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PLOS One logoLink to PLOS One
. 2023 Jan 13;18(1):e0279479. doi: 10.1371/journal.pone.0279479

The association between low-level viraemia and subsequent viral non-suppression among people living with HIV/AIDS on antiretroviral therapy in Uganda

Nicholus Nanyeenya 1,2,*, Larry William Chang 3, Noah Kiwanuka 1, Esther Nasuuna 4, Damalie Nakanjako 5, Gertrude Nakigozi 6, Simon P S Kibira 7, Susan Nabadda 2, Charles Kiyaga 2, Fredrick Makumbi 1
Editor: Chika Kingsley Onwuamah8
PMCID: PMC9838846  PMID: 36638086

Abstract

Background

Uganda’s efforts to end the HIV epidemic by 2030 are threatened by the increasing number of PLHIV with low-level viraemia (LLV). We conducted a study to determine the prevalence of LLV and the association between LLV and subsequent viral non-suppression from 2016 to 2020 among PLHIV on ART in Uganda.

Method

This was a retrospective cohort study, using the national viral load (VL) program data from 2016 to 2020. LLV was defined as a VL result of at least 50 copies/ml, but less than 1,000 copies/ml. Multivariable logistic regression was used to determine the factors associated with LLV, and cox proportional hazards regression model was used to determine the association between LLV and viral non-suppression.

Results

A cohort of 17,783 PLHIV, of which 1,466 PLHIV (8.2%) had LLV and 16,317 (91.8%) had a non-detectable VL was retrospectively followed from 2016 to 2020. There were increasing numbers of PLHIV with LLV from 2.0% in 2016 to 8.6% in 2020; and LLV was associated with male sex, second line ART regimen and being of lower age. 32.5% of the PLHIV with LLV (476 out of 1,466 PLHIV) became non-suppressed, as compared to 7.7% of the PLHIV (1,254 out of 16,317 PLHIV) with a non-detectable viral load who became non-suppressed during the follow-up period. PLHIV with LLV had 4.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL (adjusted hazard ratio was 4.1, 95% CI: 3.7 to 4.7, p < 0.001).

Conclusion

Our study indicated that PLHIV with LLV increased from 2.0% in 2016 to 8.6% in 2020, and PLHIV with LLV had 4.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL. Hence the need to review the VL testing algorithm and also manage LLV in Uganda.

Introduction

The introduction of antiretroviral therapy (ART) in the late 1980’s and 1990’s led to a marked improvement in HIV/AIDS care across the world, transforming the originally fatal and AIDS defining HIV epidemic into a manageable chronic condition with improved quality of life [1, 2]. Numerous efforts have been devoted to scale up access to ART, and an estimated 27.5 million (out of 37.7 million) PLHIV worldwide were accessing it by the end of 2020 [3]. In Uganda, about 1.2 million (out of 1.4 million) PLHIV were accessing ART by December 2019 [4]. The increase in access to ART has simultaneously led to the scale up of HIV viral load (VL) coverage in Uganda from about 2% of PLHIV on ART in 2014 to about 95% of PLHIV on ART 2020 [5]. Uganda is currently devoting enormous efforts to achieve the global targets of ending the HIV/AIDS epidemic by 2030 [6, 7], though the increasing concern of PLHIV with low-level viraemia (≥50 to <1,000 copies/ml) is posing a risk to this progress. This is because low-level viraemia (LLV) has been associated with viral non-suppression and virologic failure by the different studies elsewhere [810]. To our knowledge however, no specific study has been done to determine the association between LLV and viral non-suppression in Uganda. Similarly, we are not aware about the availability of any intervention(s) that target PLHIV with LLV in Uganda.

The goal of ART is to lead to HIV viral suppression, with an increase in the body immunity function [11]. In 2013, the World Health Orgnisation (WHO) recommended VL monitoring as the preferred way to monitor PLHIV on ART [12]. HIV viral load is the number of HIV viral RNA copies per milliliter of blood, and a threshold of 1,000 copies/ml is used to determine viral non-suppression. Hence a VL of 1,000 copies/ml or higher is crucial in early detection of either poor drug adherence or virologic treatment failure [13]. Recent studies have associated VL non-suppression with several risk factors like comorbidities, poor adherence to ART, sociodemographic and psychological factors, poor absorption of antiretroviral drugs, lack of knowledge or awareness of the benefits of viral suppression, and drug toxicity among others [1416]. Viral non-suppression has also been associated with an increased risk of fastened progression to AIDS and poor clinical outcomes [17, 18]. Despite the WHO recommendation of using a threshold of 1,000 copies/ml [17], the Centers for Disease Control and Prevention (CDC) and the International Association of Providers of AIDS Care (IAPAC) recommend use of 200 copies/ml as a threshold for determining VL non-suppression, and this has been adopted in various developed countries [19, 20].

Uganda adopted the WHO 2013 recommendation and initiated the scale up of VL testing in 2014 by establishing a national VL testing reference laboratory at Ministry of Health Central Public Health Laboratories (CPHL) [21]. Since then, VL coverage has increased from 2% of PLHIV on ART in 2014 to 95% in 2020 [5]. Like most of other Sub-Saharan African (SSA) countries, Uganda also uses a threshold of 1,000 copies to determine VL non-suppression [22], yet there have been concerns with this threshold that it could lead to accumulation of PLHIV with LLV, since it is considered as being very high [23].

Different studies have shown that LLV (≥50 to <1,000 copies/ml) can be associated with HIV virological failure and drug resistance, which may lead to accelerated disease progression [2427]. In a study to evaluate virologic failure and its predictors in four African countries including Uganda, LLV and persistent LLV were observed in 19.3% and 7.8% of PLHIV on ART respectively [9]. In this study, 57.5% of participants with persistent LLV (plasma HIV RNA > 50 copies/mL at two consecutive visits) later had confirmed virologic failure. In South African study, LLV was associated with increased hazards of virological failure and the subsequent switch to second-line ART, as compared with a non-dectectable VL of less than 50 copies/ml; and the risk of virological failure was increased more with increased ranges of LLV [10]. However there is limited data about the association of LLV and viral non-suppression in Uganda, yet this is very important to guide key policy decisions in the country.

In this study, we aimed to determine the association between low-level viraemia and subsequent viral non-suppression among PLHIV on ART in Uganda.

Methods

Study design and population

This was a retrospective cohort study involving analysis of the national VL program data from 2016 to 2020 at CPHL, to determine the association between low-level viraemia and viral non-suppression among PLHIV on ART in Uganda.

The study population comprised of PLHIV on ART with a suppressed VL (less than 1,000 copies/ml) done between January 2016 and December 2016 using plasma samples, and these were followed up to 31st December, 2020. Non-suppressed PLHIV on ART were excluded from this study. PLHIV with missing data for critical variables such as date of sample collection and results of the VL test for the follow-up years were also excluded from the study.

The HIV viral load program description

The Ministry of Health established the national VL program in 2014, and this is housed and coordinated at CPHL. CPHL has a national VL reference testing laboratory which receives VL samples from all parts of the country through use of hub sample transport system [28]. CPHL has a comprehensive data centre that hosts the Laboratory Information Management System, which enables electronic delivery of VL results to health facilities through the electronic results download module [29].

The first VL test is done for PLHIV who have been on ART for 6 months, and then another VL test is done at 12 months if the results are suppressed. PLHIV with a VL result below 1,000 copies/ml have a suppressed VL and are routinely given adherence counselling in which they are encouraged to continue with their ART; and no other intervention is given [22]. PLHIV aged 18 years and above with a suppressed VL repeat a VL test once every year to monitor the efficacy of ART annually. PLHIV below 18 years who are suppressed do VL testing every 6 months. For PLHIV with a VL of 1,000 copies/ml or more, they are considered to be having a non-suppressed VL and they are offered monthly intensive adherence counselling (IAC) sessions for three months, after which a VL test is repeated in the fourth month to determine whether they have achieved VL suppression [22]. If the repeat VL result after IAC is still non-suppressed, this is considered as virologic failure provided non-adherence is ruled out, and a switch committee is convened and the patient is switched to another ART line [22].

Data management and analysis

Routine viral load monitoring data for PLHIV on ART is archived into the laboratory information management system (LIMS) housed at CPHL. We developed and piloted a data abstraction checklist using a physical viral load result form to ensure that our checklist was comprehensive and captured all the relevant study data elements. We then extracted our study data from LIMS and the dataset included unique patient identifiers and other key variables such as age, sex, duration on ART, ART regimen, date of sample collection, type of VL sample collected, and the result of the VL test done. The dataset was extracted into a Microsoft spread sheet, cleaned by running filters to identify outliers and any other incomprehensible formats. We coded and removed duplicate records from the dataset before declaring it final for analysis. The remaining records were screened for inclusion into the study. Basing on the inclusion criteria, all PLHIV with non-suppressed results and all PLHIV with Dried Blood Spot (DBS) samples were excluded from the study.

The primary end point was viral non-suppression, and this was defined as a VL result of 1,000 copies/ml or more. The primary outcome was the proportions of PLHIV with VL non-suppression among the group with LLV and the group with a non-detectable VL. The secondary outcome was the time-to-non-suppression. The respective hazard ratios for non-suppression were also determined using Cox regression.

Our main exposure variable was level viraemia (LLV) defined as a VL result of at least 50 copies/ml but less than 1,000 copies/ml (≥50 to <1,000 copies/ml). This was stratified into four categories basing on the level of viraemia, that is; 50 to 199, 200 to 399, 400 to 599, and 600 to 999 copies/ml. We further designated PLHIV with a VL less than 50 copies/ml (non-detectable VL) as the unexposed group.

Statistical analysis

Using the approach of complete case analysis, descriptive statistics of participants with complete records were obtained where; continuous variables were summarised by mean (standard deviation) or median (Interquartile range) depending on the distribution, whereas categorical variables were summarised as frequencies and percentages. Multivariable logistic regression was used to determine the factors associated with low-level viraemia.

Cox proportional hazards regression model was used to determine the association between LLV and viral non-suppression, and schoenfeld residuals were used to test for the hazards assumption [30]. Hazard ratios, displayed as Kaplan-Meier estimators, were used to report the findings, comparing the relative risk of viral non-suppression for LLV with a non-detectable viral load. PLHIV who did not get viral non-suppression through out the follow-up period were right censored at the end of their last viral load test in 2020.

For the missing data, we determined the patterns and mechanisms of the missing data, and conducted multiple imputation using chained equations. We then ran model diagnostics to check whether the imputed results are similar to the observed results. We then derived the association between LLV and viral non-suppression for the inputed data. We conducted sensitivity analyses of both the observed and imputed results, and this showed relatively similar and consistent results. However we reported the results of complete case analysis in this study due to the large missingness of 72.2% of the data.

Stata version 14.0 was used for the statistical analysis of the data, and all the findings were reported with their respective 95% Confidence Interval levels.

Ethical consideration

We acquired ethical approval from Makerere University School of Public Health Research Ethics Committee (SPHREC) to undertake this study, and the IRB approval number was SPH-2021-144. We also acquired approval from the Uganda National Council for Science and Technology (UNCST), and the approval number was HS2008ES. Furthermore, permission to use the national viral load program data was sought from Ministry of Health. We received a waiver for the requirement of informed consent from SPHREC to use the archived national VL program data. All the program data was fully anonymized before we accessed it to ensure confidentiality of the patients.

Results

Trend of Low-level viraemia across the years

The national VL program data from 2016 to 2020 indicated increasing numbers of PLHIV with LLV from 2.0% in 2016 to 8.6% in 2020, and increasing suppression rates across the years, as shown in Fig 1 and Table 1.

Fig 1. Graph showing the trend of low-level viraemia from 2016 to 2020.

Fig 1

Table 1. Characteristics for the program data for the individual years from 2016 to 2020.

Characteristics 2016 (n = 612,006) 2017 (n = 917,460) 2018 (n = 1,051,122) 2019 (n = 1,230,992) 2020 (n = 1,119,414)
Mean Age (SD), years 36.3 (13.8) 36.0 (14.0) 36.2 (14.2) 36.5 (14.4) 37.0 (14.5)
Gender
    Female n (%) 401, 974 (65.7) 597,999 (65.2) 686,989 (65.4) 806,434 (65.5) 737,825 (65.9)
    Male n (%) 202,380 (33.1) 308,888 (33.7) 351,937 (33.5) 409,420 (33.3) 368,974 (33.0)
    Missing n (%) 7,652 (1.2) 10,573 (1.1) 12,196 (1.1) 15,138 (1.2) 12,615 (1.1)
Viral Suppression
    Suppressed n (%) 546,848 (89.4) 787,950 (85.9) 927,544 (88.2) 1,097,658 (89.2) 1,012,516 (90.5)
    Non-Suppressed n (%) 65,158 (10.6) 129,510 (14.1) 123,578 (11.8) 133,334 (10.8) 106,898 (9.5)
ART regimen
    First line regimen n (%) 561,992 (91.8) 847,117 (92.3) 927,525 (88.2) 1,091,537 (88.7) 984,407 (87.9)
    Second line regimen n (%) 25,502 (4.2) 41,236 (4.5) 72,746 (6.9) 87,566 (7.1) 84,677 (7.6)
    Other regimen n (%) 1,016 (0.2) 1,844 (0.2) 16,749 (1.6) 5,436 (0.4) 8,600 (0.8)
    Missing n (%) 23,496 (3.8) 27,263 (3.0) 34,102 (3.3) 46,453 (3.8) 41,730 (3.7)
Sample type
    Plasma 137,619 (22.5) 318,440 (34.7) 553,240 (52.6) 617,106 (50.1) 570,232 (50.9)
    DBS 474,387 (77.5) 599,020 (65.3) 497,882 (47.4) 613,886 (49.9) 549,182 (49.1)

Association between low-level viraemia and non-suppression

Based on the inclusion criteria (Fig 2), a cohort of 17,783 PLHIV was followed from 2016 to 2020; of which 11,765 (66.2%) were female; 5,765 (32.4%) were male; and 253 (1.4%) had a missing sex result. The mean age for the study cohort was 33.8 years (SD—15.2), and the median follow-up time was 4.0 years (IQR 3.8–4.2). 15,741 (88.5%) PLHIV were on a first line ART regimen; 1,710 (9.6%) on a second line ART regimen; 53 (0.3%) on other regimen (third line regimens and any other salvage regimens), and 279 (1.6%) had a missing regimen; as shown in Table 2.

Fig 2. Participants included in the study (Study profile).

Fig 2

Table 2. Characteristics of the study cohort at baseline in 2016.

Characteristics (n = 17,783)
Mean Age (SD), years 33.8 (15.2)
Age disaggregation
    Children n (%) 3,399 (19.1)
    Adults n (%) 14,242 (80.1)
    Missing n (%) 142 (0.8)
Gender
    Female n (%) 11,765 (66.2)
    Male n (%) 5,765 (32.4)
    Missing n (%) 253 (1.4)
Level of viraemia
    Non-Detectable (Below 50) n (%) 16,317 (91.8)
    Low-level viremia (≥50 to <1,000) n (%) 1,466 (8.2)
        50 to 199 copies/ml 836 (57.0)
        200 to 399 copies/ml 288 (19.6)
        400 to 599 copies/ml 129 (8.8)
        600 to 999 copies/ml 213 (14.6)
ART regimen
    First line regimen n (%) 15,741 (88.5)
    Second line regimen n (%) 1,710 (9.6)
    Other regimen n (%) 53 (0.3)
    Missing n (%) 279 (1.6)
Mean Duration on ART (SD), years 5.0 (3.3)

Low-level viraemia was identified in 1,466 PLHIV (8.2%); and of these, 836 (57.0%) were between 50 to 199 copies/ml; 288 (19.6%) were between 200 to 399 copies/ml; 129 (8.8%) were between 400 to 599 copies/ml; and 213 (14.6%) were between 600 to 999 copies/ml. Men had 1.3 times the risk of having LLV, as compared to women (risk ratio = 1.3, 95% CI: 1.2–1.4, p value < 0.001); and PLHIV on a second line ART regimen had 2.5 times the risk of having LLV, as compared to PLHIV with a first line ART regimen (risk ratio = 2.5, 95% CI: 2.2–2.8, p value < 0.001). Children had 3.1 times the risk of having LLV, as compared to adults (risk ratio = 3.1, 95% CI: 2.9–3.4, p value < 0.001). Furthermore, young PLHIV were associated with LLV (mean age for PLHIV with LLV was 29.7 years, SD—16.4, as compared to the mean age for PLHIV with a non-detectable VL, which was 34.1 years, SD– 15.0).

A total of 1,730 PLHIV (9.7%) out of 17,783 PLHIV became non-suppressed during the follow-up period. 32.5% of the PLHIV with LLV (476 out of 1,466 PLHIV) became non-suppressed, as compared to 7.7% of the PLHIV (1,254 out of 16,317 PLHIV) with a non-detectable viral load who became non-suppressed during the follow-up period. PLHIV with LLV had 4.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL (adjusted hazard ratio was 4.1, 95%CI: 3.7 to 4.7, p < 0.000), after adjusting for age, sex, and ART regimen. High ranges of LLV were associated with increased hazard ratios, as shown in Table 3. The Kaplan-Meier estimators indicated that PLHIV with LLV had increased hazards of viral non-suppression, compared to PLHIV with a non-detectable viral load, and these hazards of viral non-suppression increased with increasing ranges of viraemia, as shown by Fig 3.

Table 3. The association between low-level viraemia and viral non-suppression as determined through cox proportional hazards analysis.

Adjusted HR (95% CI) p value
Non-Detectable (Below 50 copies/ml) 1 (Reference)
Low-level viremia (≥50 to <1,000) 4.1 (3.7–4.6) < 0.001
    50 to 199 copies/ml 2.4 (2.0–2.8) < 0.001
    200 to 399 copies/ml 4.9 (4.0–5.9) < 0.001
    400 to 599 copies/ml 10.1 (8.1–12.8) < 0.001
    600 to 999 copies/ml 8.3 (6.9–10.1) < 0.001
Age:
    Adults 1 (Reference)
    Children 2.8 (2.5–3.1) < 0.001
Sex:
    Male 1 (Reference)
    Female 0.8 (0.7–0.9) < 0.001
ART Regimen:
    First line regimen 1 (Reference)
    Second line regimen 1.6 (1.4–1.8) < 0.001
    Other regimen 0.8 (0.3–1.7) 0.510

Fig 3. Kaplan-Meier estimator showing the association between LLV and viral non-suppression.

Fig 3

Discussion

In this study, we assessed the association between low-level viraemia and viral non-suppression among PLHIV on ART in Uganda. To the best of our knowledge, this is the only such study to be conducted in Uganda, as of now. The findings of this study indicated that there are increasing proportions of PLHIV with LLV, from 2.0% in 2016 to 8.6% in 2020; and LLV was found to be associated with male sex, second line ART regimen and being of lower age. Furthermore, LLV was associated with a 4.1 times hazard rate of viral non-suppression as compared to a non-detectable VL.

Our study builds on the existing literature about the emerging concern of LLV in Sub-Sahara Africa, and enriches the prevailing debate about the need to review the use of a threshold of 1,000 copies/ml to determine viral non-suppression among PLHIV on ART. The findings of our study are consistent with the findings of similar studies done in Sub-Saharan Africa, for instance a study in 4 African countries including Uganda showed high prevalences of viraemia and persistent LLV at 19.3% and 7.8% respectively among study participants [9]. This study also indicated that 57.5% of study participants with persistent viraemia had confirmed virologic failure. Similarly, the LLV study conducted in South Africa also indicated that LLV was in 23% of the study participants and LLV was associated with increased hazards of virological failure (hazard ratio of 2.6, 95% CI: 2.5–2.8; p<0.0001) [10].

Our findings indicate four main aspects that are important to note. The first aspect is that there are increasing PLHIV with LLV in Uganda over the years, from 2.0% in 2016 to 8.6% in 2020. This implies that there is an urgent need in the country to assess for the cause of this rising trend of LLV, and institute strategies to halt it. Secondly, LLV has been shown to be associated with male sex, among other factors; and this is not a surprise because men have been associated with poor health seeking behaviour, as compared to women [31]. Furthermore, different barriers like self-denial, HIV related stigma, conflicting priorities of having to work to get money to look after the family, alcohol ingestion, and perceived medication effects are key in hindering men from seeking HIV-related care, which may contribute to poor treatment outcomes like LLV [3133]. This therefore calls for concerted efforts to address these barriers, which can consequently improve treatment outcomes in males, including reduction of LLV. Furthermore, our findings show that children have increased rates of LLV, as compared to adults. This is in line with previous studies which have shown increased rates of other poor treatment outcomes like virologic failure and drug resistance among children [16, 34, 35]. These poor treatment outcomes have been associated with non-disclosure, HIV related stigma, and ART-induced side effects, among others [16, 36, 37]. Hence the need to devote efforts to address these challenges to reduce the rates of LLV and other poor treatment outcomes among children. Lastly, LLV has been associated with a 4.1 times the rate of viral non-suppression as compared to a non-detectable VL and it is important to note that this rate increases with high ranges of LLV. This indicates that higher ranges of viraemia are highly associated with viral non suppression and virologic failure, as also shown in several other studies [10], hence Uganda should consider a policy to revise the VL non-suppression threshold to at least 400 copies/ml, putting the public health perspective in mind. Though the ideal would be 200 copies/ml as recommended by CDC and IAPAC [19, 20].

Strengths and limitations

Among the various strengths of our study is that we followed up a large number of PLHIV for a long period of time of upto 5 years, in determining the association between LLV and VL non-suppression.

Our study had several limitations, the first being that this was an observational retrospective cohort analysis using the national program data for viral load testing. As a result, there was significant missing data for key variables like the date of sample collection and viral load results for the follow-up years (2017, 2018, 2019 and 2020). However we conducted a comprehensive missing data analysis. The percentage missingness was 72.2% whereby 46,107 out 63,890 PLHIV missed one of the key variables (either a date of sample or viral load result) in the follow-up years. The missing data followed a non-monotonic and multivariate pattern. Despite this pattern, it is important to note that the PLHIV who missed a date of sample collection also missed a viral load result. To determine the mechanism of the missingness, we ran the Little’s MCAR Test and the p value was < 0.001, hence the data was not missing completely at random (MCAR). We then did a logistic regression to test whether the data was missing at random (MAR), and the p value was < 0.001, hence the data was MAR. We then conducted multiple imputation using chained equations, after which we ran the model diagnostics to check whether the imputed results are similar to the observed results. Results from multiple imputation indicated that PLHIV with LLV had 6.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL (adjusted hazard ratio was 6.1, 95% CI: 5.4 to 6.8, p < 0.001). This was comparable and had similar conclusions with the findings of complete case analysis. Important to note that the standard multiple imputation approach did not account for the intra-cluster correlations of the different ranges of viraemia. Further sensitivity analysis of both the observed and imputed results gave consistent results, and due to the large missingness of 72.2%, we decided to report the results of the complete case analysis in this study.

Secondly, the other limitation is that we used the national VL program data, and this lacked results for HIV drug resistance testing, which would have provided a further understanding of LLV in this study. The national program data also lacked data on other key variables like co-morbidities which could be potential confounders. Furthermore, different assays and techniques could have been used in conducting the VL testing for the different PLHIV over the years, which could create a threat of measurement bias. However in this study, we only included participants whose VL tests were done on plasma samples, since techniques that use plasma samples give more distinct results, as compared to those that use DBS samples.

Conclusion

Our study indicated that PLHIV with LLV had 4.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL, and that this rate increased with elevated ranges of LLV. These findings indicate that there is an urgent need to review the VL testing alogarithm in Uganda, and also institute interventions such as intensive adherence counselling to manage LLV among PLHIV on ART, as per the recent 2021 WHO recommendations.

Supporting information

S1 Dataset. Dataset for the study cohort from 2016 to 2020.

(XLSX)

Acknowledgments

We extend our appreciation to Mr. Obuya Emmanuel, Mrs. Nabukenya Miriam Bamwita, Mr. Kiwanuka Julius, Mr. Ssemugabo Charles, Ms. Mary Nakafeero and Mrs. Esther Bayiga for the devoted efforts invested in the study’s data management and statistical analysis processes. Thank you very much.

Abbreviations and acronyms

AIDS

Acquired Immune Deficiency Syndrome

ART

Antiretroviral Therapy

CDC

Centres for Disease Control and Prevention

CPHL

Central Public Health Laboratories

DBS

Dried Blood Spot

HIV

Human Immunodeficiency Virus

IAC

Intensive Adherence Counselling

IAPAC

International Association of Providers of AIDS Care

LLV

Low-level viraemia

PLHIV

People Living with HIV/AIDS

VL

Viral Load

WHO

World Health Organization

Data Availability

All relevant data are within the paper and its Supporting Information files.

Funding Statement

This project was supported by NIH Research Training Grant # D43TW009340 funded by the NIH Fogarty International Center, NINDS and NIMH. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

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Decision Letter 0

Chika Kingsley Onwuamah

27 Sep 2022

PONE-D-22-22579The association between low-level viraemia and subsequent viral non-suppression among people living with HIV/AIDS on antiretroviral therapy in UgandaPLOS ONE

Dear Dr. Nanyeenya,

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Comments to the Author

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Reviewer #1: Partly

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes

**********

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: Abstract;

Background: The introductory statement is not in tandem with the aim and objective of the study. One is rather worried about HIV drug resistance in patients with low level viraemia.

Introduction;

Line - 96-97 - The introduction is satisfactory, however there are repetitions which was noticed on line 66 -68

Line 107-108 – The statement should read that we aimed to determine but not to understand the association between low level viraemia……

Line - 151-153 - Exposed to what? Is this the right word to use?

Methodology. Well presented and sufficient to allow reproducibility

Results

Line - 194 Fig 1 Not displayed

Line - 224 Fig 2 Not displayed

Line - 240 Table 3 – Include %

The manuscript did not mention the ARV regimen for the 1st/2nd line ARVs

The authors did not mention other cofounders eg comorbities in the patients/data reviewed that can affect viral suppression

The socio demographic characteristics of the reviewed data was not highlighted.

The data did not provide the age disaggregation except by gender

What do you mean by “other regimen” in table 3?

Statistical analysis is okay but not rigorously performed.

Discussion

Line - 281-282 – Repetition of statement

Line - 285 -286 - What about the fact that men may be engaged with some activities to provide for the family and may forget their medications. What about denial state. Men may have the preponderance to indulge in alcohol ingestion and may forget or interference with medications

Line - 289 -291 - Repeating the result in the discussion is not acceptable.

Line - 302 -312 - Why so much emphasis and statistical analysis on missing data which does not form part of the data presented

Line - 318-319 – Is this statement a limitation or a strength?

Line - 321-323. However, in this study, we only included participants whose VL tests were done on plasma samples, since techniques that use plasma samples give more distinct results, as compared to those that use DBS samples

Another limitation is that children were not included in the study and from reports the children are more predisposed to LLV and non-viral suppression

Conclusion

327-329 In response to the last sentence in your conclusion, would there be a need to review the drug regimen? Why WHO recommendations, Does Uganda not have National guidelines on ART? The recommendations need to be apt.

References

Authors should review reference 19 and other references and ensure it align with the journal instructions.

The fonts and characters are different what is in the text

General Comments

The authors have generally made significant effort to describe their findings on patients on ART with LLV in Uganda. The sample size is large enough to draw an inference. They have also highlighted their strength and limitations. However, I observed significant limitations of this study which obviously excluded children who are less than 18 years. Is it that within this period of study children and early adolescents did not present with low level viraemia.

There were repetitions in the write up and the figures were not in place though efforts should have been made to refer the reviewers to the appendix.

Generally, the discussion did not critically review the findings and critic those findings in relation to other studies and available literatures. The authors were instead discussing missing data. This and other queries must be addressed.

Reviewer #2: TITLE: THE ASSOCIATION BETWEEN LOW-LEVEL VIRAEMIA AND SUBSEQUENT VIRAL NON-SUPRESSION AMONG PEOPLE LIVING WITH HIV/AIDS ON ANTIRETROVIRAL THERAPHY IN UGANDA

SUMMARY OF THE PAPER

This article describes a retrospective cohort study on the association between low-level HIV viraemia and subsequent virologic non-suppression. It is a retrospective cohort study of 17,783 people living with HIV out of which 1,466 had low-level viraemia and the remaining had undetectable viral load. It was a five year follow up study (2016 - 2020). The study defined undetected viral load as viral load below 50 while low-level viral load was taken as between 51 copies and 1000 copies. The study found that during the follow up period, the incident proportion of persons with low-level viraemia increased from 2% to 8.6% and that persons with low-level viral load had 4.1 times the risk of failure to achieve viral suppression compared to those with undetected viral load. Low-level viraemia was also associated with the male gender and being on second line antiretroviral theraphy. The authors of the paper established on literature review that low-level viraemia was associated with antiretroviral drug resistance and virologic failure. The researchers employed the approach of complete case analysis and multivariate logistic regression to establish an association between low-level viraemia and virologic non-suppression. They also used the cox proportional hazard regression model to identify the association between low-level viraemia and viral suppression. Study limitations included the fact that a large part of the cohort about 72% had missing data that was essential to the study and that resistance testing was not available for the cohort.

ASSESSMENTS

This study is important for giving the reader an insight into the challenges of managing people living with HIV in Uganda. Although the title describes what was actually carried out in the study , it does not capture an important aspect of what the researchers tried to contribute. The researchers were obviously concerned and objected to a continued policy of accepting a viral load of 1000 as threshold for satisfactory treatment response. And related to this, the need for greater attention to be paid to persons with low-level viraemia especially the young male on second line antiretroviral theraphy.

This aspect of the manuscript is one of the major strengths i.e pointing out the weakness of current policy and providing data to challenge it. The authors however did not make a strong enough connection between their findings and the need for a review of this policy. The major weakness of this study is the treatment of missing data that was essential to the study.

IMPRESSION OF PAPER/RECOMMENDATION

The overall arrangement of the paper is good, the language is sytematic and scientific, the evidence was well brought out and the conclusions matched the evidence. However, the recommendation which had to do with the need for policy change was not well argued. The authors make an overall good impression and the paper is worthy of dissemination in peer reviewed journals.It should be Accepted with revisions as follows.

MAJOR ISSUES

1.[Line 304 to 316] Author needs to clarify the treatment of missing data to show the proportion of people with missing date of sample and the proportion of people with missing viral load result because the effect of a missing viral load result would not necessarily be the same as the effect of a missing sample date.

MINOR ISSUES

1.Table 3 does not include age which is already identified as a significant factor.

2. The paper did not give the reader the rational for using ‘virologic non-suppression’ rather than ‘virologic failure’.

REVIEWER: Dr. Harry OHWODO

**********

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Reviewer #1: No

Reviewer #2: Yes: Harry Ohwodo

**********

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PLoS One. 2023 Jan 13;18(1):e0279479. doi: 10.1371/journal.pone.0279479.r002

Author response to Decision Letter 0


14 Oct 2022

First and foremost, we greatly and humbly thank you all for taking off time to carefully read our manuscript and giving us very insightful review comments. We greatly believe that addressing these comments has been very key in improving our manuscript. Thank you very much once again.

We hereby humbly submit the responses to the different review comments raised, as shown below;

1. ACADEMIC EDITOR

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

a) Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at

https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf.

� Thank you very much for this comment. We have read through PLOS ONE’s style requirements and revised the manuscript to meet these requirements. Thank you very much.

b) In the ethics statement in the manuscript and in the online submission form, please provide additional information about the patient records/samples used in your retrospective study. Specifically, please ensure that you have discussed whether all data/samples were fully anonymized before you accessed them and/or whether the IRB or ethics committee waived the requirement for informed consent. Please clearly state which ethics committee provided the waiver for the requirement of informed consent.

� This is a key comment. Thank you very much. We have revised the ethics statement in the manuscript as shown in lines 179 to 185, and in the online submission to incorporate these key aspects highlighted in this comment.

c) We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match.

� Thank you for this observation. This has been addressed. Thank you very much.

d) When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

� Thank you very much for this. We have addressed this, as per your guidance.

2. REVIEWER #1

a) Background: The introductory statement is not in tandem with the aim and objective of the study. One is rather worried about HIV drug resistance in patients with low level viraemia.

� Thank you very much for this comment. We have revised the introductory statement, as shown in lines 94 to 96.

b) Introduction;

i. Line - 96-97 - The introduction is satisfactory, however there are repetitions which was noticed on line 66 -68

� Thank you very much. This has been addressed and revised as shown in lines 63 to 65.

ii. Line 107-108 – The statement should read that we aimed to determine but not to understand the association between low level viraemia……

� Thanks for this guidance. This has been revised as shown in lines 105.

iii. Line - 151-153 - Exposed to what? Is this the right word to use?

� Thank you very much. The exposure was low-level viraemia. However, following this comment, the sentence has been revised to make it clear, as shown in lines 150 to 151.

c) Methodology. Well presented and sufficient to allow reproducibility

� Thank you very much.

d) Results

i. Line - 194 Fig 1 Not displayed

� Thank you very much. We desired to place all the figures in the manuscript however following the guidance from the journal, figure 1 was separately uploaded into the system. Thanks very much.

ii. Line - 224 Fig 2 Not displayed

� Thank you very much. We also desired to place this figure in the manuscript however following the guidance from the journal, this figure was also separately uploaded into the system. Thanks very much.

iii. Line - 240 Table 3 – Include %

� Thank you for this comment. We humbly request you to note that Table 3 represents the adjusted hazards ratios, which do not require %. However we have noted that we had included ‘n (%)’ on the ‘other regimen’ by mistake, and we have corrected this, as shown in Table 3. Thanks indeed for this comment.

iv. The manuscript did not mention the ARV regimen for the 1st/2nd line ARVs

� Thank you very much. It would really be great to mention the ARV regimens, however Uganda has over 20 ARV regimens for the first and second line, which made mentioning them not so feasible. Therefore, we decided to follow literature where many other similar articles mainly stratify ARVs up to the level of first and second line only, without mentioning the respective regimens. Thank you very much.

v. The authors did not mention other cofounders e.g. comorbities in the patients/data reviewed that can affect viral suppression

� This is a very insightful comment. Thank you very much. We used national VL program data which did not have complete data for some variables like comorbidities. However in the data analysis, we addressed confounding by stratification, as evidenced by the reported adjusted hazards ratios in Table 3. Following this comment, a discussion of using national program data with missing data on probable confounders has been added to the Discussion section, as shown by line 314 to 315. Thank you very much.

vi. The socio demographic characteristics of the reviewed data was not highlighted.

� Thank you for this comment. We humbly request you to note that Table 1 on line 205 shows the socio demographic characteristics of the reviewed data for the VL program for the individual years from 2016 to 2020. Table 2 on line 232 also shows the socio demographic characteristics of the Study Cohort at baseline in 2016. Thank you very much.

vii. The data did not provide the age disaggregation except by gender

� Thank you very much for this perfect comment. We have realized that including the age disaggregation would add much value to the manuscript. Following the guidance from this comment, we have repeated the data analysis, to include the disaggregation by age (children versus adults). We have revised the manuscript to report on the children, as shown in lines 220 to 223, Table 2 on line 232, and Table 3 on line 244. We have also included this in our discussion as shown in lines 277 to 282. Greatly thank you for this key comment.

viii. What do you mean by “other regimen” in table 3?

� Thanks very much. The national ART guidelines in Uganda refer to any third line regimen or any other salvage ART combination (regimen) used in management of drug resistance, as ‘other regimen’. This has been further clarified in the manuscript, as shown in lines 213 to 214.

e) Statistical analysis is okay but not rigorously performed.

� Thanks very much.

f) Discussion

i. Line - 281-282 – Repetition of statement

� Thanks very much. This comment is well noted. We are humbly informing you that these are two different studies, however this comment is very true because it looked like a repetition. We have revised these statements in the manuscript following this comment to ensure that they do not look like a repetition, as shown in line 263 to 265.

ii. Line - 285 -286 - What about the fact that men may be engaged with some activities to provide for the family and may forget their medications. What about denial state. Men may have the preponderance to indulge in alcohol ingestion and may forget or interference with medications

� Thanks for this comment. We humbly note that this is very useful guidance, and we have done further literature review to incorporate these factors. The manuscript has been revised following this guidance, as shown in lines 272 to 276.

iii. Line - 289 -291 - Repeating the result in the discussion is not acceptable.

� Thank you very much. This has been revised in the manuscript as shown in lines 282 to 284. Thanks.

iv. Line - 302 -312 - Why so much emphasis and statistical analysis on missing data which does not form part of the data presented

� Thanks very much. We humbly note this comment however our team feels that it is important to include these details in the discussion, to show how we managed missing data, since it was a key weakness of our study. However as per your guidance in the other comments, we have improved the other sections of the discussion to make it better. Thank you.

v. Line - 318-319 – Is this statement a limitation or a strength?

� Thanks. This statement is a limitation. However this statement has been revised in the manuscript to make it clear, as shown in line 312. Thank you very much.

vi. Line - 321-323. However, in this study, we only included participants whose VL tests were done on plasma samples, since techniques that use plasma samples give more distinct results, as compared to those that use DBS samples

� Thank you very much. We used this statement to explain how we tried to solve the limitation of different assays used for viral load testing, which could lead to measurement bias. Thank you very much.

g) Another limitation is that children were not included in the study and from reports the children are more predisposed to LLV and non-viral suppression

� Thanks very much for this insightful comment. The inclusion criteria for the study was people living with HIV (PLHIV) on ART with a suppressed viral load, done using a plasma sample. By this criteria, children were included into the study. However we acknowledge that we had not extensively included them in the data analysis and had not reported on them. We have done the data analysis again, and reported on children, as shown in lines shown in lines 220 to 223, Table 2 on line 232, and Table 3 on line 244. We have also included this in our discussion as shown in lines 277 to 282. Thank you.

h) Conclusion:

i. 327-329 In response to the last sentence in your conclusion, would there be a need to review the drug regimen? Why WHO recommendations, Does Uganda not have National guidelines on ART? The recommendations need to be apt.

� Thank you very much for this. For this study, we think that there may be no need to review the drug regimens since Dolutegravir-based regimens have just been rolled out within the previous 3 years in Uganda, and other sub-Sahara African countries. However we agree that further research and studies should be done to review drug regimens.

� Thanks for hinting about the WHO recommendation. In 2021, WHO recommended use of intensive adherence counselling (IAC) in management of low-level viraemia (LLV). However many countries including Uganda are still very reluctant to initiate IAC for LLV, and it is actually not yet incorporated in the Ugandan HIV consolidated guidelines. And that is why we emphasize that interventions like IAC should be instituted in management of LLV, basing on the WHO recommendation. However following this comment, we have clarified the last sentence to indicate the year of the WHO recommendation, as shown in line 332.

i) References

i. Authors should review reference 19 and other references and ensure it align with the journal instructions.

� Thanks for this comment. This has been revised in the manuscript, as shown in lines 382 to 383. Thank you very much.

ii. The fonts and characters are different what is in the text

� Thank you very much. This has been addressed in manuscript, as shown in the reference section.

j) General Comments

The authors have generally made significant effort to describe their findings on patients on ART with LLV in Uganda. The sample size is large enough to draw an inference. They have also highlighted their strength and limitations. However, I observed significant limitations of this study which obviously excluded children who are less than 18 years. Is it that within this period of study children and early adolescents did not present with low level viraemia.

There were repetitions in the write up and the figures were not in place though efforts should have been made to refer the reviewers to the appendix.

Generally, the discussion did not critically review the findings and critic those findings in relation to other studies and available literatures. The authors were instead discussing missing data. This and other queries must be addressed.

� Thank you very much for all the comments raised. The manuscript has been revised following the guidance from the comments. The data has been re-analysed to include the children, and the discussion has also been improved, in addition to addressing the other comments. Thank you very much.

3. REVIEWER #2

a) Summary of the paper

This article describes a retrospective cohort study on the association between low-level HIV viraemia and subsequent virologic non-suppression. It is a retrospective cohort study of 17,783 people living with HIV out of which 1,466 had low-level viraemia and the remaining had undetectable viral load. It was a five year follow up study (2016 - 2020). The study defined undetected viral load as viral load below 50 while low-level viral load was taken as between 51 copies and 1000 copies. The study found that during the follow up period, the incident proportion of persons with low-level viraemia increased from 2% to 8.6% and that persons with low-level viral load had 4.1 times the risk of failure to achieve viral suppression compared to those with undetected viral load. Low-level viraemia was also associated with the male gender and being on second line antiretroviral therapy. The authors of the paper established on literature review that low-level viraemia was associated with antiretroviral drug resistance and virologic failure. The researchers employed the approach of complete case analysis and multivariate logistic regression to establish an association between low-level viraemia and virologic non-suppression. They also used the cox proportional hazard regression model to identify the association between low-level viraemia and viral suppression. Study limitations included the fact that a large part of the cohort about 72% had missing data that was essential to the study and that resistance testing was not available for the cohort.

b) Assessments

This study is important for giving the reader an insight into the challenges of managing people living with HIV in Uganda. Although the title describes what was actually carried out in the study, it does not capture an important aspect of what the researchers tried to contribute. The researchers were obviously concerned and objected to a continued policy of accepting a viral load of 1000 as threshold for satisfactory treatment response. And related to this, the need for greater attention to be paid to persons with low-level viraemia especially the young male on second line antiretroviral therapy.

This aspect of the manuscript is one of the major strengths i.e pointing out the weakness of current policy and providing data to challenge it. The authors however did not make a strong enough connection between their findings and the need for a review of this policy. The major weakness of this study is the treatment of missing data that was essential to the study.

c) Impression of paper/recommendation

The overall arrangement of the paper is good, the language is systematic and scientific, the evidence was well brought out and the conclusions matched the evidence. However, the recommendation which had to do with the need for policy change was not well argued. The authors make an overall good impression and the paper is worthy of dissemination in peer reviewed journals. It should be Accepted with revisions as follows.

d) Major issues

i. [Line 304 to 316] Author needs to clarify the treatment of missing data to show the proportion of people with missing date of sample and the proportion of people with missing viral load result because the effect of a missing viral load result would not necessarily be the same as the effect of a missing sample date.

� Thanks very much for raising this very critical comment. Largely, PLHIV with a missing date, also missed a viral load result for example in 2017, 61.5% of PLHIV missed the date of sample collection while 58.7% missed a viral load result. In 2018, 63.2% of the PLHIV missed both the date of sample collection and the viral load result. In 2019, 66.2% of the PLHIV missed both, while in 2020, 70.3% of the PLHIV missed both the date of sample collection and viral load results. This indicates a loss-to-follow up of these participants. We imputed all these missing variables to assess the impact of the missingness, and this is why we described the full steps that we used to manage the missing data in the discussion. We have made further clarification in the manuscript about this, as shown in line 298 to 299. Once again, thank you for highlighting this comment.

d) Minor issues

i. Table 3 does not include age which is already identified as a significant factor.

� Thank you for this key comment. We acknowledge that we had missed out data analysis on age disaggregation (children versus adults). However this has been addressed as shown in Table 3 on line 244.

ii. The paper did not give the reader the rational for using ‘virologic non-suppression’ rather than ‘virologic failure’.

� Thank you very much for this comment. We had desired to use virologic failure in this study, however we used the national viral load program data, which had a limitation of a lot of missing data, and hence we would not ascertain the virologic failure very well. However virologic non-suppression is a major predictor of virologic failure, according to literature, and actually key stakeholders like CDC define virologic failure as the inability to achieve or maintain suppression of viral replication to HIV-RNA level <200 copies/mL, which is the same as virologic non-suppression (https://clinicalinfo.hiv.gov/en/guidelines/hiv-clinical-guidelines-adult-and-adolescent-arv/virologic-failure).

Once again, thank you very much for the comments.

Attachment

Submitted filename: Response to Reviewers.pdf

Decision Letter 1

Chika Kingsley Onwuamah

8 Dec 2022

The association between low-level viraemia and subsequent viral non-suppression among people living with HIV/AIDS on antiretroviral therapy in Uganda

PONE-D-22-22579R1

Dear Dr. Nanyeenya,

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Reviewers' comments:

Acceptance letter

Chika Kingsley Onwuamah

4 Jan 2023

PONE-D-22-22579R1

The association between low-level viraemia and subsequent viral non-suppression among people living with HIV/AIDS on antiretroviral therapy in Uganda

Dear Dr. Nanyeenya:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

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on behalf of

Dr. Chika Kingsley Onwuamah

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Dataset. Dataset for the study cohort from 2016 to 2020.

    (XLSX)

    Attachment

    Submitted filename: Response to Reviewers.pdf

    Data Availability Statement

    All relevant data are within the paper and its Supporting Information files.


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