or body fluid exposure. Of these, 43.8% were health care workers (HCWs) and 57.2% were not HCWs. Most (52.0%) of the exposures were nonsexual. HIV PEP was offered to 21.0% and accepted and received by 9.4% of all patients. HIV PEP was offered more often after significant exposures, exposures to known HIV-infected sources, when time elapsed after the exposure was shorter, if the patients were HCWs, adults, presented to a teaching hospital, presented during the latter years of the study, or sustained nonsexual exposures. Once offered HIV PEP, patients who were male, adult, sustained a significant exposure, knew the source was HIV infected, sustained a nonsexual exposure, or were HCWs had a greater odds of accepting and receiving HIV PEP. Even when controlling for exposure significance, HIV status, and time elapsed since the exposure, several factors such as gender and type of hospital that are unrelated to the exposure appeared to influence the initiation of HIV PEP. ED providers should ensure that these factors do not inappropriately restrict its initiation.
PMCID: PMC3206608  PMID: 18095841
13.  Disparities in the Provision of Sexually Transmitted Disease and Pregnancy Testing and Prophylaxis for Sexually Assaulted Women in Rhode Island Emergency Departments 
Journal of women's health (2002)  2008;17(4):619-629.
To determine how often sexually assaulted adult female emergency department (ED) patients are being offered testing and prophylaxis for sexually transmitted diseases (STDs) and pregnancy and identify factors associated with the offering of tests and prophylaxis.
This is a retrospective study of ED visits for adult female sexual assault in all Rhode Island EDs from January 1995 through June 2001. The percentage of patients offered testing and prophylaxis was calculated. Multivariable logistic regression was used to identify factors related to testing and prophylaxis use for women sustaining an anal/vaginal assault.
Of the 780 patients, 78.2% sustained anal/vaginal penetration, 5.0% genital touching only, and 3.7% oral sex only, and 13.1% did not know what happened to them. Of those women anal/vaginally assaulted, 83.8% were offered chlamydia/gonorrhea testing, 69.4% syphilis testing, 82.9% pregnancy testing, 77.0% chlamydia/gonorrhea prophylaxis, 47.6% emergency contraception, and 19.2% HIV prophylaxis. In multivariable logistic regression models, patients evaluated at the state’s women’s hospital instead of academic or community hospitals and those who sustained anal/vaginal assault instead of other assaults had a greater odds of being offered testing and prophylaxis. In some cases, older women were offered testing and prophylaxis less often than younger women.
Testing and prophylaxis for chlamydia/gonorrhea were used much more often than prophylaxis for emergency contraception and HIV, even for patients who were anal/vaginally assaulted. Disparities in testing and prophylaxis exist by type of hospital and, in some cases, by age. Educational campaigns should be instituted to ensure that all women receive adequate testing and prophylaxis commensurate with the exposure they sustained from a sexual assault.
PMCID: PMC3180868  PMID: 18346000
14.  Drug resistance patterns and virus re-suppression among HIV-1 subtype C infected patients receiving non-nucleoside reverse transcriptase inhibitors in South Africa 
Journal of AIDS & clinical research  2011;2(117):1000117.
Emergence of HIV-1 drug resistance is at times an inevitable and anticipated consequence of antiretroviral therapy (ART) failure. We examined drug resistance patterns and virus re-suppression among subtype C-infected South African patients receiving first-line ART.
Treatment records of 431 patients on NNRTI-containing regimens for a median of 45 months were analyzed. Patients with viral load (VL) >400 copies/mL were followed and drug resistance mutations (DRM) were re-assessed. Associations between clinical/demographic measures and drug resistance/virologic outcomes were examined using Fisher exact and ordinal and logistic regression.
Ten percent of patients (43/431) were viremic at enrollment (98% previously suppressed); sequences were obtained from 38/43. Of those, 82% had 1–7 DRM. In bivariate analysis remote exposure to single-dose nevirapine or prior ART; higher CD4 counts; lower VL; and >6 months of virologic failure were significantly associated with number of DRM. Of 25 viremic patients followed for a median of 8 months on a continued first-line regimen, 12 (48%) re-suppressed, six with K103N and three with M184V. Thirteen (52%) had continued virologic failure which was significantly associated with detectable VL>6 months prior to enrollment and number of DRM.
Among these HIV-1 subtype C-infected patients, DRM numbers and patterns were associated with prior exposure to sub-optimal ART, adherence and duration of virologic failure. Viral re-suppression in the presence of K103N and M184V challenges assumptions about drug resistance. In resource-limited settings, where genotyping and alternative drug options are unavailable, continuing first-line treatment, reinforcing adherence and regular virologic monitoring may be effective even after virologic failure.
PMCID: PMC3174802  PMID: 21927716
HIV-1; Subtype C; drug resistance; mutations; NNRTI; first-line ART; South Africa; ART experienced
15.  Benefit of intravenous antibiotic therapy in patients referred for treatment of neurologic Lyme disease 
We have shown previously that extended intravenous antibiotic therapy is associated with low morbidity and no mortality in patients referred for treatment of neurologic Lyme disease. In this study, we evaluated the benefit of extended intravenous antibiotic therapy in patients with symptoms of neurologic Lyme disease.
Patients with significant neurologic symptoms and positive testing for Borrelia burgdorferi were treated with intravenous antibiotics, and biweekly evaluation of symptom severity was performed using a six-level ordinal scale. Four symptoms were selected a priori as primary outcome measures in the study, ie, fatigue, cognition, myalgias, and arthralgias. Patients were placed into five groups according to time on treatment (1–4, 5–8, 9–12, 13–24, and 25–52 weeks), and changes in the primary symptoms as a function of time on treatment were analyzed using a mixed-effects proportional odds model.
Among 158 patients with more than one follow-up visit who were monitored for up to 1 year, there were on average 6.7 visits per person (median 5, range 2–24). The last follow-up day was on average 96 days after enrollment (median 69, range 7–354 days), corresponding to the length of antibiotic therapy. Each primary symptom was significantly improved at one or more time points during the study. For cognition, fatigue, and myalgias, the greatest improvement occurred in patients on the longest courses of treatment (25–52 weeks) with odds ratios (OR) for improvement of 1.97 (P = 0.02), 2.22 (P < 0.01), and 2.08 (P = 0.01), respectively. In contrast, arthralgias were only significantly improved during the initial 1–4 weeks of therapy (OR: 1.57, P = 0.04), and the beneficial effect of longer treatment did not reach statistical significance for this symptom.
Prolonged intravenous antibiotic therapy is associated with improved cognition, fatigue, and myalgias in patients referred for treatment of neurologic Lyme disease. Treatment for 25–52 weeks may be necessary to obtain symptomatic improvement in these patients.
Video abstract
PMCID: PMC3177589  PMID: 21941449
Lyme disease; Borrelia burgdorferi; intravenous antibiotics; neurologic symptoms
17.  HIV Risk Behavior Before and After HIV Counseling and Testing in Jail: A Pilot Study 
Jail incarceration represents an opportunity to deliver HIV counseling and testing (C&T) services to persons at increased risk of infection. However, jails can be chaotic with rapid turnover of detainees. We conducted a pilot study to investigate the feasibility of comparing the effect of different approaches to HIV counseling and testing (C&T) in jail on subsequent HIV risk behaviors among persons testing HIV-negative.
Consecutive cohorts of newly incarcerated jail detainees were recruited with 132 subjects completing standard HIV C&T as per jail protocol and 132 subjects completing rapid testing with an individualized counseling session. Risk behavior was assessed and compared at baseline and six weeks following jail release.
Among the 264 male participants, pre-incarceration substance use and sexual risk were common. The follow-up visit was completed by 59% of eligible participants. There were no differences in post-release HIV risk behavior between the two arms but there was an overall decrease in risk behavior following jail release for the cohort. In addition, all participants in the rapid arm received rapid HIV test results compared to participants receiving 28% of conventional test results.
Jail incarceration represents an important public health opportunity to deliver HIV C&T. This study demonstrated (1) feasibility in delivering rapid HIV testing combined with individualized counseling to jail detainees, (2) improved test result delivery rates, and (3) success with evaluating risk behaviors during the transition from jail to the community. Further research is needed to determine the optimal approach to HIV C&T in jail with the goal of increasing awareness of HIV serostatus and decreasing HIV risk behavior.
PMCID: PMC2837107  PMID: 20035232
HIV counseling and testing; HIV prevention; correctional facilities; jail
19.  TREAT Asia Quality Assessment Scheme (TAQAS) to standardize the outcome of HIV genotypic resistance testing in a group of Asian laboratories 
Journal of virological methods  2009;159(2):185-193.
The TREAT Asia (Therapeutics, Research, Education, and AIDS Training in Asia) Network is building capacity for Human Immunodeficiency Virus Type-1 (HIV-1) drug resistance testing in the region. The objective of the TREAT Asia Quality Assessment Scheme – designated TAQAS – is to standardize HIV-1 genotypic resistance testing (HIV genotyping) among laboratories to permit rigorous comparison of results from different clinics and testing centres. TAQAS has evaluated three panels of HIV-1-positive plasma from clinical material or low-passage, culture supernatant for up to 10 Asian laboratories. Laboratory participants used their standard protocols to perform HIV genotyping. Assessment was in comparison to a target genotype derived from all participants and the reference laboratory’s result. Agreement between most participants at the edited nucleotide sequence level was high (>98%). Most participants performed to the reference laboratory standard in detection of drug resistance mutations (DRMs). However, there was variation in the detection of nucleotide mixtures (0–83%) and a significant correlation with the detection of DRMs (p < 0.01). Interpretation of antiretroviral resistance showed ~70% agreement among participants when different interpretation systems were used but >90% agreement with a common interpretation system, within the Stanford University Drug Resistance Database. Using the principles of external quality assessment and a reference laboratory, TAQAS has demonstrated high quality HIV genotyping results from Asian laboratories.
PMCID: PMC2863146  PMID: 19490972
HIV; Drug resistance; TAQAS; Quality assessment; Genotyping
20.  Genital Tract Leukocytes and Shedding of Genital HIV Type 1 RNA 
The mechanism of human immunodeficiency virus (HIV) transmission via heterosexual intercourse is unknown. We sought to determine whether the presence of inflammatory cells in the vagina is associated with the presence of genital tract HIV type 1 (HIV-1) RNA.
Analysis of a longitudinal prospective cohort was performed. Women with HIV-1 infection were assessed with use of paired plasma and cervicovaginal lavage specimens. Viral load measurements were performed using nucleic acid sequence—based amplification. White blood cells found in the genital tract (GT WBCs) were quantified using a hemacytometer. Common lower genital tract infections assessed for association with viral shedding (i.e., genital tract viral load [GTVL]) included bacterial vaginosis, candidiasis, and trichomoniasis. Generalized estimating equations were used to estimate the prevalence and odds of detectable GTVL by GT WBC. The association was examined both in the presence and in the absence of lower genital tract infections.
A total of 97 women and 642 visits were included in the analysis. Median duration of follow-up was 30.4 months. Thirty women (31%) had detectable GTVL at any visit. The median CD4 cell count at baseline was 525 cells/μL. Most women were antiretroviral therapy naive at baseline. After adjustment for plasma viral load, the odds of detectable GTVL increased as GT WBC increased, with an odds ratio of 1.36 (95% confidence interval, 1.1–1.7) per 1000-cell increase in GT WBC among women without lower genital tract infections. After adjustment for plasma viral load and lower genital tract infections by incorporating them in a regression model, GT WBC remained significantly associated with GTVL, with an adjusted odds ratio of 1.22 (95% confidence interval, 1.08–1.37).
The presence of GT WBC is associated with an increased risk of detectable GTVL.
PMCID: PMC2714169  PMID: 18808359
21.  HIV infection in refugees: a case–control analysis of refugees in Rhode Island 
The number of HIV-infected refugees entering the USA is increasing. There is little data describing the HIV-infected refugee population and the challenges encountered when caring for them. We performed a retrospective case–control analysis of HIV-infected refugees in order to characterize their co-morbidities, baseline HIV characteristics, and longitudinal care compared to HIV-infected non-refugees.
A retrospective chart review was performed of HIV-infected refugees and non-refugees who were matched for gender, age, and time of establishment of initial HIV care.
The refugee population studied was largely from West Africa. Refugees were more likely than non-refugees to have heterosexual risk for HIV infection, latent tuberculosis infection, and active hepatitis B. Refugees were less likely than non-refugees to have a history of substance use, start antiretrovirals, and be enrolled in a clinical study. The baseline CD4 counts and HIV plasma viral loads were similar between the two groups.
Clinicians caring for West African HIV-infected refugees should be knowledgeable about likely co-morbidities and the impact of cultural differences on HIV care. Further studies are needed to develop culturally competent HIV treatment, education, and prevention programs for refugees who are beginning a new life in the USA.
PMCID: PMC2704558  PMID: 18771943
HIV infection; Refugee; HIV treatment; HIV care

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