Genotyping of B and non-B subtypes of human immunodeficiency virus type 1

Companion and complementary diagnostics for infectious diseases

INTRODUCTION

Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents.

AREAS COVERED

This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests.

EXPERT OPINION

CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.

Pitfalls of antiretroviral drug resistance genotyping of HIV-1 Group M and Group N from Cameroon by sequenced-based assays

Background:

HIV-1 genotyping for antiretroviral drug resistance mutations (DRMs) were developed based basically on subtype B HIV-1 Group M, which represents only 10% of HIV strains worldwide. In sub-Saharan Africa, non-B subtypes HIV-1 largely predominate and HIV-1 genetic diversity could affect the performance of drug resistance genotyping assays. We compared prospectively the performance of the ViroSeq^® and Trugene^® genotyping assays to detect DRM in HIV-1-infected adult patients living in Douala, Cameroun.

Materials and Methods:

DRM in protease (P) and reverse transcriptase (RT) genes were assessed in parallel using both ViroSeq^® and Trugene^® assays in plasma samples from 45 first-line antiretroviral treatment-experienced patients in Douala, Cameroon.

Results:

Trugene HIV-1 Genotyping Assay^® (Siemens Health Care Diagnostics, NY, USA) and ViroSeq HIV-1 Genotyping System^®(Celera Diagnostics, CA, USA) assessed equivalently antiretroviral DRMs in P and RT genes from non-B HIV-1 Group M in 44 Cameroonian adults in virological failure; Trugene^® was slightly more sensitive than ViroSeq^® (100% vs. 91%). One patient infected by HIV-1 Group N was successfully amplified only by the Trugene HIV-1 Genotyping assay^®, while ViroSeq HIV-1 Genotyping System v2.0^® assay could not.

Conclusion:

Results showed the higher performance of the Trugene^® system to detected and amplify P and RT genes targeting DRM to the principal antiretroviral drugs used in sub-Saharan Africa. Discrepancies between the results of HIV viral load assays and molecular tests should alert clinicians and virologists to the possibility of infection by an atypical variant virus, especially in Central Africa where very broad HIV-1 genetic diversity exists.

Viral Genetic Diversity and Polymorphisms in a Cohort of HIV-1-Infected Patients Eligible for Initiation of Antiretroviral Therapy in Abuja, Nigeria

Studying the genetic diversity and natural polymorphisms of HIV-1 would benefit our understanding of HIV drug resistance (HIVDR) development and predict treatment outcomes. In this study, we have characterized the HIV-1 genetic diversity and natural polymorphisms at the 5' region of the pol gene encompassing the protease (PR) and reverse transcriptase (RT) from 271 plasma specimens collected in 2008 from HIV-1-infected patients who were eligible for initiating antiretroviral therapy in Abuja (Nigeria). The analysis indicated that the predominant subtype was subtype G (31.0%), followed by CRF02-AG (19.2 %), CRF43-02G (18.5%), and A/CRF36-cpx (11.4%); the remaining (19.9%) were other subtypes and circulating (CRF) and unique (URF) recombinant forms. Recombinant viruses (68.6%) were the major viral strains in the region. Eighty-four subtype G sequences were further mainly classified into two major and two minor clusters; sequences in the two major clusters were closely related to the HIV-1 strains in two of the three major subtype G clusters detected worldwide. Those in the two minor clusters appear to be new subtype G strains circulating only in Abuja. The pretreatment DR prevalence was <3%; however, numerous natural polymorphisms were present. Eleven polymorphic mutations (G16E, K20I, L23P, E35D, M36I, N37D/S/T, R57K, L63P, and V82I) were detected in the PR that were subtype or CRF specific while only three mutations (D123N, I135T, and I135V) were identified in the RT. Overall, this study indicates an evolving HIV-1 epidemic in Abuja with recombinant viruses becoming the dominant strains and the emergence of new subtype G strains; pretreatment HIVDR was low and the occurrence of natural polymorphism in the PR region was subtype or CRF dependent.

Current molecular epidemiology and recombination of HIV type 1 subtypes in northern Thailand

HIV subtype characterization is an important tool to monitor the genetic variation of the HIV epidemic. This study investigated the current HIV subtype distribution and recombination among the northern Thai population. An in-house genotypic assay of HIV protease and reverse transcriptase genes was performed on 420 plasma specimens from HIV-infected patients residing in several northern Thai provinces. HIV subtyping was determined by phylogenetic analysis. Three hundred and ninety-eight sequences (94.8%) were identified as CRF01_AE with the genetic distance of 1.848 ± 0.957% and 12 (2.9%) as subtype B with the genetic distance of 4.186 ± 0.849%. In addition, two sequences (0.5%) of HIV subtype C were found, suggesting that these patients were either immigrants from another country or were infected through heterosexual contact with HIV-infected subjects from another country. Bootscan analysis showed that there were eight (1.9%) unique recombinant forms (URFs) consisting of a recombinant of CRF01_AE with subtype B or subtype C. The information from this study is useful for prevention programs to halt the onward transmission of a particular HIV outbreak. However, characterization of the full genome of these CRF01_AE/B and CRF01_AE/C intersubtype recombinants, and also subtype C, is required for confirmation and elucidation.

Genetic diversity among human immunodeficiency virus-1 non-B subtypes in viral load and drug resistance assays

The tremendous diversity of human immunodeficiency virus (HIV)-1 strains circulating worldwide has an important impact on almost all aspects of the management of this infection, from the identification of infected persons, through treatment efficacy and monitoring, and prevention strategies such as vaccine design. The areas where HIV-1 genetic diversity is highest are those where the majority of patients in need of treatment and biological monitoring live. With increased access to treatment in these areas, it is expected that the demand for monitoring tools such as viral load assays and resistance tests will also increase, and their reliability will be critical. Regular updates of these assays during the last two decades have aimed at improving their performances in different ways that include their reliability with different HIV-1 strains. We here review to what extent HIV-1 genetic diversity still limits or not the use of currently available viral load and resistance tests.

High failure rate of the ViroSeq HIV-1 genotyping system for drug resistance testing in Cameroon, a country with broad HIV-1 genetic diversity

The ViroSeq HIV-1 genotyping system is used in many African countries for drug resistance testing. In this study, we used a panel of diverse HIV-1 group M isolates circulating in Cameroon to show that the performance of this assay can be altered by the sequence variation of non-B HIV-1 strains that predominate in African settings.

Development and application of a broadly sensitive dried-blood-spot-based genotyping assay for global surveillance of HIV-1 drug resistance

As antiretroviral therapy (ART) is scaled up in resource-limited countries, surveillance for HIV drug resistance (DR) is vital to ensure sustained effectiveness of first-line ART. We have developed and applied a broadly sensitive dried-blood-spot (DBS)-based genotyping assay for surveillance of HIV-1 DR in international settings. In 2005 and 2006, 171 DBS samples were collected under field conditions from newly diagnosed HIV-1-infected individuals from Malawi (n = 58), Tanzania (n = 60), and China (n =53). In addition, 30 DBS and 40 plasma specimens collected from ART patients in China and Cameroon, respectively, were also tested. Of the 171 DBS analyzed at the protease and RT regions, 149 (87.1%) could be genotyped, including 49 (81.7%) from Tanzania, 47 (88.7%) from China, and 53 (91.4%) from Malawi. Among the 70 ART patient samples analyzed, 100% (30/30) of the Chinese DBS and 90% (36/40) of the Cameroonian plasma specimens were genotyped, including 8 samples with a viral load of <400 copies/ml. The results of phylogenetic analyses indicated that the subtype, circulating recombinant form (CRF), and unique recombinant form (URF) distribution was as follows: 73 strains were subtype C (34%), 37 were subtype B (17.2%), 24 each were CRF01_AE or CRF02_AG (11.2% each), 22 were subtype A1 (10.2%), and 9 were unclassifiable (UC) (4.2%). The remaining samples were minor strains comprised of 6 that were CRF07_BC (2.8%), 5 that were CRF10_CD (2.3%), 3 each that were URF_A1C and CRF08_BC (1.4%), 2 each that were G, URF_BC, and URF_D/UC (0.9%), and 1 each that were subtype F1, subtype F2, and URF_A1D (0.5%). Our results indicate that this broadly sensitive genotyping assay can be used to genotype DBS collected from areas with diverse HIV-1 group M subtypes and CRFs. Thus, the assay is likely to become a useful screening tool in the global resistance surveillance and monitoring of HIV-1 where multiple subtypes and CRFs are found.

Clinical utility of genotypic resistance tests for HIV-1-infected patients with low-level virological failure

The usefulness of genotypic resistance tests (GRT) among HIV-1 patients with low-level virological failure (LLVF) was evaluated. Up to 78% of samples with <1,000 copies/ml were sequenced successfully. For samples with 50 to 200 copies/ml, the success rate was as high as 69%. LLVF should not deter clinicians from requesting GRT.

Antiretroviral resistance in different HIV-1 subtypes: impact on therapy outcomes and resistance testing interpretation

PURPOSE OF REVIEW

This review summarizes our knowledge of HIV-1 subtype-related differences associated with antiretroviral drug resistance and its interpretation, and with clinical, immunological and virological therapy outcomes. It also addresses the problem that subtypes are only a crude classification of the genetic diversity relevant to these topics.

RECENT FINDINGS

Subtype-related variability is responsible for differences in drug resistance. Baseline drug susceptibility and resistance pathways vary between subtypes; such variation is mainly related to differences in the prevalence of specific polymorphisms. The clinical impact of these findings is rather limited, but with the increasing genetic diversity of HIV-1, they have the potential to impact the accuracy of the 'algorithm' concept for genotypic drug resistance test interpretation negatively.

SUMMARY

Severe limitations exist in the data describing the association of HIV-1 subtypes with resistance and treatment outcomes, because most data are the result of retrospective observational studies. Even with these limitations, the knowledge gathered allows us to assume that differences in the short-term response to treatment in different subtypes should not greatly affect treatment strategies. As for the interpretation of genotypic resistance testing, new tools are needed, taking into account the entire genomic context and thus overcoming the problem of genetic diversity.

Molecular epidemiology of HIV type 1 in northern Brazil: identification of subtypes C and D and the introduction of CRF02_AG in the Amazon region of Brazil

The molecular epidemiology of HIV-1 strains circulating in Belem-PA and Macapa-AP, in the Northern region of Brazil, is described using sequences of the C2V3 segment of the env and the pro gene of HIV-1 from patients of the Reference Unit for Special Infectious and Parasitary Diseases (URE-DIPE) in Belem-PA and the Central Laboratory (LACEN) in Macapa-AP. Subtype B was the most frequently found in relation to pro (88.3%) in Belem and in Macapa (97.1%) and env (88.3% in Belem and 100% in Macapa). Subtype F was also described in Belem (9.3% pro and 8.3% env) and Macapa (2.8% pro). Subtype D was described for the first time in the Northern region of the country as well as the recent entry of CRF02_AG. Furthermore, several possible recombinant forms among the various subtypes were found in both cities. The results support the hypothesis that HIV-1 infection is associated with the epidemic of the virus in the Southeast region of the country and that the city of Belem is the most important route for HIV-1 entry in the Northern region of Brazil.

Multicenter performance evaluation of a new TaqMan PCR assay for monitoring human immunodeficiency virus RNA load

A TaqMan real-time PCR assay, the COBAS TaqMan human immunodeficiency virus (HIV) (HPS-CTMHIV) PCR assay, recently developed for the quantification of HIV type 1 RNA in plasma, was evaluated in comparison with the licensed COBAS AMPLICOR HIV-1 MONITOR (CAHIM) assay. In this study, we have analyzed the tests' sensitivities, precisions, and linearities using multiple replicates of a standard panel of HIV RNA covering a 7-logarithm range of concentrations, as well as serial threefold dilutions of high-titer clinical samples. The subtype inclusivity was also investigated, using a panel of subtypes A to H, while a collection of 160 clinical samples was analyzed to assess the tests' specificities and the systems' similarities. The results of these experiments showed that the HPS-CTMHIV assay has a sensitivity of 53 copies/ml (95% hit rate), 100% specificity, and good intra- and interassay precision. The results of the HPS-CTMHIV assay were linear in the 50- to 10(7)-copies/ml range, with a correlation coefficient (R) for expected versus observed results of 0.98. Compared to the CAHIM assay, the HPS-CTMHIV assay showed a high correlation (R=0.99) across the dynamic range of RNA concentrations that, for the CAHIM assay, requires two different sample preparations. Equivalent performances were also observed for the two systems in the detection and quantification of HIV subtypes A to H. These data indicate that the HPS-CTMHIV assay may be one of the tests of choice for monitoring viral load throughout the course of HIV infection and during highly active antiretroviral therapy.

Performance evaluation of the two protease sequencing primers of the Trugene HIV-1 genotyping kit

This article describes the performance of the two protease sequencing modules available in the Trugene HIV-1 genotyping Kit on a sample population with a high prevalence of HIV-1 non-B subtypes (n=110). The relevance of the algorithm recommended by the kit was also evaluated. The results indicated a high sequencing failure rate of the PR module (34%). Forty-five percent of the failed sequences derived from non-B subtype viruses. Furthermore, no PR sequence could be obtained from any of the HIV-1 subtype A and C infected samples that were tested. In contrast, a sequence could be obtained from the entire panel using the P2 module. The data indicated that the high rate of sequencing failures of the PR module was related to both the HIV-1 non-B subtypes as well as lower levels of RNA viral load. In six out of the 73 samples for which both protease modules were successful, discrepancies between the two protease sequences were observed, which led to discordant resistance reports in two cases. The data highlight the problems and the clinical implications that may occur during resistance genotyping of clinical samples with a high prevalence of HIV-1 non-B subtypes.

K65R and Y181C are less prevalent in HAART-experienced HIV-1 subtype A patients

The vast majority of HIV-1 infections globally are caused by subtype A or C, although little is known about their drug resistance profiles. We found that HAART-experienced patients infected with subtype A had a lower prevalence of K65R and Y181C than those with subtypes B or C, despite similar exposure to antiretroviral agents that select for these mutations. If confirmed, this information may be important in the planning of antiretroviral regimens in patients infected with HIV-1 subtype A.