Identification of human immunodeficiency virus type 1 non-B subtypes and antiretroviral drug-resistant strains in United States blood donors

The infection staging and profile of genotypic distribution and drug resistance mutation among the human immunodeficiency virus-1 infected blood donors from five Chinese blood centers, 2012-2014

The increasing complexity and diversity of the human immunodeficiency virus-1 (HIV-1) infections challenge the disease control and anti-retrovirus treatment in China. The infection stages and molecular characteristics of HIV-1 from infected Chinese blood donors were examined to shed light on the HIV genotype distribution and the status of drug resistance mutations (DRMs) in the changing HIV epidemic in China. Western blot (WB) confirmed HIV-1 positive plasma samples were collected from blood donors at five Chinese blood centers from April 16, 2012, through June 30, 2014. The HIV infection stages were determined using the Lag-avidity assay. HIV Pol regions including whole protease and partial reverse transcriptase (RT) were amplified and sequenced to establish the profile of genotype distribution and drug resistance mutations (DRMs). Viral loads were determined using the ROCHE COBAS system. Of the 259 HIV-1 positive samples tested by the Lag-avidity assay, 23.6% (61/259) were identified as recent infections. A total of 205 amplified sequences displayed the following genotype distributions: circulating recombinant form (CRF) 07_BC (61.5%), CRF08_BC (8.3%), CRF01_AE (20%), B (6.3%), and 01B (3.9%). There was no significant difference in genotype distribution between recent and long-term infections. 31 DRMs were identified from 27 samples including four protease inhibitors (PIs) accessory DRMs, two PIs major DRMs (M46I), two nucleoside RT inhibitors DRMs (K219R and K70Q), and 23 nonnucleoside RT inhibitors DRMs. 27 samples had DRMs, yielding a drug resistance prevalence of 13.2% (27/205). Our findings provide important information for developing strategies for comprehensive HIV control and improving anti-retroviral treatment in China.

Molecular Testing in Emerging Infectious Diseases

It was widely believed in the late 1960s that infectious diseases had been conquered by vaccines and antibiotics and humans were no longer under threat by microbial pathogens. Yet, since that time more than 60 pathogens have been discovered that can cause serious emerging infectious diseases. Molecular methods have played critical roles in the discovery, monitoring, and clinical diagnostics of emerging pathogens. In this chapter, we present well-recognized emerging pathogens. We provide examples of the utility of molecular assays in research and clinical care of emerging infectious diseases. We also discuss some theoretical and practical limitations of molecular tests and the future prospects of expanding molecular diagnostics for emerging pathogens based on new advances of knowledge and technologies.

Phylogenetic and geospatial evaluation of HIV-1 subtype diversity at the largest HIV center in Rhode Island

Individuals infected with HIV-1 non-B subtypes are understudied in the United States. Their characterization may augment prevention and treatment interventions. We examined the regional molecular epidemiology of non-B subtypes using a combined phylogenetic and geospatial approach. HIV-1 pol sequences and clinical data obtained for routine clinical care were aggregated from 2004 to 2011 at the largest HIV center in Rhode Island. Subtyping was performed by neighbor-joining and maximum-likelihood phylogeny and compared across eight commonly used tools (HIVdb, REGA, RIP, NCBI, Geno2Pheno, EuResist, jpHMM and STAR) using proportional odds ordinal regression. Individuals with non-B subtypes were characterized according to demographics and risk factors for infection, intra-subtype clustering by maximum-likelihood phylogeny, and geospatial hotspot analysis using Getis-Ord Gi(∗) statistics. Of 1277 unique sequences, phylogenetic subtyping demonstrated 8.3% (N=106, 95% CI 6.8-10%) non-B subtypes and circulating recombinant forms (CRFs): CRF02_AG=46; A=15; C=15; CRF01_AE=6; CRF06_CPX=5; CRF14_BG=5; G=3; CRF43_02G=3; D=3; CRF24_BG=3; CRF11_CPX=1; F1=1. Compared to phylogeny, Geno2Pheno was the most concordant (86% exact match) followed by REGA (85%), EuResist (85%) and STAR (82%). Of 106 individuals with non-B subtypes, 50% were male, 71% acquired infection through heterosexual transmission; 76%, were born in Africa, 6% Southeast Asia, 5% the United States, 3% Central America, 1% Europe, and 9% unknown. Eighty percent of CRF02_AG, 93% of A and 87% of C sequences were from African-born individuals. Twenty-two percent of non-B subtypes formed transmission clusters, including a significant number of younger individuals with perinatally-acquired infection. Geospatial analyses revealed hotspots of B and non-B subtypes in the state capital with a more concentrated focus among non-B subtypes. Molecular examination of regional HIV diversity revealed a larger than expected non-subtype B infected population, mostly born in Africa, with low ongoing regional transmission. Phylogenetic and geospatial characterization of infection clusters is helpful to identify targets for treatment and prevention interventions.

Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) has significant implications for diagnosis, vaccine development, and clinical management of patients. Although HIV-1 subtype B is predominant in the United States, factors such as global travel, immigration, and military deployment have the potential to increase the proportion of non-subtype B infections. Limited data are available on the prevalence and distribution of non-B HIV-1 strains in the United States. We sought to retrospectively examine the prevalence, geographic distribution, diversity, and temporal trends of HIV-1 non-B infections in samples obtained by ARUP Laboratories, a national reference laboratory, from all regions of the United States. HIV-1 pol sequences from 24,386 specimens collected from 46 states between 2004 and September 2011 for drug resistance genotyping were analyzed using the REGA HIV-1 Subtyping Tool, version 2.0. Sequences refractory to subtype determination or reported as non-subtype B by this tool were analyzed by PHYLIP version 3.5 and Simplot version 3.5.1. Non-subtype B strains accounted for 3.27% (798/24,386) of specimens. The 798 non-B specimens were received from 37 states and included 5 subtypes, 23 different circulating recombinant forms (CRFs), and 39 unique recombinant forms (URFs). The non-subtype B prevalence varied from 0% in 2004 (0/54) to 4.12% in 2011 (201/4,884). This large-scale analysis reveals that the diversity of HIV-1 in the United States is high, with multiple subtypes, CRFs, and URFs circulating. Moreover, the geographic distribution of non-B variants is widespread. Data from HIV-1 drug resistance testing have the potential to significantly enhance the surveillance of HIV-1 variants in the United States.

Prevalence of drug-resistant HIV type 1 at the time of initiation of antiretroviral therapy in Portland, Oregon

The presence of transmitted drug-resistant HIV-1 (TDR) at the time of antiretroviral therapy (ART) initiation is associated with failure to achieve viral load suppression. Rates of TDR in ART-naive patients have been reported from various parts of the world through ongoing national, regional, and global evaluations; however, surveillance of TDR in Portland, Oregon has not been previously described. We describe the prevalence of TDR in patients in the Portland area who have recently entered care. Genotypic data were obtained from plasma specimens collected between 2003 and 2009 from 165 recently identified HIV-1-positive, ART-naive adults in care at the Multnomah County Health Department. Median time from diagnosis to first genotype was 2.7 months. Mutations associated with TDR were observed in 33 (20.0%) patients. Mutations associated with resistance to nucleoside reverse transcriptase (RT) inhibitors (NRTI), nonnucleoside RT inhibitors (NNRTI), and protease inhibitors (PI) were found in 15 (9.1%), 17 (10.3%), and 5 (3.0%) patients, respectively (p=0.013 for NNRTI vs. PI, and 0.035 for NRTI vs. PI, Fisher exact test). Dual class resistance was observed in four (2.4%) patients. Predominant RT mutations included M41L, T215C or S, and K103N. The prevalence of HIV-1 with NRTI resistance-associated mutations increased from 2006 to 2008-2009 (p=0.004) based on date of diagnosis. These data indicate relatively high rates of drug resistance present prior to ART initiation among patients in the Portland area, and support continued surveillance of local trends of TDR to inform optimal individual treatment strategies and public health decisions.

Universal profiling of HIV-1 pol for genotypic study and resistance analysis across subtypes

BACKGROUND

The increased use of anti-HIV-1 treatments in developing countries primarily infected by non-B subtypes necessitates development of novel tools to assess susceptibility and resistance. HIV-1 genomes are highly polymorphic and present challenges for the development of universal protocols capable of screening across subtypes. Currently available viral genotyping methods are useful for viral quantification, but are inadequate for sequence profiling or comprehensive mutation detection in the variable regions of HIV polymerase (pol).

METHODS

A novel set of universal primers within pol, with consensus among a variety of HIV-1 subtypes, was developed. One-round amplification was performed by one-step reverse transcription PCR on 79 samples from HIV-1 subtypes. Using a second set of primers, the amplified fragment was sequenced and assembled to produce a profile database per sample.

RESULTS

First-round amplification using universal primers generated a unique amplicon encompassing the major pol regions in all tested HIV-1 subtype samples. Sequence analysis of the amplified fragment not only confirmed the subtype of each HIV-1 isolate but also identified resistance mutations in the pol genes of HIV-1, including protease, reverse transcriptase, connection, RNase H, and integrase. Last, some of these primers were used to develop a viral load test using quantitative real time-PCR.

CONCLUSIONS

A novel protocol was produced to effectively identify and simultaneously generate extensive sequence profiles of pol genes across HIV-1 subtypes. This protocol allows for expeditious and cost-effective mutation detection, genotypic evaluation and viral load determination in multiple HIV-1 subtypes.

Genetic diversity of recently acquired and prevalent HIV, hepatitis B virus, and hepatitis C virus infections in US blood donors

BACKGROUND

Genetic variations of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and hepatitis B virus (HBV) can affect diagnostic assays and therapeutic interventions. Recent changes in prevalence of subtypes/genotypes and drug/immune-escape variants were characterized by comparing recently infected vs more remotely infected blood donors.

METHODS

Infected donors were identified among approximately 34 million US blood donations, 2006-2009; incident infections were defined as having no or low antiviral antibody titers. Viral genomes were partially sequenced.

RESULTS

Of 321 HIV strains (50% incident), 2.5% were non-B HIV subtypes. Protease and reverse transcriptase (RT) inhibitor resistance mutations were found in 2% and 11% of infected donors, respectively. Subtypes in 278 HCV strains (31% incident) yielded 1a>1b>3a>2b>2a>4a>6d, 6e: higher frequencies of 3a in incident cases vs higher frequencies of 1b in prevalent cases were found (P = .04). Twenty subgenotypes among 193 HBV strains (26% incident) yielded higher frequencies of A2 in incident cases and higher frequencies of A1, B2, and B4 in prevalent cases (P = .007). No HBV drug resistance mutations were detected. Six percent of incident vs 26% of prevalent HBV contained antibody neutralization escape mutations (P = .01).

CONCLUSIONS

Viral genetic variant distribution in blood donors was similar to that seen in high-risk US populations. Blood-borne viruses detected through large-scale routine screening of blood donors can complement molecular surveillance studies of highly exposed populations.

The human immunodeficiency virus-1 genotype diversity and drug resistance mutations profile of volunteer blood donors from Chinese blood centers

BACKGROUND

The global human immunodeficiency virus (HIV)-1 epidemic is becoming increasingly diverse and complex. Molecular epidemiologic characteristics were studied for HIV-1-infected blood donors from five Chinese regions to determine genotype diversity and drug resistance mutations (DRMs) profile.

STUDY DESIGN AND METHODS

HIV-1 confirmed-reactive serum samples were collected from 172 blood donors from five blood centers during 2007 to 2010. HIV-1 Pol including whole protease and partial reverse transcriptase genes was amplified, sequenced, and analyzed for the subtype determination and drug resistance profile description.

RESULT

A total of 113 amplified sequences including 82 from Kunming blood center and 31 from four other blood centers had the following genotype characteristics: G (0.9%), B (2.7%), circulating recombinant form (CRF) 01_AE (32.7%), CRF07_BC (22.1%), and CRF08_BC (41.6%). Female donors represent 45.1% of all cases and 63.9% cases with DRMs. The prevalence of samples with potential low or higher resistance among Chinese blood donors is 4.4%.

CONCLUSION

HIV-1 infection in Chinese blood donors is genetically diverse and the subtype distribution reflects that from the high-risk populations. Our results support continuous molecular epidemiologic surveillance for HIV-1 in blood donors as a part of a comprehensive HIV control program.

Seroconverting blood donors as a resource for characterising and optimising recent infection testing algorithms for incidence estimation

Introduction

Biomarker-based cross-sectional incidence estimation requires a Recent Infection Testing Algorithm (RITA) with an adequately large mean recency duration, to achieve reasonable survey counts, and a low false-recent rate, to minimise exposure to further bias and imprecision. Estimating these characteristics requires specimens from individuals with well-known seroconversion dates or confirmed long-standing infection. Specimens with well-known seroconversion dates are typically rare and precious, presenting a bottleneck in the development of RITAs.

Methods

The mean recency duration and a ‘false-recent rate’ are estimated from data on seroconverting blood donors. Within an idealised model for the dynamics of false-recent results, blood donor specimens were used to characterise RITAs by a new method that maximises the likelihood of cohort-level recency classifications, rather than modelling individual sojourn times in recency.

Results

For a range of assumptions about the false-recent results (0% to 20% of biomarker response curves failing to reach the threshold distinguishing test-recent and test-non-recent infection), the mean recency duration of the Vironostika-LS ranged from 154 (95% CI: 96–231) to 274 (95% CI: 234–313) days in the South African donor population (n = 282), and from 145 (95% CI: 67–226) to 252 (95% CI: 194–308) days in the American donor population (n = 106). The significance of gender and clade on performance was rejected (p−value = 10%), and utility in incidence estimation appeared comparable to that of a BED-like RITA. Assessment of the Vitros-LS (n = 108) suggested potentially high false-recent rates.

Discussion

The new method facilitates RITA characterisation using widely available specimens that were previously overlooked, at the cost of possible artefacts. While accuracy and precision are insufficient to provide estimates suitable for incidence surveillance, a low-cost approach for preliminary assessments of new RITAs has been demonstrated. The Vironostika-LS and Vitros-LS warrant further analysis to provide greater precision of estimates.

Expanded evaluation of blood donors in the United States for human immunodeficiency virus type 1 non-B subtypes and antiretroviral drug-resistant strains: 2005 through 2007

BACKGROUND

In a previous study of 66 human immunodeficiency virus (HIV)-infected US blood donors from 1999 to 2005, HIV-1 non-B and antiretroviral drug-resistant strains accounted for 4.7 and 6.5% of HIV infections, respectively. This study was expanded to include an additional 11 recently acquired infections and 197 established infections collected from January 2005 through December 2007.

STUDY DESIGN AND METHODS

HIV-infected donors were detected using FDA-licensed assays. Drug resistance profiles for protease and reverse transcriptase (RT) genes were determined using a genotyping system (ViroSeq, Celera Diagnostics); genetic subtype was determined by phylogenetic analysis of these sequences.

RESULTS

Drug resistance profiles were obtained for 203 of 208 specimens; 9.9% had mutations that confer drug resistance. Ten showed resistance to a single drug class: nine to nonnucleoside RT inhibitors (NNRTIs) and one to nucleoside RT inhibitors (NRTIs). Eight showed two drug class resistance: five NRTI plus NNRTI, two NRTI plus protease inhibitor (PI), and one NNRTI plus PI. Two showed three drug class resistance. Non-B strains were identified in 2.5% of donors and consisted of subtypes A1 and D, CRF02_AG, CRF43-02G, and URF_BF.

CONCLUSIONS

Data from this and the previous study show that antiretroviral drug-resistant HIV-1 is present in 9.1% of HIV-infected donors from 1999 through 2007; 9.3% of established infections and 6.9% of recent infections. Diverse HIV-1 non-B strains presently account for 3.0% of HIV infections in US donors.

HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir

Viruses were sequenced from 75 antiretroviral therapy (ARV)-naïve and from 75 ARV-treated patients who subsequently received a raltegravir-containing regimen. No major integrase inhibitor (INI)-resistance mutations were present in the 150 integrase (IN) sequences. Four ARV-naïve (5.3%) and two ARV-treated patients (2.7%) had one of the following minor INI-resistance mutations: L74M, E157Q, G163R, and R263K but there was no association between baseline raltegravir genotype and subsequent response to raltegravir treatment. We also combined our sequences with 4170 previously published group M IN sequences from INI-naïve patients to assess IN sequence variability and compared our findings with those of a study we performed in 2008 using data from 1563 patients. The number of polymorphic IN positions increased from 40% to 41% between the two studies. However, none of the major INI-resistance mutations was found to be polymorphic in either study and there were no significant changes in the prevalence of any of the minor INI-resistance mutations.

Two independent epidemics of HIV in Maryland

BACKGROUND

HIV-1 subtype B virus is the predominant subtype in HIV-infected individuals in the United States. However, increasing evidence suggests that prevalence of non-B subtypes may be on the rise in the West, and this may have implications for HIV-1 disease surveillance and treatment. The state of Maryland currently has the fourth highest AIDS case report rate in the United States. The goal of this study was to evaluate the prevalence of HIV-1 non-B subtypes in Maryland. The study population included individuals diagnosed with HIV in 2007 through the voluntary counseling and testing sites at the Maryland Department of Health and Mental Hygiene and HIV-infected patients who had genotyping performed at the University of Maryland Medical Center.

RESULTS

At the Department of Health and Mental Hygiene sites, 47 unique non-B subtype strains were identified representing a non-B prevalence of 12.9%. These non-B subtypes included CRF02_AG (n = 20), C (n = 11), A (n = 7), G (n = 5), D (n = 1), and unique recombinant forms (n = 3). The non-B patients were predominantly non-Hispanic black (95.7%) with 63.8% female. Although the majority of the HIV subtype B cases (65.3%) were identified from the Baltimore metropolitan area, most (80.9%) of the non-B cases were from the Maryland suburbs of Washington, DC. Among University of Maryland Medical Center patients, there were 30 non-B subtypes, representing a non-B prevalence of 1.9%. The non-B subtypes detected were CRF02_AG (n = 14), C (n = 6), A (n = 6), G (n = 2), D (n = 1), and unique recombinant forms (n = 1). Phylogenetic analysis of the non-B subtypes revealed that viral sequences from both sources were intermixed, confirming that both sampling frames were drawing from the same overall population.

CONCLUSIONS

Multiple HIV-1 subtypes exist in the Baltimore-Washington metropolitan area with a significant non-B-infected population in the Maryland suburbs of Washington, DC, suggesting 2 independent epidemics of HIV in Maryland. Population-based surveillance inclusive of groups at higher risk of non-B strains is essential to monitor the prevalence and variations of HIV subtypes in Maryland and the United States.

Prevalence, incidence, and residual risk of human immunodeficiency virus and hepatitis C virus infections among United States blood donors since the introduction of nucleic acid testing

BACKGROUND

Nucleic acid testing (NAT) for human immunodeficiency virus (HIV) and hepatitis C virus (HCV) was introduced for blood donation screening in the United States in 1999. This study analyzes temporal trends of these two infections since NAT introduction.

STUDY DESIGN AND METHODS

Donation data from 1999 to 2008 were analyzed; each donation was tested for antibodies and viral RNA for HIV and HCV. Incidence for first-time (FT) donors was derived by multiplying that among repeat (RP) donors by the ratio of NAT yield rates between FT and RP donors. Incidence for all donors was the weighted mean based on percentage of FT and RP donors. Residual risk (RR) was determined using the window-period model.

RESULTS

During the 10-year period approximately 66 million donations were screened with 32 HIV (1:2 million) and 244 HCV (1:270,000) NAT yield donations identified. HCV prevalence among FT donors decreased by 53% for 2008 compared to 1999. HIV and HCV incidence among RP donors increased in 2007 through 2008 compared to 2005 through 2006. During 2007 through 2008, HIV incidence was 3.1 per 10(5) person-years (py), with an RR estimate of 0.68 per 10(6) (1:1,467,000) donations; HCV incidence was 5.1 per 10(5) py, with an RR estimate of 0.87 per 10(6) (1:1,149,000). The increase in HIV incidence was primarily among 16- to 19-year-old, male African American donors and that in HCV was primarily among Caucasian donors of 50 or more years. Donors from the Southern United States had higher incidence rates.

CONCLUSION

HCV prevalence decreased significantly since NAT introduction. The increase in HIV and HCV incidence in 2007 through 2008 warrants continued monitoring and investigation.

Young pregnant women living with HIV/AIDS in Criciuma, Southern Brazil, are infected almost exclusively with HIV type 1 clade C

Southern Brazil has the highest prevalence rate of AIDS in the country and is the only region in the Americas where HIV-1 C prevails. Metropolitan areas and harbor cities have been evaluated, but limited information is available for small towns and specific populations. We studied women attending the obstetric outpatient clinic of Criciuma, State of Santa Catarina in 2007 to evaluate the molecular epidemiology of HIV-1 among pregnant women living with HIV/AIDS. Forty-two cases had partial pol gene sequenced and additional partial gag and/or env genes from nine women. HIV subtyping was evaluated by phylogenetic methods and antiretroviral (ARV) drug resistance mutations (DRMs) at the Stanford Database. DRMs to one or more ARV class was observed in 20/42, 48% of cases, with 15/41, 37% with viral load <500 copies/ml. Subtype C at pol was identified in 33/42, 78.6% (95% CI: 64-89%), C mosaics (CB, CF) in 2, 4.8% (95% CI: 0.8-19%), F in 4, 9.5% (95% CI: 3-21%), and B in 3, 7.1% (95% CI: 1.8-18%). Discordance in concatenated gag/pol/env or intraregion mosaic was observed in 1/9, 11% of HIV-1 C genomes. The proportion of HIV-1 C in this study is the highest rate described in the Americas. Molecular surveillance in specific populations is instrumental for a better understanding of the Brazilian HIV epidemic.

Results of the Abbott RealTime HIV-1 assay for specimens yielding "target not detected" results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test

No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding "target not detected" results by CTM.

Transmitted drug resistance in nonsubtype B HIV-1 infection

HIV-1 nonsubtype B variants account for the majority of HIV infections worldwide. Drug resistance in individuals who have never undergone antiretroviral therapy can lead to early failure and limited treatment options and, therefore, is an important concern. Evaluation of reported transmitted drug resistance (TDR) is challenging owing to varying definitions and study designs, and is further complicated by HIV-1 subtype diversity. In this article, we discuss the importance of various mutation lists for TDR definition, summarize TDR in nonsubtype B HIV-1 and highlight TDR reporting and interpreting challenges in the context of HIV-1 diversity. When examined carefully, TDR in HIV-1 non-B protease and reverse transcriptase is still relatively low in most regions. Whether it will increase with time and therapy access, as observed in subtype-B-predominant regions, remains to be determined.