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35 protocols using realtime hiv 1

1

Monitoring CD4+ and Viral Load in DTG-based HAART

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The CD4 + cell counts and viral load data were obtained from the patients’
laboratory data. The viral load was measured using the Abbott Real-Time HIV-1
(Abbott Molecular Diagnostics, Wiesbaden, Germany) with a minimum detection
level of <50copies/ml. These data were collected at baseline, 6 months, and 1
year after initiation of the DTG-based HAART regimen.
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2

Viral Load Suppression in HIV Patients

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VL suppression was defined as HIV-1 RNA levels ≤1000 copies/mL by week 24.8
HIV VLs were performed on either: COBAS® AmpliPrep/COBAS® TaqMan® HIV-1
Test, version 2.0 or Abbott real-time HIV-1 (Automated), version m2000sp.
According to national guidelines, VLs are recommended 24 weeks after initiation
while on or with any change in ARV regimen. Data showed variation in timing
possibly due to clinician management decisions, test availability, and clinic
attendance. Therefore, VLs done 8 weeks before or after scheduled initial VL at
24 weeks were considered “24 weeks,” while any VL outside this time frame was
considered an “any other VL measurement.”
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3

HIV Confirmatory Testing Techniques

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HIV confirmatory tests are used to verify the positive results of HIV screening tests by combining several techniques, including the HIV antibody test, antigen test, neutralization test, Western blot, and NAT. The HIV indeterminate samples from the 17 PIHEs were sent to the KDCA for HIV reconfirmation. The PIHEs used an HIV-1/2 antigen/antibody (VIDAS HIV DUO Ultra [HIV5]; bioMérieux SA, Marcy l’Etoile, France), HIV-1 antigen (VIDAS HIV P24 II [P24]; bioMérieux SA), and HIV-1/2 Western blot method (HIV Blot 2.2 Western Blot Assay; MP Biomedicals Asia Pacific Pte Ltd, Singapore) for HIV confirmatory testing, whereas the KDCA used an HIV p24 antigen neutralization test (VIDAS HIV P24 II Confirmation; bioMérieux SA) and NAT test (Abbott RealTime HIV-1; Abbott Molecular Inc, Des Plaines, IL) in addition to the three tests by PIHE to augment the detection of early HIV infections. Since May 2015, the KDCA has performed HIV NAT and p24 antigen neutralization tests on indeterminate samples for acute infection (antigen-positive and antibody-negative or Western blot-indeterminate cases), false positive in immunoassays, and the final stage of patients with AIDS requested by the PIHEs.
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4

Comparative HIV-1 Viral Load Assays

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The study was conducted in Cameroon in the CREMER Virology Laboratory in Yaoundé, Cameroon, a national reference laboratory and accredited by WHO for HIV antiretroviral resistance surveillance. HIV-1 RNA VL results were compared for 474 samples from HIV-1 positive patients on first-line antiretroviral treatment (ART). Patients were attending HIV services of the Central and Military Hospitals of Yaoundé in Cameroon for the screening visit prior to inclusion in the ANRS12169/2-LADY Trial, designed to evaluate the efficiency of different second-line ART regimens (Ciaffi et al., 2015 (link)). Whole blood was collected on EDTA tubes and sent within six hours to the laboratory of CREMER. After centrifugation, at least three plasma aliquots of 1 mL were stored at −80 °C when sufficient material was available. One aliquot was used for routine VL testing with the Abbott RealTime HIV-1 (Abbott molecular, IL, USA), the second one was used for VL testing with the recently developed HIV-1/SIVcpz/SIVgor RT-qPCR assay and the last one was kept as backup for further analyses (i.e viral load control test, genotypic drug resistance testing). The freeze/thaw cycles until use were the same for each assay.
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5

HIV-1 and HIV-2 RNA Quantification

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HIV-1 RNA was quantified on the Abbott m2000 platform (Abbott RealTime HIV 1, version 9.00, Abbott Molecular Inc, Abbott Park, USA). As previously described [26] (link) HIV-2 RNA was quantified using an in-house method. For both analyses, the detection limit was 50 copies/mL.
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6

Ultrasensitive HIV RNA Quantification

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HIV RNA levels were measured in previously frozen cell-free CSF and
plasma using the ultrasensitive (50 copies/mL lower limit of detection) Amplicor
HIV Monitor (version 1.5; Roche Molecular Diagnostic Systems, Branchburg, NJ),
or the Abbott RealTime HIV-1 (Abbot Laboratories, Abbot Park, IL, USA) assays.
Paired blood and CSF measurements were made using the same assay, in the same
PCR run.
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7

Factors Influencing Adolescent Sexual Maturation

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The gender (male vs. female) and skin color (white vs. brown and black) of the participants, income (wages), and education (years of schooling) was recorded. Sexual maturation was self-reported based on the observation of the images of Tanner stages after participants received instructions from a same-gender researcher. For the HIV group, information about ART (untreated vs. non- PI-ART vs. PI-ART), HIV-1 viral load measured by RNA quantification (Abbott RealTime® HIV -1; Abbott, Rungis, France), and CD4 T-cell count measured by flow cytometry (Facscalibur® Multitest; BD Biosciences, San José, CA, USA), were obtained from medical records. The body mass (kg) and height (cm) were measured using a Tanita® electronic scale (BF683W; Arlington Heights, Illinois, USA), and an Alturaexata® stadiometer (Belo Horizonte, Brazil), respectively.
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8

Ultrasensitive HIV-RNA Quantification

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HIV-RNA levels were measured in previously frozen CSF and plasma using the ultrasensitive (20 copies/mL lower limit of detection) Amplicor HIV Monitor (version 1.5; Roche Molecular Diagnostic Systems, Branchburg, NJ) or the Abbott RealTime HIV-1 (Abbot Laboratories, Abbot Park, IL, USA) assays. Paired blood and CSF measurements were made in the same PCR run.
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9

Ultrasensitive HIV-RNA Quantification

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HIV-RNA levels were measured in previously frozen CSF and plasma using the ultrasensitive (20 copies/mL lower limit of detection) Amplicor HIV Monitor (version 1.5; Roche Molecular Diagnostic Systems, Branchburg, NJ) or the Abbott RealTime HIV-1 (Abbot Laboratories, Abbot Park, IL, USA) assays. Paired blood and CSF measurements were made in the same PCR run.
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10

HIV Prevalence in Blood Donations

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From January 2016 to December 2017, a total of 199 blood donations collected from 24 blood screening laboratories were confirmed as HIV viral load positive by the Abbott RealTime HIV-1 (Abbott Molecular Diagnostics, Des Plaines, IL, USA) test or serologically reactive by the Abbott ARCHITECT HIV Ag/Ab Combo test (Abbott Diagnostics, Weisbaden, Germany). These samples were tested non-reactive for Hepatitis B surface antigen (HBsAg), antibody to Hepatitis C Virus (anti-HCV) and antibody to treponema pallidum (anti-TP) in blood screening laboratories. Of these, at least two HIV regions were successfully sequenced for 179 plasma samples (Supplementary materials Table S1). Geographical localizationof blood screening laboratories in the study and the number of blood donations in these laboratories from January 2016 to December 2017 were shown in Fig. S4.
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