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Rapid decline of HIV-1 DNA and RNA in infants starting very early antiretroviral therapy may pose a diagnostic challenge

Veldsman, Kirsten, A.a; Maritz, Jeana,b; Isaacs, Shahiedaa; Katusiime, Mary, G.a; Janse van Rensburg, Anitac,d; Laughton, Barbarac,d; Mellors, John, W.e; Cotton, Mark, F.c,d; van Zyl, Gert, U.a,b

doi: 10.1097/QAD.0000000000001739

Objective: Birth diagnosis of HIV-1 infection offers an ideal opportunity for early antiretroviral therapy (ART) to limit HIV-1 reservoir size and limit disease progression. Although data on cellular HIV-1 DNA decay exist for children commencing treatment from 2 to 3 months of age, data are lacking for starting shortly after birth.

Design: We studied infants who initiated ART within 8 days after birth to assess HIV-1 DNA levels longitudinally.

Methods: Children were recruited from public health clinics in Cape Town where birth diagnosis of HIV-1 coupled with early ART initiation occurred. Total cellular HIV-1 DNA levels were determined using a sensitive quantitative PCR targeting a conserved region in integrase.

Results: Of 11 infants diagnosed and beginning ART within 8 days of birth with detectable pre-ART HIV-1 DNA, three subsequently had undetectable HIV-1 DNA after 6 days, 3 months and 4 months on treatment, respectively. In seven who had virologic suppression (defined as a continuous downward trend in plasma HIV-1 RNA, and <100 copies/ml after 6 months) total HIV-1 DNA continued to decay over 12 months [mean half-life of 64.8 days (95% confidence interval: 47.9–105.7)].

Conclusion: In infants initiated on ART within 8 days of life the combination of maternal ART, and early ART for prophylaxis and treatment contribute to rapid decline of HIV-1 infected cells to low or undetectable levels. However, rapid decline of HIV-1 RNA and DNA may complicate definitive diagnosis when confirmatory testing is delayed.

aDivision of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Cape Town

bNational Health Laboratory Service, Cape Town

cDepartment Paediatrics and Child Health, Stellenbosch University, Faculty of Medicine and Health Sciences, Cape Town

dTygerberg Children's Hospital, Cape Town, South Africa

eDepartment of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

Correspondence to Gert U. van Zyl, MBChB, MMed, FCPath(SA), PhD, National Health Laboratory Service, Cape Town, South Africa; Division of Medical Virology, Faculty of Medicine and Health Sciences, Cape Town, South Africa. Tel: +27 21 938 9691; fax: +27 21 938 9361; e-mail:

Received 18 September, 2017

Revised 12 December, 2017

Accepted 13 December, 2018

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Most intrauterine HIV-1 infections occur during the last weeks of gestation [1]. Infant diagnosis by sensitive HIV-1 nucleic acid testing at birth offers a unique opportunity to diagnose infection as soon as possible to begin therapy and linkage to care as infant HIV-1 disease is rapidly progressive with high mortality [2–5]. Early antiretroviral therapy (ART) can also limit the HIV-1 reservoir size [6–9]. Low reservoir sizes are associated with a delayed rebound after ART discontinuation, most likely due to stochastic activation of rare infected cells containing intact proviruses [10]. This was evident from a prolonged period without rebound viremia, despite absent detectable immune response in the Mississippi child and adult Boston hematopoietic stem cell transplant patients [10–13]. Early therapy may also provide an opportunity to achieve ART-free remission due to a small reservoir size and intact immune system: in adults, early therapy followed by interruption resulted in post-treatment control in about 15% in the Visconti cohort [14], but data from the SPARTAC study suggest that the effect of early treatment may have been inflated by the natural occurrence of transient control early after infection [15,16]. Nevertheless, the proportion remains higher than naturally occurring elite controllers (<1%). Post treatment control was also observed in perinatally infected individuals: in two children beginning ART within the first 3 months of life [17,18] and a young adult who started therapy, after perinatal infection, at 3.5 years of age [19].

In children who initiated ART between 0.5 and 2.6 months of age a study described that HIV-1 DNA concentration decayed to 1.0–1.5 log10 copies/million cells at 1–2 years of age [20]. Two other studies described median HIV-1 DNA half-lives of 53 [21] and 107 days [22], in children initiating ART around a median of 2 months or before 3 months, respectively. We have previously shown that therapy before 2 months of age reduces the number of infected cells and their transcriptional activity measured by unspliced cellular RNA [23]. However, information on the early decay of HIV-1 DNA in infants who began ART shortly after birth is limited. Our aim was therefore to investigate changes in total HIV-1 DNA in infants starting ART within 8 days after birth.

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Children were diagnosed through a public health sector birth HIV-1 diagnosis program in Cape Town, South Africa, and initiated ART as soon as feasible. Parents or legal guardians provided informed consent. The study was approved by the Stellenbosch University's Health Research Ethics Committee (reference: M14/07/029).

HIV-1 infection was confirmed with at least two positive HIV nucleic acid tests on separate samples (qualitative and/or quantitative) with Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 v2.0 or HIV-1 Qualitative v2 (CAP/CTM) (Roche Molecular Diagnostics, Pleasanton, California, USA). Subsequently the infants enrolled in a study of HIV-1 reservoirs and neurodevelopment in infants and children. We studied total cell associated HIV-1 DNA kinetics in infants beginning ART within 8 days of birth. Other inclusion criteria were having detectable baseline HIV-1 DNA and at least two stored peripheral blood mononuclear cell (PBMC) samples on treatment.

PBMCs and plasma were processed at 3 monthly visits. Samples were processed and stored according to the HANC Cross-Network PBMC processing SOP ( HIV-1 total DNA was extracted and measured through a sensitive quantitative PCR adapted for HIV-1 subtype C, targeting a conserved region in HIV-1 integrase (iCAD; limit of detection: 3 copies/million PBMCs; Supplementary Table 1, [24,25]. HIV-1 RNA was quantified with the CAP/CTM v2.0, with a 100 copies/ml limit of detection for a 200-μl plasma input. We defined virologic suppression as a continuous downward trend in plasma HIV-1 RNA and no HIV-1 RNA more than 100 copies/ml at the first measurement after 6 months on ART. Infants not meeting these criteria were classified as viremic.

As pretreatment PBMCs were unavailable, we assayed pretreatment dried blood spots (DBS), routinely stored in the diagnostic laboratory, to confirm assay detectability. The PBMC extraction method was adapted for DBS nucleic acid extraction: A solution comprising proteinase K and guanidinium hydrochloride was added to the DBS, sonicated immediately for 10 s, incubated at 37 °C overnight and followed by extraction and total HIV-1 DNA quantification as described [25].

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Kinetics were modeled with log-linear regression. To predict total HIV-1 DNA (log copies/ml), mixed effect models (participant as random effect and time-treated as fixed effect) were compared and random intercept models were found to be optimal (adding random slopes did not improve Akaike information criterion or Bayesian information criterion). Goodness of fit was assessed with a conditional generalized linear least square method and confidence intervals were calculated with bootstrapping [26,27]. Graphics and statistics were performed with R version 3.3.1 Vienna, Austria [28]. We expressed decay rates as half-lives (t½) which allows for an intuitive comparison between different phases of decay and with published studies.

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Fifteen infants started ART between 0 and 8 days (median 4 days) after birth (Table 1) and had at least three samples collected (a pre-ART DBS and at least two on-treatment PBMC samples). After enrollment, two infants had no detectable plasma HIV-1 RNA and cellular HIV-1 DNA samples, and another two had detectable plasma HIV-1 RNA only. The remaining 11 had at least one baseline assay-detectable HIV-1 DNA sample (pre-ART samples were from DBS) to allow longitudinal HIV-1 DNA observation, seven of these were suppressed ‘S’ and four viremic ‘V’ participants (Fig. 1; Supplementary Table 2,

Table 1

Table 1

Fig. 1

Fig. 1

Plasma HIV-1 RNA decay kinetics: Average baseline HIV-1 RNA was 3.9 (range 2.6–4.7) log 10 copies/ml in the 11 infants. In the seven suppressed infants, HIV-1 RNA was undetectable (<100 copies/ml for 200-μl input) in three children within 3.4 months, and in one child it was 120 copies at 3.5 months. In the remaining three patients, the first undetectable plasma HIV-1 RNA loads were recorded between 6 and 7 months.

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Cellular HIV-1 DNA decay kinetics

HIV-1 DNA decay slopes were characterized in the seven suppressed infants. As pre-ART DBS samples contained cells other than PBMCs we used it only to assess that HIV-1 DNA could be detected by our assay but could not characterize the decay between pre-ART and the first on-ART time point. Thereafter HIV-1 DNA time slopes showed a good log-linear correlation [mean t½ (95% confidence interval (CI)): 64.8 (47.9–105.7) days; conditional R2 (95% CI): 0.77 (0.53–0.91); Fig. 1]. At the end of the observation period at a median of 6.9 months (95% CI 3.5–11.6 months), in six of seven suppressed infants, HIV-1 DNA loads dropped to less than 10 copies/million PBMCs. In one of these six HIV-1 DNA was undetectable at the second visit, 3.5 months on ART (participant S9) in another HIV-1 DNA remained detectable, but unquantifiable at less than 3 copies/million PMBCs, at 11.6 months (participant S3). The ‘suppressed’ child whose HIV-1 DNA remained more than 10 copies/million PBMCs (participant S6), had delayed viremia suppression (145 HIV-1 RNA copies at 4 months on treatment) with HIV-1 DNA load reaching 47.8 HIV-1 DNA copies/million PBMCs at 6 months. Two ‘viremic’ infants had early undetectable HIV-1 DNA at their first visits, respectively, 6 days (participant V5) and 4 months (participant V3) with subsequent viremia; participant V5 had continued viremia with accompanied HIV-1 DNA increase, whereas participant V3 had a single episode of viremia with HIV-1 DNA remaining undetectable.

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In infants with a rapid plasma HIV-1 RNA load suppression, here defined as HIV-1 RNA less than 100 copies/ml within 3.5 months, who had assay detectable HIV-1 DNA, total HIV-1 DNA became undetectable in three of 11 infants, respectively at 6 days, 3.5 months and 4 months on treatment. The rate of initial HIV-1 DNA decay from treatment initiation to study enrolment could not be accurately assessed since only DBS were available pretreatment. Thereafter total HIV-1 DNA in PBMC cells decayed with a t½ of 65 days during the remainder of the first year of life with all but one of seven suppressed infants reaching a total HIV-1 DNA load of less than 10 copies/million PBMCs within 13 months of birth. Rapid decay of HIV-1 DNA was observed in adults treated in Fiebig stage I and II (t½ of 21 days in the first 2 weeks). Thereafter, the second phase decay was much slower (t½ of 198 days) [29]. In children treated around 2 months of life the total HIV-1 DNA t½ in the first 24 weeks of life was 53 days, where after it was 124 days between 24 and 48 weeks [21]. Another study that defined early treatment as before 3 months of life found a t½ of 107 days in the first year of life [22].

The mechanism of rapid HIV-1 DNA decline to low or undetectable levels in infants treated shortly after birth is unknown and requires further investigation. Mechanisms could include the following: low numbers of pretreatment infected cells due to maternal ART and infant prophylaxis, possible rapid loss of cells with unintegrated virus [29]; high CD4+ cell turnover with a large proportion of short-living infected CD4+ cells that decay rapidly [30] or a large proportion of surviving cells with integrated HIV-1 DNA that may have defective genomes harboring deletions, and as our assay detects HIV-1 integrase, these genomes may not be detectable [31].

Our study had the following limitations: First, infants diagnosed at birth and who initiated on early ART were recruited from the public health sector and often only enrolled later into our study. Second, having only a DBS sample pre-ART, we could not accurately assess decay up to the first on-treatment visit, as although HIV-1 DBS DNA levels were normalized for amplifiable cell equivalents, it contained multiple cell types and there was a limited recovery of total nucleic acid, precluding a comparison with subsequent HIV-1 DNA levels measured in PBMC. This combined with not having more frequent sampling prevented us from determining whether the earliest HIV-1 DNA decay was log-linear or biphasic. Third, adherence in young infants is challenging, evident from the high number of viremic children and some having had delayed HIV-1 RNA suppression, limiting our ability to study HIV-1 DNA decay under optimal conditions.

Despite the difficulty of treating infants, HIV-1 DNA decayed very rapidly in most infants and reached very low levels in the first year of life. As HIV is rapidly progressive in infants, it requires early diagnosis and treatment [5]. Moreover, very early ART could result in infants with small HIV reservoirs, who may be good candidates for future immunological interventions aimed at remission or cure. Rapid HIV-1 RNA and DNA decay poses a diagnostic challenge. The combined result of maternal ART (effectively intrauterine treatment of infected babies), extensive neonatal prophylaxis and possibly some antiretroviral absorption through breastfeeding [32], may together contribute to suppression of viral replication and result in undetectable HIV-1 DNA and RNA levels early in life and false negative diagnostic tests. It is therefore crucial that a definitive diagnosis is established as soon as possible after birth before HIV-1 DNA or plasma HIV-1 RNA become undetectable.

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We thank the participants, their parents and the clinical Study Team.

Author contributions: G.U.v.Z. and K.A.V. planned the investigation. A.J.v.R., B.L. and M.F.C. oversaw patient recruitment and data collection. J.M. oversaw the DBS extraction method. K.A.V., S.I. and M.G.K. processed samples. K.A.V. and S.I. performed the assays for HIV-1 DNA. J.W.M. and M.F.C. provided scientific and technical advice. G.U.v.Z. drafted the article with input from K.A.V., J.W.M. and M.F.C. All authors approved of the final article.

NIMH: 1R01MH105134-01; NCI: 1U01CA200441-01; Poliomyelitis Research Foundation, University of Pittsburgh: Centre for Global Health; SAMRC Collaborating Centre for HIV Laboratory Research.

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Conflicts of interest

There are no conflicts of interest.

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HIV-1 DNA decay; HIV-1 reservoirs; infant early antiretroviral treatment; infant HIV diagnosis; perinatal HIV infection

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