Open Access

High level of HIV-1 drug resistance among patients with HIV-1 and HIV-1/2 dual infections in Guinea-Bissau

  • Sanne Jespersen1, 2Email author,
  • Martin Tolstrup2,
  • Bo Langhoff Hønge1, 2, 3,
  • Candida Medina4,
  • David da Silva Té4,
  • Svend Ellermann-Eriksen5,
  • Lars Østergaard2,
  • Christian Wejse2, 6,
  • Alex Lund Laursen2 and
  • for The Bissau HIV cohort study group
Virology Journal201512:41

https://doi.org/10.1186/s12985-015-0273-9

Received: 25 December 2014

Accepted: 26 February 2015

Published: 11 March 2015

Abstract

Background

With the widespread use of antiretroviral treatment (ART) in Africa, the risk of drug resistance has increased. The aim of this study was to evaluate levels of HIV-1 resistance among patients with HIV-1 and HIV-1/2 dual infections, treated with ART, at a large HIV clinic in Guinea-Bissau.

Findings

Patients were selected from the Bissau HIV cohort. All patients had HIV-1 or HIV-1/2 dual infection, a CD4 cell count performed before and 3–12 months after starting ART, and a corresponding available plasma sample. We measured viral load in patients with HIV-1 (n = 63) and HIV-1/2 dual (n = 16) infections a median of 184 days after starting ART (IQR: 126–235 days). In patients with virological failure (defined as viral load >1000 copies/ml) and with sufficient plasma available, we performed an HIV-1 genotypic resistance test. Thirty-six patients (46%) had virological failure. The CD4 cell count did not predict treatment failure. Of the 36 patients with virological failure, we performed a resistance test in 15 patients (42%), and nine patients (9/15; 60%) had resistance mutations. The most common mutation was K103N, which confers high-level resistance to non-nucleoside reverse transcriptase inhibitors (NNRTI). No major mutations against protease inhibitors (PI) were found.

Conclusions

Our results showed that patients with HIV-1 and HIV-1/2 dual infections in Guinea-Bissau had a high rate of virological failure and rapid development of NNRTI resistance. It remains to be determined whether a more robust, PI-based treatment regimen might benefit this population more than NNRTIs.

Keywords

HIV-1 HIV-1/2 dual infection Sub-Saharan Africa Drug resistance Antiretroviral treatment Guinea-Bissau

Findings

Widespread use of antiretroviral treatment (ART) in Africa has increased the risk of drug resistance [1]. Factors that contribute to drug resistance include lack of plasma viral load monitoring [2], treatment interruptions due to drug stocking discontinuities [3], and drug interactions [4].

Most patients in Africa initiate ART with two nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and one non-nucleoside reverse transcriptase inhibitor (NNRTI) [5]. Africans have a high risk of developing the K103N NNRTI mutation, which is connected to poor adherence, due to a common genetic polymorphism that causes slow plasma NNRTI clearance and functional NNRTI monotherapy, when treatment is interrupted [6].

The West African country, Guinea-Bissau, has the highest HIV-2 prevalence worldwide [7-9]. HIV-2 is naturally resistant to NNRTIs [10], hence, patients with HIV-2 or HIV-1/2 dual infections must be treated with a protease inhibitor (PI)-based regimen. Differences in HIV-1 and HIV-2 resistance patterns may lead to complex drug resistance challenges for ART options in HIV-1/2 dual infections. This study is the first to report data on HIV resistance in Guinea-Bissau among patients with HIV-1 and HIV-1/2 dual infections. Based on data from neighboring countries, we suggest that HIV resistance may be a substantial problem [11-13].

Methods

This retrospective, follow-up study accessed data from a clinical HIV cohort at Hospital Nacional Simão Mendes, in Bissau, the capital of Guinea-Bissau [14].

Whenever a CD4 cell count is performed, surplus plasma is stored in a biorepository in Aarhus, Denmark. From this repository, we identified data for adult patients with HIV-1 or HIV-1/2 dual infections that had CD4 cell counts and stored plasma samples acquired before and after 3–12 months of ART. HIV-1/HIV-2 discrimination was performed with a SD Bioline HIV 1/2 3.0 test (Standard Diagnostics Inc, Kyonggi-do, South Korea). All stored plasma from patients with HIV-1/2 dual infections underwent an immunofluorescence discriminatory HIV-test (INNO-LIA; Innogenetics, Ghent, Belgium) [15]. When INNO-LIA and Bioline produced divergent results, INNO-LIA was considered the gold standard.

HIV-1 viral load was measured at the Department of Clinical Microbiology, Aarhus University Hospital, Denmark, with COBAS® AmpliPrep/COBAS® TaqMan® (Roche Diagnostics GmbH, Mannheim, Germany). The lower limit of detection was 20 copies/ml. Virological failure was defined as a viral load >1000 copies/ml [5].

When sufficient plasma was available, we studied HIV-1 genotypic resistance in patients with virological failure by sequencing the protease and reverse transcriptase genes with ViroSeq® 2.0 (Abbott Laboratories, Illinois, USA). Mutations were classified as minor or major according to ART resistance consensus statements from the Stanford HIV RT and Protease Sequence database [16]. Subtype classifications were extracted from the Stanford database.

We used the Chi-square test for categorical variables to compare characteristics of patients with HIV-1 and HIV-1/2 dual infections, and patients with or without virological failure. We compared continuous variables with the Wilcoxon rank-sum test (non-normal distributions). The significance level was set at 0.05. Statistical analyses were performed with Stata IC 11.0 (StataCorp, College Station, Texas, USA).

All patients provided voluntary, signed, dated, informed consent, or fingerprints when illiterate, prior to enrolment into the cohort. The ongoing HIV cohort studies were approved by the national ethics committee of Guinea-Bissau (Parecer NCP/No.15/2007).

Results

Viral load was measured in stored plasma samples from patients with HIV-1 (n = 63) and HIV-1/2 dual (n = 16) infections, acquired before and 3 to 12 months after (median 184 days, interquartile range (IQR): 126–235 days) starting ART (Table 1). No patient was pregnant and no information was available regarding ART during previous pregnancies.
Table 1

Patient characteristics

Characteristic

Number of patients (%), unless other indicated (total N = 79)

Sex

 

Females

47 (59)

Males

32 (41)

Age at inclusion, median years (IQR)

36 (28–43)

HIV-type

 

HIV-1

63 (80)

HIV-1/2

16 (20)

Baseline CD4 cell count, median cells/μl (IQR)

134 (62–207)

Baseline viral load, median copies/ml (IQR)

73,473 (3,798-264,033)

Baseline ART

 

2 NRTIs + 1 NNRTI

53 (67)

2 NRTIs + 1 PI

23 (29)

3 NRTIs

3 (4)

Post ART CD4 cell count, median cells/μl (IQR)

217 (157–310)

Post ART viral load, median copies/ml (IQR)

203 (0–25.153)

IQR: Interquartile range.

Patients with HIV-1 and HIV-1/2 dual infections showed no significant differences in HIV-1 viral load (85,373 vs. 39,555 copies/ml, p = 0.37) or CD4 cell count (114 vs. 177 cells/μl, p = 0.10). At 3–12 months after starting ART, 36 patients (46%) developed virological failure (Figure 1), but these patients were distributed similarly between HIV-1 and HIV-1/2 dual infection groups (30/63 = 48% vs. 6/16 = 38%, respectively; p = 0.47). The presence or absence of virological failure did not affect the proportion of patients (14% vs. 16%, respectively; p = 0.77) that showed decreased CD4 cell counts after starting ART.
Figure 1

Flow chart of patient selection. ART: antiretroviral treatment; NNRTI: non-nucleoside reverse transcriptase inhibitors; NRTI: nucleoside/nucleotide reverse transcriptase inhibitors; PI: protease inhibitors.

Of the 36 patients with virological failure, we performed successful resistance tests in 15 (42%). Of these, eight (60%) showed resistance to at least one antiretroviral drug: one (7%) patient was resistant to NRTIs, four (27%) to NNRTIs, and four (27%) to both. No patient showed major PI resistance.

Twelve patients were taking NNRTIs; of these, seven (58%) were resistant to NNRTIs. The most common NNRTI resistance mutation was K103N (5/12, 42%), which caused high-level resistance against efavirenz and nevirapine. One male patient with NNRTI resistance had not received NNRTI treatment but PI treatment. Among the 15 patients tested for resistance (Table 2), the most common NRTI mutation was M184V (4/15 patients, 27%). Only one patient (1/15, 7%) had thymidine analogue mutations (TAMs). All resistance mutations are shown in Table 2. The most common HIV-1 subtype was circulating recombinant form 02_AG (CRF02_AG), found in 13/15 (87%) patients. After one year of ART, no patient had switched to second-line therapy.
Table 2

Distribution of resistance-associated mutations among 15 patients with viral loads > 1000 copies/ml, at 3–12 months after ART initiation

Patient

Sex

HIV type

HIV-1 subtype

Initial CD4

Baseline viral load

ART

Time from ART to re-sistance test (days)

NNRTI resistance

NRTI resistance

PI resistance

Predicted resistance to the following agents

1

M

HIV-1

CRF02_AG

32

132,355

AZT + 3TC + EFV

319

K103N

M184M/V

None

EFV/NVP, 3TC/FTC.

2

F

HIV-1

CRF02_AG

33

61,978

AZT + 3TC + NVP

362

K103N Y188CY

None

L10I/V/F/R/Y

EFV/NVP. Resistance to most PIs when present with other mutations.

3

F

HIV-1/2

CRF02_AG

279

11,348

AZT + 3TC + IND/r

177

None

None

None

None

4

M

HIV-1/2

CRF02_AG

50

360,158

AZT + 3TC + IND/r

161

K101E

None

K20R/M/I/T/V

Intermediate NVP. Low-level ETR, RPV, EFV. Potentially low-level NFV resistance.

5

M

HIV-1

CRF02_AG

207

55,650

AZT + 3TC + EFV

114

None

None

None

None

6

M

HIV-1

CRF02_AG

46

360,978

AZT + 3TC + EFV

203

K103N K101E/K

M184MV

None

High-level 3TC/FTC.

Low-level ddI, ABC.

High-level EFV/NVP.

Low-level EFV, ETR, RPV.

7

F

HIV-1

A

40

216,270

AZT + 3TC + NVP

126

K103N

M184V

L10I/V/F/R/Y

High-level 3TC/FTC.

High-level EFV/NVP.

Resistance to most PIs when present with other mutations.

8

F

HIV-1/2

CRF02_AG

258

46,763

AZT + 3TC + IND/r

189

None

None

None

None.

9

M

HIV-1

CRF02_AG

159

869,295

AZT + 3TC + EFV

281

None

None

None

None.

10

F

HIV-1

CRF02_AG

94

485,983

AZT + 3TC + NVP

98

V106A Y188C

None

K20R/M/I/T/V

High-level NVP, low-level EFV. Potentially low-level NFV resistance.

11

F

HIV-1

CRF02_AG

149

212,560

AZT + 3TC + NVP

344

K103N

None

None

High-level EFV/NVP.

12

M

HIV-1

CRF02_AG

107

34,698

AZT + 3TC + EFV

193

None

M184MV M184 V/I

K20R/M/I/T/V

High-level 3TC/FTC.

Low-level ABC, ddI. Potentially low-level NFV resistance.

13

F

HIV-1

A

71

25,000,000

D4T + 3TC + NVP

98

Y181C

T69D

L10I/V/R/Y

Low-level ddI.

High-level NVP.

Resistance to most PIs when present with other mutations.

14

M

HIV-1

CRF02_AG

147

185

AZT + 3TC + NVP

91

None

None

L33F

Contributed resistance to FPV/r, DRV/r, LPV/r, ATV/r, TPV/r.

15

M

HIV-1

CRF02_AG

252

Un-detectable

AZT + 3TC + EFV

185

None

None

None

None.

M: Male, F: Female, AZT: Zidovudine, D4T: Stavudine, 3TC: Lamivudine, NVP: Nevirapine, EFV: Efavirenz, IND/r: Ritonavir-boosted indinavir, ABC: Abacavir, ddI: Didanosine, FPV: Fosamprenavir, DRV: Darunavir, LPV: Lopinavir, ATV: Atazanavir, TPV: Tipranavir, NFV: Nelfinavir, ETR: Etravirine, RPV: Rilpivirine.

Discussion

The main finding of this study was that a large proportion of HIV-1 and HIV-1/2 dual infections developed virological failure (46%) after a median follow-up of six months. Furthermore, over half of these patients developed resistance - predominantly to NNRTIs. The CD4 cell count was not an effective indicator of treatment failure.

In the context of ART rollout, the most important drug resistance mutations in HIV-1 were single amino-acid mutations that conferred high-level resistance to NNRTIs. This finding was not surprising, because first-line ART and strategies for preventing mother-to-child transmission were based on NNRTIs. In this study, over half the patients with NNRTI resistance harbored the K103N mutation; thus, detection of this sentinel mutation may be useful in expanded surveillance activities for estimating the prevalence of NNRTI resistance.

Although nine patients developed clinically important mutations to either NRTIs or NNRTIs or both, none had been identified and switched to second-line therapy. The CD4 cell count was a poor predictor of treatment failure, which underscored the need for implementing virological measures.

This was the first study on HIV-1 resistance in Guinea-Bissau. Knowledge is scarce about resistance mutations in patients with HIV-1/2 dual infections. Thus, despite the small sample size, our results provided valuable information about this relatively unexplored population. Some patients with HIV-1 infections had been coincidentally treated with a first-line PI-based regimen, because they were assumed initially to be infected with HIV-1/2. This provided the opportunity to examine resistance in the context of a PI-based, rather than an NNRTI-based regimen.

Unfortunately, we could not successfully measure resistance in all patients with virological failure, due to the lack of stored plasma or difficulties with the PCR assay for some samples. The latter problem could have been due to poor sample storage in Guinea-Bissau, where electricity is intermittent. Thus, we may have underestimated the proportion of patients with resistance.

No baseline resistance tests had been performed; consequently, we could not determine whether the observed resistance was transferred or acquired. The one patient with an NNRTI-resistant virus that did not receive an NNRTI may represent a case of transmitted resistance; however, it also may represent a previous, unrecorded exposure to ART. In Senegal, the prevalence of transmitted drug resistance was 4.16% for NRTIs and 1.04% for PIs [13]. In Guinea-Conacry, the prevalence of primary resistance was 8.6% in patients naïve to ART [12]. In our study, at ART initiation, patients had low CD4 cell counts; this only occurs several years after primary infection. This finding argues against transferred resistance, because it is unlikely that this can be detected many years after a primary infection.

Studies in low- and middle-income countries have indicated, that after 12 months of ART, 82-91% of patients achieve viral suppression [17]. However, a review of 89 studies from Sub-Saharan Africa showed 78% viral suppression after six months of ART [18]. The present study, showed only 54% viral suppression; however, our shorter follow-up time made comparisons with other studies difficult.

A previous survey of acquired resistance showed that, among those experiencing therapy failure, 60-70% had developed drug resistance [17]. We identified drug resistance in 60% of patients with virological failure; this finding suggested that 40% developed treatment failure for reasons other than resistance. Thus, when viral load is used as the only indicator for switching to costlier second-line regimens, a large proportion of patients may switch unnecessarily.

The majority of patients was infected with the CRF02_AG subtype, and a minority harbored subtype A, consistent with previous studies in this region [19]. Genetic differences between subtypes might influence drug resistance pathways; therefore it may be difficult to generalize our results to studies performed in different geographic regions [20,21].

In conclusion, we found a high virological failure rate and rapid development of NNRTI resistance among patients with HIV-1 and HIV-1/2 dual infections in Guinea-Bissau. It remains to be determined whether a more robust PI-based treatment regimen might benefit this population more than NNRTIs. Further studies are warranted on drug resistance in patients with HIV-1/2 dual infections.

Abbreviations

ART: 

Antiretroviral treatment

CRF02_AG: 

Circulating recombinant form 02_AG

IQR: 

Interquartile range

NNRTI: 

Non-nucleoside reverse transcriptase inhibitor

NRTI: 

Nucleoside/nucleotide reverse transcriptase inhibitors

PI: 

Protease inhibitor

TAMs: 

Thymidine analogue mutations

Declarations

Acknowledgements

Financial support from Aarhus University is gratefully acknowledged. The Global Fund to Fight AIDS, TB and Malaria supported the data collection during 2009–2010, provided through the ‘Secretariado Nacional de Luta contra o Sida’ in Guinea-Bissau. The authors are grateful to the health care staff at the HIV clinic at HNSM for providing medical care to the patients with HIV infections and for allowing us access to data for this study. We extend special thanks to the West African Platform for HIV Intervention Research (WAPHIR) and the International Epidemiologic Databases to Evaluate AIDS (IeDEA) for their collaboration and for financial support for The Bissau HIV cohort. We acknowledge The National Cancer Institute (NCI), the Eunice Kennedy Shriver National Institute of Child Health & Human Development (NICHD) and the National Institute of Allergy and Infectious Diseases (NIAID) of the U.S. National Institutes of Health (NIH), for supporting the International Epidemiologic Databases to Evaluate AIDS (IeDEA) under Award Number U01AI069919.

The Bissau HIV cohort study group comprises: Amabelia Rodrigues, David da Silva, Zacarias da Silva, Candida Medina, Ines Oliviera-Souto, Lars Østergaard, Alex Laursen, Morten Sodemann, Peter Aaby, Anders Fomsgaard, Christian Erikstrup, Jesper Eugen-Olsen and Christian Wejse (chair).

Authors’ Affiliations

(1)
Bandim Health Project, Indepth Network
(2)
Department of Infectious Diseases, Aarhus University Hospital
(3)
Department of Clinical Immunology, Aarhus University Hospital
(4)
National HIV Programme, Ministry of Health, Bissau
(5)
Department of Clinical Microbiology, Aarhus University Hospital
(6)
GloHAU, Center for Global Health, School of Public Health, Aarhus University

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© Jespersen et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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