Gueudin2016 PDF

JAIDS Journal of Acquired Immune Deficiency Syndromes Publish Ahead of Print
DOI: 10.1097/QAI.0000000000001003
Performance Evaluation of the new HIV-1 quantification assay, Xpert HIV-1 Viral Load,
on a wide panel of HIV-1 variants
Marie Gueudin1,2$, Adeline Baron1$, Elodie Alessandri-Gradt1,2, Vronique Leme1, Thomas

Mourez1,2, Manuel Etienne2,3, Jean Christophe Plantier1,2*
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$ : equal contribution
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Affiliations:
1- Laboratoire de Virologie Associ au Centre National de Rfrence du VIH, Hpital Charles
Nicolle, CHU de Rouen, Rouen, France;
2- GRAM, Equipe dAccueil 2656, Facult de Mdecine-Pharmacie, Institut de Recherche et
dInnovation en Biomdecine, Universit de Rouen, Rouen, France;
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3- COREVIH Haute-Normandie, Hpital Charles Nicolle, CHU de Rouen, Rouen, France
*Corresponding author:
Correspondence to Pr JC PLANTIER
Laboratoire de Virologie, Institut de Biologie Clinique, Hpital Charles Nicolle, CHU de
Rouen, 1 rue de Germont, 76031 Rouen, France.
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Tel: +33 2 32 88 14 62; fax: +33 2 32 88 04 30;

e-mail: jc.plantier@chu-rouen.fr
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Running title: HIV-1 VL Xpert evaluation
Conflicts of Interest/Sources of Funding: The authors have no conflicts of interest to disclose.

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The work was supported by Cepheid, the Institut de Veille Sanitaire (InVS) and the CHU de
Rouen.
Presented in part as a poster presentation at the 18th Annual Meeting of European Society for
Clinical Virology, 9th12th September 2015, Edinburg, Scotland.
Copyright 2016 Wolters Kluwer Health, Inc. Unauthorized reproduction of this article is prohibited.
3 ABSTRACT
4 Objective
5 To evaluate the quantification performance of the new Cepheid GeneXpert HIV-1 Viral Load
6 assay, on a wide panel of HIV-1 variants.
7 Methods
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8 Clinical performance was evaluated relative to the Abbott RealTime HIV-1 assay on 285 HIV-1
9 seropositive samples selected to cover the assays quantification range (40 cp/mL to 10,000,000
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10 copies/mL), and included RNA undetectable or detected seropositive samples. The panel
11 comprised 120 subtype B, 150 non-B and 15 non-typable clinical samples; serial dilutions of 18
12 viral supernatants representative of the divergent viruses of HIV-1 groups N, O and P were also
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13 tested.
14 Results
15 Based on samples selected according to the Abbott assay viral loads (VL), the Cepheid assay
16 detected or quantified 222/285 (78%) samples and the Abbott assay 240/285 (84%). Xpert
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17 yielded VLs for 162 (76%) of the 213 quantifiable samples with Abbott. This difference
18 corresponded to 51 samples with VL >40 cp/mL by the Abbott assay (all below 200 cp/mL) but
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19 detected (n=40) or undetectable (n=11) by the Cepheid assay. VL of samples quantifiable by both
20 assays (n=162) showed very strong correlation, with a Spearmans correlation coefficient of
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21 0.985 and a Bland-Altmans mean of differences of -0.01. Performance for quantification of the
22 non-M samples showed very good correlation, with significantly higher values with Cepheid for
23 the group N and 2 group O samples.
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26 Conclusion
27 Our study showed that the Xpert HIV-1 VL assay offered very good performance for detection
28 and quantification of the current HIV-1 genetic diversity; differences reported at the threshold
29 could be an issue and requires further evaluations. The practicability of this new assay makes it
30 suitable for low income countries, where it could facilitate and improve follow-up of patients, as
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31 well as for high income regions.
Key words: HIV viral load, GeneXpert, genetic diversity
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33 INTRODUCTION
34 Plasma viral load (VL) is a key element of the virological follow-up for patients infected with
35 HIV to measure the intensity of viral replication in untreated patients, as well as for assessing
36 virological response to antiretroviral drugs. Assessment of HIV-1 VL has been performed for
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37 many years by different techniques, initially the measurement of p24 antigen, and currently using
38 the measurement of the RT enzymatic activity [1] or more largely by molecular techniques such
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39 as nucleic acid sequence based amplification (NASBA), transcription mediated amplification
40 (TMA) or real-time reverse transcriptase polymerase chain reaction (RT-PCR) [2-6].
41 These different technologies use relatively impressive high capacity platforms, combining a
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42 separate system of extraction and amplification of the viral genome. Automation improved the
43 reproducibility of results, facilitated technical work components, avoided contamination and
44 allowed savings due to processing of batched sets of samples. These platforms are advantageous
45 for large laboratories but may be inadequate or difficult to implement in smaller laboratories or in
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46 field conditions in low income countries, due to required technical expertise, cost, and
47 maintenance of the instruments. In addition, traditional batched samples systems are not able to
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48 perform HIV VL in real time or for emergency cases.
49 The GeneXpert (Cepheid, Sunnyvale, CA) technology is based on cartridges used in individual
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50 modules that perform the extraction and quantitative RT-PCR in a unique instrument system [7].
51 This technology has been developed for different markers such as mycobacterium tuberculosis,
52 hepatitis C virus (HCV), methicillin-resistant Staphylococcus aureus (MRSA), for
53 oncohaematology and others applications. A new assay, Xpert HIV-1 Viral Load (Xpert HIV-1
54 VL), has been developed for use on the Cepheid GeneXpert Instrument System. Due to its
55 simplicity and ease of use, this new HIV-1 VL assay could be an alternative to the current large
56 analytical platforms, for laboratories that do not have sufficient numbers of samples to perform
57 VL testing on large instruments in a cost-effective manner. It also could be interesting for larger
58 laboratories wishing to conduct their high volume viral load tests in real time, and for emergency
59 cases if necessary.
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60 To be successful, a new test for quantifying HIV-1 must have analytical performance and a
61 threshold of sensitivity comparable to what is currently available (20 to 40 copies/ml plasma
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62 depending on the assay). Due to the intrinsic genetic properties of HIV-1, an assay must also be
63 able to detect and quantify the wide genetic diversity of the pandemic HIV-1 group M viruses.
64 Moreover, quantifying divergent viruses of groups N, O and P, as is the case with the Abbott
65 RealTime HIV-1 and Roche CAP/CTM Cobas Taqman HIV-1 assays [8], would be an additional
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66 desired feature, and would be essential for the effective monitoring of the patients infected with
67 these more rare groups of HIV-1.
68 The aim of this study was to conduct a performance evaluation of the Xpert HIV-1 VL assay
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69 relative to the Abbott RealTime HIV-1 assay on a wide panel of HIV-1 variants representative of
70 the current genetic diversity of HIV-1, as well as its practicability.

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71 METHODS AND SAMPLES
72 Cepheid Xpert assay
73 The Xpert HIV-1 VL assay is performed on the Cepheid GeneXpert instrument systems. These
74 systems automate and integrate sample preparation, nucleic acid amplification, and detection of
75 the target sequence (3-LTR region) in samples using real-time reverse transcription PCR (RT-
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76 PCR). The systems require the use of single-use disposable GeneXpert cartridges that include
77 reagents as well as High (IQSH) and Low (IQSL) internal controls and a Probe Check Control
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78 (PCC). The IQSH and IQSL are present to control for adequate processing of the target sample
79 and to monitor the presence of inhibitors in the RT and PCR reactions as well as for
80 quantification of HIV-1. The PCC verifies reagent rehydration, PCR tube filling in the cartridge,
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81 probe integrity, and dye stability. External controls used during the study consisted of one HIV-1
82 negative, one low HIV-1 positive containing the 8E5 LAV strain in EDTA based normal human
83 plasma matrix (expected range 2.95-4.15 Log copies/mL), and one high HIV-1 positive control
84 (expected range 5.48-6.44 Log copies/mL). The negative control was made of HIV-1 negative
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85 human plasma matrix. Controls were tested with the Xpert HIV-1 VL on each day that specimens
86 were tested prior to analyzing any study specimens. The run time for one sample is 90 minutes.
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87 The input volume of plasma (ACD-A or EDTA) is 1 mL. The range of quantification in human
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88 plasma is from 40 to 10,000,000 copies/mL (1.6 Log cp/mL to 7 Log cp/mL), and the limit of
89 detection (LOD) is determined to be 40 cp/mL for HIV-1 subtype B in EDTA and ACD plasma.
90 Results of INVALID (e.g., failure of IQSH and/or IQSL), ERROR (test failure due to Probe
91 Check: FAIL*; all or one of the probe check results fail or insufficient volume) or NO RESULT
92 (insufficient data collected, e.g. a test in progress was stopped) are defined as indeterminate
93 results.
94 Abbott Assay
95 For comparison, all specimens were tested using the Abbott RealTime HIV-1 Assay, as
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96 recommended by the manufacturer. This technique is based on an automated-system of extraction
97 of the nucleic acid (m2000 SP) and an amplification system (m2000RT) using real-time reverse
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98 transcription PCR (RT-PCR); the detection is performed in the Integrase region and the linear
99 range is 40 cp/mL to 10,000,000 cp/mL (1.6 Log to 7 Log) and the LOD is 40 copies/mL with the
100 1.0 mL sample volume procedure.

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101 Samples for clinical performance
102 The specificity was evaluated by testing 20 plasma (EDTA) specimens from HIV-1 negative
103 blood donors.

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104 The clinical performance was assessed on 295 HIV-1 seropositive samples, collected during
105 routine viral load measurements for 285 patients managed at the Charles Nicolle Hospital,
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106 Rouen, France, and requiring no additional blood samples. They were obtained from 224 subjects
107 on antiretroviral therapy (ART) and 59 untreated patients. No ART information was available for
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108 two patients. The samples were initially quantified with the Abbott assay used routinely in the
109 laboratory, and selected to cover the quantification range (1.6 Log n=71 2 Log; 2 Log < n=
110 50 3 Log; 3 Log < n= 32 4 Log; 4 Log < n= 33 5 Log; n = 32 5 Log) and included RNA
111 undetectable (n= 47) or detected (n= 30) samples; 176 plasma (EDTA) were selected from
112 registered collection of samples frozen and stored at 80C and 119 plasma samples were
113 selected prospectively and tested fresh. Fresh samples were stored at 2-8C and tested
114 simultaneously by both techniques within 5 days of collection and separation, and frozen samples
115 were tested simultaneously within the same freeze/thaw cycle.
116 The genetic diversity of the panel was determined by grouping and subtyping using molecular
117 characterization, i.e. by sequencing the Pol region (Protease and Reverse Transcriptase) on an
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118 automated capillary CEQ 8000 DNA sequencer (Beckman Fullerton, CA), followed by
119 phylogenetic analyses as previously described [9]. Their genetic distribution was as follows:
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120 subtypes A=15, B=120, C=9, D=6, F=6, G=6, H=6, J=1, K=1, CRF02_AG=43, other CRFs=36,
121 Unique Recombinant Forms (URFs)=21, non-typable (NT)=15 (these latter corresponded to
122 samples without genetic material, i.e. undetectable or very low viral load making the molecular
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123 analysis impossible). In addition, 18 viral supernatants from cell cultures representative of non-
124 pandemic HIV-1 non-M groups, i.e. group O (n=15), group N (n=2) and group P (n=1) were
125 tested; they were obtained from strains characterized, isolated and propagated in the laboratory,
126 from samples genetically characterized as HIV-1 non-M groups. The supernatants were diluted
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127 with human plasma HIV negative, to obtain reference viral loads using the Abbott assay, between
128 3 to 4 Log cp/mL, 4 to 5 Log cp/mL, and 5 to 6 Log cp/mL.

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129
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130 Statistical Analysis
131 Samples with HIV-1 RNA quantitative results within the linear range of both the Xpert HIV-1
132 VL and the Abbott RealTime HIV-1 Assay were compared using MedCalc Statistical Software
133 version 15.11.4 (MedCalc Software bvba, Ostend, Belgium; https://www.medcalc.org; 2015). A
134 Passing-Bablok regression was calculated and a Bland-Altman graph was generated. A maximum
135 difference less than 0.5 Log between the two assays was considered as acceptable.
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137 RESULTS
138 Specificity
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139 None of the 20 negative samples were found positive thus the specificity of Xpert HIV-1 VL was
140 100% (95% CI: 83.9-100.0).
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142 Clinical concordance
143 Xpert HIV-1 VL tests were successful on the first attempt for 96.6% (285/295) of the samples.
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144 The 10 indeterminate cases reported included 3 ERROR, 6 INVALID, and 1 NO RESULT;
145 corresponding VL obtained with the Abbott assay was undetectable (n=2), detected at < 40
146 copies/mL but not quantifiable (n=3), and from 1.7 to 5.3 Log cp/mL (n=5). None of these
147 indeterminate cases was retested due to insufficient sample volume.

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148 The results of the 285 specimens with valid results by both VL assays are presented in table 1.
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149 They are classified as follows: HIV-1 undetectable; HIV-1 detected at < 40 copies/mL but not
150 quantifiable, and HIV quantifiable at 40 copies/mL. In both techniques, the HIV-1 VL was
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151 undetectable for 38 samples, detected for 13 plasmas and quantifiable for 162 plasmas, leading to
152 overall concordance of 74.7% (213/285).
153 Taking into account that samples were initially selected on the Abbott VL, the Cepheid assay
154 detected or quantified HIV RNA in 222/285 (78%) samples, and the Abbott assay detected or
155 quantified HIV RNA in 240/285 (84%) samples. Xpert yielded VLs for 162 (76%) of the 213
156 quantifiable samples selected with the Abbott assay; this difference corresponded to 51 samples
157 that were quantifiable with the Abbott assay but only detected or undetectable with the Cepheid
158 assay.
159 Regarding the genetic diversity of the 222 samples detected or quantified by Cepheid, 84 (38%),
160 135 (61%) and 3 (1%) were subtype B, non-B and NT respectively; among the 240 samples
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161 detected or quantified by Abbott, 94 (39%), 139 (58%), and 7 (3%) were of subtype B, non-B
162 and NT respectively. Regarding the 162 samples quantified by Cepheid, 58 (36%) and 104 (64%)
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163 were subtype B and non-B respectively; among the 213 samples quantified by Abbott, 84 (39%),
164 124 (58%), and 5 (3%) were subtype B, non-B and NT respectively. No difference was thus
165 observed in terms of distribution of subtype B vs subtype non-B clinical samples among data
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166 obtained by both techniques.
167 Among the 51 samples not quantifiable with the Cepheid assay, forty were detected with Cepheid
168 (i.e. detected at < 40 copies/mL but not quantifiable). These samples had a low VL with the
169 Abbott assay, with a range of 40 cp/mL (1.6 Log) to 170 cp/mL (2.23 Log), a median of 56
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170 cp/mL (1.75), and an average of 61 cp/mL (1.76 Log). There were 11 samples quantifiable with
171 the Abbott assay that were undetectable with Cepheid Xpert HIV-1 VL. These samples also had a
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172 low VL with a range of 41 cp/mL (1.61 Log) to 77 cp/mL (1.89 Log), a median of 55 cp/mL
173 (1.74 Log) and an average of 54 cp/mL (1.73 Log). Regarding the genetic diversity of these 51
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174 different samples, 26 were subtype B, 10 were CRF02_AG, 5 were URFs, 5 were NT, and there
175 was 1 for D, F1, CRF01, CRF06, CRF11, each.
176 There were 14 samples detected with Abbott that were undetectable with the Cepheid kit. Of
177 these 7 were subtype B, 2 were CRF02, 2 were NT and there was 1 for A, CRF06, CRF11 each.
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178 Conversely there were 7 samples detected with Cepheid that were undetectable with Abbott. Of
179 these samples 3 were subtype B, 2 was subtype A, 1 was CRF02 and 1 was an URF.
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181 Quantitative analysis was performed for 162 clinical samples with quantifiable results by both
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182 systems (104 subtype non-B and 58 B). These samples had VLs ranging from 40 cp/mL (1.6
183 Log) to 6,800,000 cp/mL (6.83 Log). Correlation between the Cepheid Xpert HIV-1 VL and the
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184 Abbott RealTime HIV-1 Assay was performed using a Passing-Bablok regression on the 162
185 samples. Figure 1 shows very good correlation between both assays with a slope for the
186 regression line of 1.0355 [1.0114 to 1.0597] and an intercept of -0.1184 [-0.2151 to -0.03756],
187 showing a slightly higher quantification in the lowest VL for Abbott and in the highest VL for
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188 Cepheid, with a close quantification among the middle ranges of VL.
189 Using a Bland-Altman analysis (Figure 2), we observed an extremely close quantification of all
190 samples, since the mean of differences was -0.01. Values were close along the VL level, with
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191 slightly higher values for the Abbott assay in the lowest levels (between 1.6 to 2.5 Log, Figures 1
192 and 2). No dispersion or heterogeneous distribution was observed, with SD of +0.4 and -0.4,
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193 values less than 0.5 considered as the maximum difference between two techniques. Only two of
194 the 162 (1.2%) samples had a difference of quantification of more than 0.5 Log. Among them 1
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195 (CRF02_AG) had a difference of -0.53 (in the 2-2.5 Log range) in favor of Abbott. The other
196 sample (subtype B) had a difference of + 0.78 (in the 4-4.5 Log range) in favor of Cepheid.
197 Performance for detection and quantification of the HIV-1 groups non-M samples (N, O, and P)
198 was analyzed for the 3 dilutions of the 18 culture supernatants (Figure 3). Results showed a
199 median with Cepheid and Abbott of 2.80 and 2.74 for the 2-3 Log dilution, of 3.80 and 3.69 for
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200 the 3-4 Log dilution and of 4.81 and 4.74 for the 4-5 Log dilution, respectively. Globally
201 these values were linear along the dilutions for the same assay and very close between the assays
202 (slightly higher for Xpert). For 4 supernatants, we observed significantly higher values with
203 Cepheid than with Abbott. Of those found, 2 were group N samples (difference of +0.87 Log and
204 +0.74 Log each at the 3-4 Log dilutions; similar differences were found for the 2 other dilutions)
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205 and 2 of the 15 group O samples (difference of +0.87 Log and +1.83 Log at the 3-4 Log
206 dilutions; similar differences were found for the 2 other dilutions). No difference (regardless of
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207 dilutions) was observed for the unique group P sample.
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DISCUSSION
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209 The aim of this study was to evaluate the performance of the new HIV-1 viral load test
210 from Cepheid. Given the important genetic diversity of HIV-1, we wanted to evaluate
211 performance on a large panel of samples representative of the current HIV-1 diversity. We thus
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212 tested 295 clinical samples including 120 subtype B and 150 subtype non-B of HIV-1 group M,
213 as well as 18 culture supernatants derived from the diversity of the rare variants of groups N, O
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214 and P.
215 This wide panel of specimens tested demonstrated that the performance of Xpert HIV-1
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216 VL assay was globally close to that of the Abbott HIV-1 RealTime assay. Comparison of the
217 quantifiable samples (i.e. > 40 cp/mL) by both techniques showed a remarkable correlation
218 between the two systems regardless of the VL level since the mean difference was almost zero,
219 what we did not observe in previous comparisons of viral load assays [4, 6]. Contrary to data
220 reported recently by Mor et al., i.e. many samples presenting a mean difference of more than 0.5
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221 in favor of Xpert [10], only two samples in the current study were discrepant over 0.5 Log, with
222 one very close to this limit at 0.53 Log. As Mor et al. did not describe the subtype characteristics
223 of the samples involved in these differences, it is not possible to assess the impact of genetic
224 diversity from their samples; in particular, involvement of a particular subtype that will not be
225 well represented in our panel. Distribution of VL values is also highly correlated with very little
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226 scattering of points in a variance of +/-0.4 Log. This very strong correlation is even more
227 interesting given that the technologies and regions of amplification are different between the two
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228 assays. For the rarest divergent variants group N, O and P, circulating in Central Africa and in the
229 countries associated with this region, the results showed a good correlation between the two
230 assays with a more significant quantification for some samples with the Xpert HIV-1 VL kit. In
231 particular, an underquantification of group N samples by the Abbott test was observed,
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232 confirming data of a previous evaluation [4]. The most important differences observed for some
233 samples of group O showed that these variants remain problematic, and highlight the need to
234 determine what is the best tool before follow-up [11].

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235 Concerning the concordance of assay results near the limit of quantification, data showed
236 that 11 quantifiable samples above the threshold of 40 cp/mL with the Abbott technique, were
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237 undetectable with the Cepheid assay. These data seem concordant with those reported by Mor et
238 al., but rigorous comparison is difficult, since the authors did not distinguish undetectable from
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239 detected samples below 40 cp/mL and did not indicate mean or median values for these samples
240 [10]. As all of these samples in our work correspond to very low values (less than 80 cp/mL)
241 below the clinical VL cut-off of 1,000 cp/mL defined by WHO [12], this assay could improve the
242 patient monitoring in low income settings [13]. Although considering a definition of the
243 virological failure at 50 cp/mL [14, 15], these undetectable samples could be wrongly considered
244 to be a virological success following ART ; this relative sensitivity could be an issue for
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245 monitoring especially using integrase inhibitors, since virological escape was observed at low
246 viral load [16]. Low values (below 170 cp/mL) were also found for the 40 samples quantifiable
247 with the Abbott technique but detected with Cepheid. Analysis of genetic diversity of these
248 samples showed that these results were not related to a particular subtype, since it involved
249 samples of subtype B (n=26) as well as non-B subtypes (n=20) or non-typable (n=5).
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250 It is important to note that a low indeterminate rate of approximately 3% was observed
251 with the Cepheid assay. This rate, rarely shown in studies, should be considered, because it is
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252 important for questions of cost and time for results; a low indeterminate rate is an indirect
253 indicator of quality and robustness of the test. Unfortunately insufficient samples were available
254 to allow for assessment of whether invalid results were sample specific or incidental.
255 The use of this assay and its unique technology in a cartridge has proved extremely simple
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256 compared to the Abbott platform. The volume requirement of 1 mL of plasma to add to the
257 single-use disposable cartridge greatly simplifies the technical task and can be performed by any
258 staff member from reference laboratories to point of care sites. This is an extremely positive and
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259 favorable element for implementation in small laboratories or in difficult field conditions. In
260 addition, the achievement of extraction and amplification in a single cartridge within a relatively
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261 short time period (90 minutes) is also extremely important to be able to respond in emergency or
262 on demand situations, as compared to the longer and heavier workflow of the series with the
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263 Abbott platform.
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265 Other positive elements of this technology are the absence of mechanical requirements
266 (i.e. for extraction), and the ease of transport (for a module of 4 cartridges), allowing the
267 technology to be implemented anywhere, especially in low income countries. The GeneXpert can
268 also be used in larger laboratories for high-volume samples with up to 80 modules or even for
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269 emergency use since the technology is not burdened by the series process. The sample addition to
270 the cartridge remains manual compared to the automated Abbott platform. This can be a
271 disadvantage but if the test is carried out in 'real time', this manual step is equivalent to a stage of
272 manual decantation of the blood samples for freezing prior to testing on the platform.
273
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274 In conclusion, this study, using a wide panel in terms of number of samples, genetic
275 diversity and VL ranges, allowed us to evaluate this new assay in contexts representative of
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276 diverse clinical situations and genetic background. Our data showed that the Xpert HIV-1 Viral
277 Load assay offered very good performance for detection and quantification of the current HIV-1
278 genetic diversity. The samples quantifiable by the Abbott assay that were below 40 cp/mL by the
279 Cepheid technique are an issue and requires further studies with non-selected samples near the
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280 limit of quantification. It is also necessary now to compare this new test to other assays, such as
281 the Roche Cobas Taqman HIV-1, also widely used, to confirm its global performances. In
282 addition, the practicability of this new assay makes it a useful and interesting tool both for high
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283 income and in low income countries, where it could facilitate and improve follow-up of patients.
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Acknowledgments
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We thank Cepheid, the Institut de Veille Sanitaire and the CHU de Rouen for financial support.
We also thank the patients for the COREVIH Haute-Normandie and all the staff of the
laboratory, particularly Fabienne De Oliveira and Marie Leoz, for characterizing the collection
samples.
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LEGENDS
332 Figure 1. Scatter diagram and the regression line according to Passing & Bablok on the 162
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333 samples quantifiable by both the Cepheid and Abbott assays. In addition to the regression line
334 (solid line), the confidence interval for the regression line (dashed lines) is displayed. Samples
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335 are differentiated between subtype B ( , n=58), subtype CRF02_AG ( , n=19), and other non-B
336 ( , n=85).
337 Figure 2. Degree of agreement in Log cp/mL for the 162 samples quantifiable by both the
338 Cepheid and Abbott assays. In the graphical method of Bland and Altman, the differences
339 between the two techniques are plotted against the averages of the two techniques. Samples are
EP
340 differentiated between subtype B ( , n=58), subtype CRF02_AG ( , n=19), and other non-B ( ,
341 n=85).
342 Figure 3. HIV-1 VL results obtained for the 3 dilutions of supernatants of groups N, O and P. In
343 the Box-and-Whisker plot, the central box represents the values from the lower to upper quartile
344 (25 to 75 percentile) and the middle line represents the median. For each dilution, groups are
C
345 differentiated between group O ( , n=15), group N ( , n=2) and group P ( , n=1).
C
A
17
Table 1. Qualitative results for Xpert HIV-1 VL and Abbott RealTime HIV-1 assays
Abbott HIV-1 RealTime
undetectable detected quantifiable total
undetectable 38 14 11 63
D
Cepheid detected 7 13 40 60
Xpert HIV-1
VL quantifiable 0 0 162 162
TE
total 45 27 213 285
EP
C
C
A
D
TE
EP
C
C
A
D
TE
EP
C
C
A
D
TE
EP
C
C
A

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JAIDS Journal of Acquired Immune Deficiency Syndromes Publish Ahead of Print

Marie Gueudin1,2$, Adeline Baron1$, Elodie Alessandri-Gradt1,2, Vronique Leme1, Thomas

Tel: +33 2 32 88 14 62; fax: +33 2 32 88 04 30;

Running title: HIV-1 VL Xpert evaluation

Conflicts of Interest/Sources of Funding: The authors have no conflicts of interest to disclose.

6 assay, on a wide panel of HIV-1 variants.

23 the group N and 2 group O samples.

Key words: HIV viral load, GeneXpert, genetic diversity

40 (TMA) or real-time reverse transcriptase polymerase chain reaction (RT-PCR) [2-6].

43 reproducibility of results, facilitated technical work components, avoided contamination and

48 perform HIV VL in real time or for emergency cases.

52 hepatitis C virus (HCV), methicillin-resistant Staphylococcus aureus (MRSA), for

61 threshold of sensitivity comparable to what is currently available (20 to 40 copies/ml plasma

67 these more rare groups of HIV-1.

70 the current genetic diversity of HIV-1, as well as its practicability.

72 Cepheid Xpert assay

100 1.0 mL sample volume procedure.

103 blood donors.

115 were tested simultaneously within the same freeze/thaw cycle.

128 3 to 4 Log cp/mL, 4 to 5 Log cp/mL, and 5 to 6 Log cp/mL.

130 Statistical Analysis

140 100% (95% CI: 83.9-100.0).

142 Clinical concordance

147 indeterminate cases was retested due to insufficient sample volume.

152 overall concordance of 74.7% (213/285).

175 was 1 for D, F1, CRF01, CRF06, CRF11, each.

234 determine what is the best tool before follow-up [11].

263 Abbott platform.

284 1. Labbett W, Garcia-Diaz A, Fox Z, Clewley GS, Fernandez T, Johnson M, et al.

309 1. Clin Microbiol Rev 2013,26:448-461.

Abbott HIV-1 RealTime

undetectable detected quantifiable total

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