Skip to main content
PLOS One logoLink to PLOS One
. 2021 Sep 10;16(9):e0257049. doi: 10.1371/journal.pone.0257049

The impact of the 2014 Ebola epidemic on HIV disease burden and outcomes in Liberia West Africa

Soka J Moses 1,#, Ian Wachekwa 2,#, Collin Van Ryn 3, Greg Grandits 3, Alice Pau 4, Moses Badio 1, Stephen B Kennedy 1, Michael C Sneller 4, Elizabeth S Higgs 4, H Clifford Lane 4, Mosoka Fallah 5, Stephen A Migueles 4, Cavan Reilly 3,*
Editor: Graciela Andrei6
PMCID: PMC8432817  PMID: 34506540

Abstract

Background

Detailed longitudinal studies of HIV-positive individuals in West Africa are lacking. Here the HIV prevalence, incidence, all-cause mortality, and the proportion of individuals receiving treatment with cART in two cohorts of participants in Ebola-related studies are described.

Setting

Individuals of all ages were enrolled and followed at four sites in the area of Monrovia, Liberia.

Methods

Two cohorts identified in response to the Ebola epidemic are described to provide insights into the current state of the HIV epidemic. HIV testing was performed at baseline for participants in both cohorts and during follow-up in one cohort.

Results

Prevalence and incidence of HIV (prevalence of 3.1% for women and 1.4% for men and incidence of 3.3 per 1,000) were higher in these cohorts compared to 2018 national estimates (prevalence of 1.3% and incidence of 0.39 per 1,000). Most participants testing positive did not know their status prior to testing. Of those who knew they were HIV positive, 7.9% reported being on antiretroviral treatment. The death rate among those with HIV was 12.3% compared to 1.9% in HIV-negative individuals (adjusted odds ratio of 6.87). While higher levels of d-dimer were associated with increased mortality, this was not specific to those with HIV, however lower hemoglobin levels were associated with increased mortality among those with HIV.

Conclusion

These findings point to a need to perform further research studies aimed at fulfilling these knowledge gaps and address current shortcomings in the provision of care for those living with HIV in Liberia.

Introduction

Despite some progress, HIV infection continues to take a heavy toll in western and central Africa [1]. While annual new HIV infections declined by 13% and the number of AIDS-related deaths decreased by 29% between 2010 and 2018, those declines are lower than seen elsewhere. In eastern and southern Africa over this same period, the number of new infections declined by 28% and the number of AIDS-related deaths decreased by 44%. The most recent western and central African incidence-prevalence ratio of 5.5% [3.7–8.3%] is almost double the epidemic transition benchmark of 3%, the threshold below which the total population of people living with HIV will gradually fall. This metric also lags behind the value of 3.9% [3.0–5.1%] reported for eastern and southern Africa [1]. In the West African country of Liberia, there were an estimated 39,000 (36,000–44,000) people living with HIV in 2018; the HIV prevalence in the general population aged 15–49 years was 1.3% (1.1–1.4%) and the incidence was 0.39 (0.38–0.41) per 1,000 people [1]. HIV prevalence appears to be higher in urban settings (2.6%) compared to rural settings (0.8%), especially in the capital city Monrovia (3.2%) [2]. With an estimated incidence-prevalence ratio of 4.9% according to recent epidemic transition metrics, the HIV epidemic in Liberia remains an inadequately addressed public health problem [1].

HIV treatment in Liberia is provided vertically and free of charge by the Liberian Ministry of Health (MoH) through its National AIDS and Sexually Transmitted Infection Control Program (NACP). Even though efforts intensified within the last decade by the MoH to better organize services to treat and control the spread of HIV infection, numerous challenges have remained to combating the HIV epidemic in Liberia. These include lack of awareness of HIV status, low condom use, poverty, lack of education, and widespread stigma surrounding HIV/AIDS [3]. In addition, clinicians do not have regular access to measurements of CD4 counts and levels of HIV plasma viremia. Healthcare provision is also hampered by shortages of trained staff, especially in rural areas, erratic availability of HIV testing kits, and inconsistent access to combination antiretroviral therapy (cART) [3, 4]. The 2014–16 Ebola Virus Disease (EVD) outbreak in Liberia further strained the fragile healthcare system, including the NACP, which had already been weakened by years of civil strife. Thousands of patients living with HIV appear to have been lost to follow-up during and after the outbreak, with major declines estimated in access to HIV counselling, testing and treatment [57]. These factors may have led to increases in HIV transmission, resistance to cART, and accelerated disease progression [8, 9]. In 2016, only 19% of the people living with HIV in Liberia were accessing cART, and approximately 13% had suppressed viral loads [10]. In addition to the lack of services in some communities and low uptake of services even in places where they are available, data collection and health facility reporting are incomplete [11]. For these reasons, current in-depth information about the HIV epidemic in Liberia is lacking and significant gaps persist that minimize the likelihood of achieving the 95-95-95 targets that have been set for 2030.

Longitudinal studies of people living with HIV in western Africa are lacking. Such studies could provide valuable information about aspects of the HIV epidemic specific to this location. In this report, we investigated HIV/AIDS in participants of two large research studies established after the beginning of the EVD outbreak in Liberia in 2014: a clinical trial of two Ebola vaccines and an EVD natural history study. Our aim was to describe HIV prevalence, incidence, all-cause mortality, and the proportion of individuals receiving treatment with cART in these cohorts in an effort to gain better insight into the HIV epidemic in Liberia.

Methods

Participants: PREVAIL cohorts

The two cohorts used in the analysis described here have been followed for up to four years (with some individuals in one cohort followed for as little as two years). Both cohorts were initiated under the auspices of the Partnership for Ebola Virus Research in Liberia (PREVAIL), an effort coordinated between the US Government and the MoH in response to the 2013–16 EVD outbreak in West Africa. All participants provided written informed consent or written informed consent was provided by parents or guardians, and written assents were obtained in accordance with international clinical research ethical norms. All protocols received approval from the NIAID Institutional Review Board and the National Research Ethics Board of Liberia.

PREVAIL I (ClinicalTrials.gov Identifier: NCT02344407) is a single center, double-blind, randomized, placebo-controlled study whose original objective was to determine the safety and efficacy of two experimental Ebola Virus (EBOV) vaccines compared to a common control. Vaccinations took place from February to April 2015. The details have been published elsewhere [12]. Due to the end of the outbreak, safety and immunogenicity objectives were substituted for the initial objective of efficacy. The enrollment, which was originally projected to exceed 28,000 participants was revised to 1,500. Only individuals with no history of EBOV infection and age 18 and over were enrolled and most participants were men. HIV and syphilis tests were conducted at baseline. Although the safety endpoint has been established, participants are still being followed under a modified protocol that seeks to assess long-term immunogenicity (participants consented to the modified protocol at the 1-year timepoint). To this end, participants have returned to the clinic on an annual basis and at these return visits, adverse events and survival are assessed and a blood draw is conducted for serology for EBOV (HIV tests were only conducted at baseline). Follow-up has been excellent with 98% of participants having been successfully followed for one year and with 1,251 (83%) returning for the year four visit.

PREVAIL III is a longitudinal cohort study whose primary objective was to determine the sequelae of EBOV infection. To this end, 1,144 EVD survivors and 2,784 controls were enrolled starting in June 2015. Enrollment took place at three sites that did not participate in PREVAIL I. The details of this study have also been described elsewhere [13]. To qualify as a survivor a participant needed to be listed on the MoH’s listing of individuals recorded as positive for EBOV at an Ebola treatment unit during the outbreak. To qualify as a contact, one needed to be selected by a survivor as someone who had close contact with the survivor during the survivor’s acute illness or had sexual contact after acute illness. Individuals of all ages were included, and the majority of participants were women. All participants return for a visit once every six months and at this visit, a blood draw for HIV and syphilis testing, a complete blood count with differential and common chemistries is conducted (blood draws were optional for participants less than 12 years of age). HIV and syphilis testing was done serum using the SD BIOLINE HIV/Syphilis Duo (06FK30, 06FK35) point-of-care diagnostic test (Standard Diagnostic, South Korea) [14]. The test is a solid phase immunochromatographic assay that qualitatively detects all antibody isotopes (IgG, IgM, IgA) specific to HIV 1/2 and/or Treponema pallidum (TP) simultaneously in human serum, plasma, or whole blood. The sensitivity and specificity of the tests against HIV 1/2 and syphilis were previously found to be 100% in an African population of commercial specimens [1416]. An extensive interview is conducted in which medication use (including cART) is determined, a detailed assessment of symptoms is collected, and a physical exam is conducted. In addition, deaths and hospitalizations are recorded based on self- or contact-reports. Follow-up has been good with 87.9% returning for the year two visit (the year three visit windows were still open for some participants when the analysis dataset was assembled).

According to the national guidelines, participants who tested HIV-positive were initially referred to an HIV clinic of their choice for treatment and care. All participants received HIV counselling at each study visit. Participants with a positive syphilis test or other clinically significant findings were referred to their primary care provider for treatment according to the national standard of care [17]. Both cohorts utilized the same laboratory resources and procedures and followed a common set of data management procedures. They also both relied on a group of community-based participant trackers who encouraged participants to return to the clinics for appointments. These commonalities provide for consistency across many aspects of the two cohorts, but participants were enrolled under different protocols designed for different objectives. Follow-up is still ongoing for both studies. The analysis presented here uses data up through April 2019.

Statistical methods

Continuous measures were summarized by medians and quantiles while categorical variables were summarized with percentages. Tests for differences between individuals with and without HIV at baseline and between those who died or not were conducted using generalized mixed effects models which modeled correlations among measurements from related groups of survivors and contacts using an independence correlation structure and used generalized estimating equations to obtain parameter estimates [18]. Models for binary outcomes used logit link functions and those for continuous outcomes used linear link functions. Proportional hazards models [19] were used to test for covariates that may impact the incidence of HIV. Time to event analysis was conducted to estimate the impact of being HIV positive (at baseline or during follow-up) on survival and time until lost to follow-up. Kaplan Meier curves were computed, and log-rank tests were conducted. Cox proportional hazards were fit with covariate-time interaction terms [20] and Schoenfeld residuals [21] were examined to assess the proportionality assumption. All adjusted analyses controlled for age (treated as continuous), sex, site, and survivor status. A significance level of 0.05 was used to assess statistical significance and no correction for test multiplicity was used. Given the small number of hypothesis tests performed here corrections for test multiplicity were deemed unnecessary. There was no attempt to define certain data points as outliers.

Survival time was calculated as the number of months from study enrollment to date of death, or, if censored for death, date of the last study visit. PREVAIL III participants were considered lost to follow-up if they voluntarily discontinued follow-up or if their last study visit occurred more than 12 months prior to April 2019. PREVAIL I participants who did not consent to follow-up visits beyond 12 months were considered lost to follow-up if they missed the 12-month follow-up visit. PREVAIL I participants who consented to follow-up visits beyond 12 months were considered lost to follow-up if they missed both the 36 and 48-month follow-up visits. Time to lost-to-follow-up was calculated as the number of months from study enrollment to date of the last study visit plus nine months if lost to follow-up, or, if not lost to follow-up, date last seen. All statistical calculations were conducted using R version 3.2.

Results

HIV prevalence and incidence

The cohorts in PREVAIL I (vaccine recipients) and PREVAIL III (EVD survivors and contacts) had different gender compositions and HIV prevalence at baseline. At baseline in PREVAIL I, 78 (5.2%) of participants were HIV+ and 549 (36.6%) of participants were women (Table 1). The prevalence of HIV among women was 9.8% while the prevalence among men was 2.5%. At baseline, 76 (2.3%) of the participants enrolled on the PREVAIL III protocol were HIV+ and 1,836 (56.3%) of participants were women. The prevalence of HIV among women was 3.1% and the prevalence among men was 1.4%. We found an overall prevalence of 3.2% (Table 1). In PREVAIL I, 11.5% of those who were HIV positive at baseline self-reported as such while in PREVAIL III this was 6.6%.

Table 1. Summary of characteristics, as well as number of deaths and number lost to follow-up, between HIV-positive and HIV-negative participants at PREVAIL I and PREVAIL III baseline.

PREVAIL I PREVAIL III Combined cohorts
Overall HIV- HIV+ p-value Overall HIV- HIV+ p-value Overall HIV- HIV+ p-value
Overall 1500 1422 (94.8) 78 (5.2) 3263 3187 (97.7) 76 (2.3) 4763 4609 (96.8) 154 (3.2)
 Female 549 (36.6) 495 (34.8) 54 (69.2) 1836 (56.3) 1780 (55.9) 56 (73.7) 2385 (50.1) 2275 (49.4) 110 (71.4)
 Age in years at enrollment 30 (24–38) 29 (24–38) 31 (26.2–39) 27 (18–38) 28 (20–39) 35 (28–41.2) 28 (20–38) 29 (22–39) 33.5 (27–41)
 On ART 9 (0.6) 0 (0) 9 (11.5) 7 (0.2) 1 (0) 6 (7.9) 16 (0.3) 1 (0) 15 (9.7)
 Deaths 65 (4.3) 54 (3.8) 11 (14.1) < 0.001 43 (1.3) 35 (1.1) 8 (10.5) < 0.001 108 (2.3) 89 (1.9) 19 (12.3) < 0.001
 Lost to follow-up 77 (5.1) 71 (5) 6 (7.7) 0.404 315 (9.7) 302 (9.5) 13 (17.1) 0.03 392 (8.2) 373 (8.1) 19 (12.3) 0.02

Data are no. (%) or median value (interquartile range).

PREVAIL I models adjusted for sex and age. PREVAIL III and combined cohort models additionally adjusted for survivor status and enrollment site and used a generalized estimating equations approach to adjust for relationships between survivors and controls. PREVAIL I participants were categorized as controls in combined cohorts.

Participants in PREVAIL III were retested for HIV every six months thereby allowing for computation of the incidence. Of the 3,187 participants with a median of 36 months of follow-up (quartiles 30 and 41), 29 new cases have been detected (Table 2), which implies an incidence of 3.3 cases per 1,000 person-years (95% CI: 2.2, 4.7 per 1,000 person-years).

Table 2. Adjusted hazard ratios for HIV infection during PREVAIL III follow-up.

PREVAIL III participants
HIV-negative at baseline
(n = 3187)
N (%) Contracted HIV 29 (0.9)
 Males 12 (0.4)
 Females 17 (0.5)
Cases per 1000 person-years (95% CI) 3.3 (2.2, 4.7)
 Males 3.1 (1.6, 5.4)
 Females 3.4 (2, 5.5)
Variable
 Indicator: female 1.11 (0.53, 2.34)
 Age in years at enrollment 1.02 (0.99, 1.04)
 Indicator: self-declared survivor 0.87 (0.39, 1.97)
 Enrollment site
  Site 2 reference
  Site 3 1.84 (0.72, 4.67)
  Site 4 1.84 (0.73, 4.65)

Data are hazard ratio (95% confidence interval) unless otherwise indicated.

Hazard ratios and confidence intervals were estimated by fitting a Cox proportional hazards model that included a random effect for relationships between survivors and contacts.

Death rates and loss to follow-up

Death rates were significantly higher among HIV+ individuals in both studies (Table 3; Fig 1). In PREVAIL I, the odds ratio for death associated with being HIV+ at baseline was 4.15 (95% CI, 1.87, 8.51), while in PREVAIL III, the odds ratio for death associated with HIV+ at baseline was 10.57 (95% CI, 4.08, 24.34). There were no deaths among the 29 participants identified as HIV positive during follow-up in PREVAIL III. Odds ratios adjusted for sex, age, survivor status and site also revealed significant associations between being HIV+ and death in both studies (PREVAIL I: adjusted OR = 4.87, 95% CI: 2.33, 10.17 and PREVAIL III: adjusted OR = 11.82, 95% CI: 4.93, 28.33). The association was highly significant in analyses that pooled data across studies (adjusted OR = 6.87, 95% CI: 3.78, 12.48).

Table 3. Adjusted hazard ratios and 95% confidence intervals for all-cause mortality by cohort.

Variable PREVAIL I PREVAIL III Combined cohorts
(n = 1500) (n = 3509) (n = 5009)
HR (95% CI) HR (95% CI) HR (95% CI)
Indicator: HIV+ at baseline 3.62 (1.85, 7.08) 13.31 (5.71, 31) 8.21 (4.38, 15.4)
Indicator: female 0.76 (0.45, 1.28) 0.57 (0.31, 1.07) 0.65 (0.42, 1)
Age in years at enrollment 1.06 (1.04, 1.07) 1.06 (1.04, 1.08) 1.06 (1.05, 1.08)
Indicator: self-declared survivor 1.08 (0.56, 2.07) 1.08 (0.57, 2.07)
Enrollment site
 Site 1 ref.
 Site 2 ref. 0.41 (0.22, 0.77)
 Site 3 0.66 (0.27, 1.61) 0.27 (0.11, 0.64)
 Site 4 1.47 (0.72, 2.99) 0.59 (0.3, 1.2)

Abbreviations: HR, hazard ratio; CI, confidence interval; ref., reference level. Hazard ratios and confidence intervals were estimated by fitting Cox proportional hazards models. PREVAIL III models and combined cohort models included a random effect for relationships between survivors and contacts.

Fig 1. Probability of survival over time by baseline HIV status.

Fig 1

In time to event analyses that examined death based on baseline HIV status, the hazard rate for death in PREVAIL I was 3.62 (95% CI: 1.85, 7.08) and 13.31 (95% CI: 5.71, 31.00) in PREVAIL III (Table 3). A hazard rate of 8.21 (95% CI: 4.38, 15.4) was found in pooled time to event analyses. Female gender and younger age were also identified to be protective from death (p<0.05).

One difference between the two studies was the substantial loss to follow-up in PREVAIL III associated with being diagnosed as HIV+ (Table 1; Fig 2). Among those who were HIV+, 13 (17.1%) were lost to follow-up compared to 302 (9.5%) among those who were HIV- (adjusted analyses: p = 0.03, OR = 1.98, 95% CI: 1.07, 3.64).

Fig 2. Probability of loss to follow-up over time for participants in PREVAIL III by HIV status.

Fig 2

Treatment and prognosis

Self-reported cART use was very low in both cohorts. In PREVAIL I, 9 (11.5%, 95% CI: 5.4%, 20.8%) HIV+ participants reported use of cART while in PREVAIL III, 6 (7.9%, 95% CI: 3.0%, 16.4%) reported use of cART at baseline. The proportion in PREVAIL III was significantly lower (p<0.01) than the UNAIDS reported value for Liberia of 19% (15–24%). Many of the participants in PREVAIL III initiated cART after being diagnosed, with 69.7% of participants reporting use during follow-up and 100% reporting continued use after first reported use.

In pooled analyses that adjusted for demographics, d-dimer levels were a factor of 1.5 higher among HIV+ individuals (p = 0.012, Table 4). Hemoglobin was about 10% lower among HIV+ individuals (p<0.001, Table 4). In addition, AST levels were significantly elevated among those with HIV (p = 0.015, Table 4) as was the prothrombin time (p = 0.002, only measured in PREVAIL III, Table 4). While these latter two differences were statistically significant, the magnitude of the differences was small and not suggestive of clinically significant differences that would be relevant for patient care. We did not detect significant differences in ALT (95% CI in HIV+ (9.4, 14.7) and HIV- (10.3, 12.3)) or eGFR (95% CI in HIV+ (106.2, 113.0) and HIV- (106.5, 108.5)).

Table 4. Summary of baseline laboratories between HIV-positive and HIV-negative participants in PREVAIL I and PREVAIL III.

Laboratory PREVAIL I PREVAIL III Combined cohorts
HIV- HIV+ p-value HIV- HIV+ p-value HIV- HIV+ p-value
d-dimer (μg/mL) 0.36 (0.27–0.57) 0.56 (0.4–0.88) 0.066 0.4 (0.3–0.7) 0.7 (0.4–1.1) 0.027 0.4 (0.3–0.6) 0.6 (0.4–1) 0.012
eGFR (mL/min/1.73m2) 107.6 (91.9–124.1) 106.3 (91.5–127.2) 0.943 105.4 (89.3–124.8) 110.4 (98–123.6) 0.073 106 (90.1–124.4) 110.2 (95.3–124.8) 0.223
ALT (U/L) 6 (3–12) 6 (2–11.8) 0.473 6 (3–11) 7 (3–12) 0.222 6 (3–11) 6 (2.2–12) 0.538
AST (U/L) 13 (10–18) 13 (10–19) 0.999 13 (10–17) 15 (11.8–21.2) 0.009 13 (10–17) 14 (11–20) 0.015
Hgb (g/dL) 13.6 (12.5–14.6) 12.1 (10.7–13.4) < 0.001 13.2 (12.1–14.5) 12.1 (10.7–13.1) < 0.001 13.4 (12.2–14.6) 12.1 (10.7–13.3) < 0.001
PT (sec) 13.9 (13.3–14.5) 14.1 (13.6–14.8) 0.002

Data are median value (interquartile range).

Abbreviations: eGFR, estimated glomerular filtration rate; ALT, alanine transaminase; AST, aspartate transaminase; Hgb, hemoglobin; PT, prothrombin time.

Table p-values are from generalized linear models that used an identity link function. PREVAIL I models adjusted for sex and age. PREVAIL III and combined cohort models additionally adjusted for survivor status and enrollment site and used a generalized estimating equations approach to adjust for relationships between survivors and controls.

PREVAIL I participants were categorized as controls in combined cohort models.

Analyses that investigated the impact of d-dimer, hemoglobin and AST levels on all-cause mortality found significant effects for d-dimer (adjusted analyses: p = 0.004, OR = 1.14 for each standard deviation increase, 95% CI: 1.04, 1.24) and hemoglobin (adjusted analyses: p = 0.001, OR = 0.65 for each standard deviation increase, 95% CI: 0.5, 0.84) but failed to detect a significant effect for AST (adjusted analyses: p = 0.52, OR = 1.04 for each standard deviation increase, 95% CI: 0.92, 1.17). Analyses that investigated the potential for an interaction between HIV status and plasma biomarker levels failed to detect a significant interaction for d-dimer but did detect a significant interaction for hemoglobin (p = 0.02 for the interaction, OR = 0.77 among HIV negative participants, 95% CI: 0.57, 1.05 and OR = 0.28 among HIV positive participants, 95% CI: 0.13, 0.6). These results indicate that while d-dimer was predictive of mortality, this association was not restricted to those who were HIV positive, whereas the predictive utility of hemoglobin was restricted to HIV-positive individuals.

Discussion

In this report, we investigated sub-populations from 5,428 individuals enrolled on two PREVAIL research protocols in Liberia. We found an overall prevalence of 3.2% and an annual incidence of 3.3 per thousand per year. Only 9.7% of those who were HIV positive were on ART and overall individuals who were HIV positive were over six times more likely to die. Because participants enrolled in these two non-HIV research studies were not selected based on HIV risk factors, their risk of being HIV positive or acquiring HIV was unlikely to differ from that of the general population in the communities where they lived. However, we note that being HIV positive may increase the likelihood of EBOV infection due to immunosuppression and it may decrease the likelihood of surviving EVD. In fact the proportion of survivors who were HIV+ was lower than the proportion of contacts who were HIV+ but the difference failed to reach statistical significance [13]. This difference in rates may lead to a slight underestimate of prevalence overall. Due to ongoing health complications, which include reduced libido [13], the incidence of HIV among survivors might be less than the incidence in the overall population. We would not expect these potential differences in prevalence and incidence to impact the nature of the associations presented. Prevalence and incidence of HIV (prevalence of 3.1% for women and 1.4% for men and incidence of 3.3 per 1000) were higher in these cohorts compared to 2018 estimates (prevalence of 1.3% and incidence of 0.39 per 1000). We observed that if men and women had been represented equally in these two cohorts, the overall prevalence of HIV at baseline would have been 6.2% (95% CI: 4.8%, 7.5%) in PREVAIL I and 2.2% (95% CI: 1.7%, 2.7%) in PREVAIL III. Both are higher than previous national and county-level estimates [1, 22]. Similarly, based on proportional hazards models that examined the impact of sex, age at enrollment, self-declared survivor status, and enrollment site, the incidence of the disease over 36 months of follow-up was 3.3 cases per 1,000 person-years. This is more than eight times higher than the USAID and UNAIDS estimates for Liberia and the highest for any country in the West African sub-region compared to the UNAIDS 2018 estimates [23, 24].

We also observed that the hazard for death associated with being HIV+ was 8.2 in analyses that combined data across the cohorts. This likely reflected advanced HIV-associated immunodeficiency in untreated participants. This might have been indirectly potentiated by the impact of the EVD outbreak on the fragile healthcare system [5].

One difference between the PREVAIL I and PREVAIL III studies was the substantial preferential loss to follow-up of HIV-infected individuals in PREVAIL III. At the time of study entry, many of these individuals claimed to not know they were HIV+. Perhaps discovery of this and the subsequent emotional impact may have limited further participation. We note that this results in a negative bias in the difference of the death rates between HIV+ and HIV-, such that the odds ratio for death might be even larger than the numbers reported here.

Like Liberia, most countries in western and central Africa have a low prevalence of HIV ranging from 1–3.5% despite a relatively high incidence. This is likely a consequence of high mortality rates resulting partly from weak health systems due to inadequate investment in health [25]. High HIV/AIDS-associated morbidity and mortality is characteristic of a low prevalence epidemic [26]. Liberia is in the process of developing updated guidelines for prevention, testing, and treatment based on current global recommendations. The new treatment and care guidelines are widely expected to institutionalize the global test-and-start treatment approach and adapt current best practices in the care of HIV disease. Better access to treatment will lead to more people living with HIV/AIDS and a higher prevalence. Paradoxically, this will be a sign of improvement.

Consistent with other studies, we found that d-dimer levels were significantly elevated in HIV-positive patients compared with HIV-negative participants and were predictive of mortality. The odds ratio for mortality associated with a standard deviation increase in d-dimer levels was 1.14 (95% CI: 1.04, 1.24), however, this was not specific to HIV-infected individuals. Hemoglobin was lower in HIV+ participants and was also associated with mortality. The odds ratio associated with a standard deviation increase in hemoglobin levels was 0.65 (95% CI: 0.5, 0.84). Unlike d-dimer, while this association was significant in analyses that pooled HIV positive and negative individuals, analyses that did not pool these groups found the association was restricted to HIV positive individuals. Hemoglobin levels have been previously reported to be correlated with clinical progression of HIV and persistent anemia is an independent predictor of mortality [2729]. While the observed differences for AST and prothrombin time were not clinically significant, elevated liver transaminases are frequently reported among HIV-infected individuals [3033], however, these differences were not associated with differences in survival.

The main limitation of our study was that the two protocols were not designed a priori to study HIV/AIDS. Hence, the results should be interpreted with caution. In addition, little HIV-related information beyond what was described herein was collected, such as WHO clinical stage, CD4 counts, plasma HIV viral loads, resistance to antiretroviral drug regimens and the prevalence of HIV-related diseases. Finally, cART use, deaths and hospitalizations are self- or contact-reported.

Despite these limitations, to our knowledge, this is the largest longitudinal study with systematic collection of HIV status, treatment and mortality in research participants in West Africa. It creates opportunities to expand HIV research locally to help address some of the unanswered questions and provide a better understanding of the HIV epidemic in Liberia. More recently, a prospective observational cohort study of people living or newly diagnosed with HIV/AIDS was initiated in Liberia called PREVAIL VIII: A cohort clinical, viral, and immunological monitoring study of people living with retroviral infection in Liberia (HONOR). Data will be collected on a cohort of 3,000 people living with HIV to describe the social, demographic, clinical, immunologic, and virologic characteristics of HIV disease in two of the most affected counties in Liberia. A major benefit for participants of the study is immediate access to plasma viral load and CD4 count measurements and other diagnostic testing to inform clinical care. This kind of research is essential to focus action and investment and reposition the country on its track to achieve the 2030 global targets for HIV elimination as a disease of public health significance.

Acknowledgments

The authors would like to thank the study participants. S.J.M. contributed to study conceptualization and data collection, I.W., A.P., S.B.K., E.S.H. and S.A.M. contributed to study conceptualization, C.V. and G.G. contributed to data analysis, M.B. contributed to data collection, M.C.S. and M.F. contributed to study design and data collection, H.C.L contributed to study design and conceptualization, and C.R. contributed to study conceptualization and data analysis. All coauthors assisted with drafting the paper and/or revision and interpretation of results. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government.

Data Availability

All relevant data are uploaded to Figshare and publicly accessible via the following DOI: 10.6084/m9.figshare.16441671.

Funding Statement

The project was funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health, under Contract No. HHSN261200800001E. This research was supported [in part] by the National Institute of Allergy and Infectious Diseases.

References

  • 1.UNAIDS. UNAIDS Data 2019. Geneva: UNAIDS, 2019 December 4, 2019. Report No.: UNAIDS/JC2959E Contract No.: UNAIDS/JC2959E.
  • 2.National AIDS Control Program. Liberia HIV&AIDS Progress Report 2016. Monrovia: National AIDS Control Program, 2016 April 2017.
  • 3.National AIDS Commission Liberia. National HIV/AIDS Strategic Plan 2015–2022. National AIDS Commission, 2014 July 2014.
  • 4.National AIDS Commission Liberia. National AIDS Commission Annual Report January-December 2016. Monrovia: National AIDS Commission, 2017 February 2017.
  • 5.Parpia AS, Ndeffo-Mbah ML, Wenzel NS, Galvani AP. Effects of the Response to 2014–2015 Ebola Outbreak on Deaths from Malaria, HIV/AIDS, and Tuberculosis, West Africa. Emerg Infect Dis. 2016;22(3):433–41. doi: 10.3201/eid2203.150977 . [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Hira S, Piot P. The counter effects of the Ebola epidemic on control and treatment of HIV/AIDS, tuberculosis, and malaria in West Africa. AIDS. 2016;30(16):2555–9. doi: 10.1097/QAD.0000000000001231 . [DOI] [PubMed] [Google Scholar]
  • 7.Loubet P, Mabileau G, Baysah M, Nuta C, Taylor M, Jusu H, et al. Likely effect of the 2014 Ebola epidemic on HIV care in Liberia. AIDS. 2015;29(17):2347–51. Epub November 2015. doi: 10.1097/QAD.0000000000000821 . [DOI] [PubMed] [Google Scholar]
  • 8.Loubet P, Charpentier C, Visseaux B, Borbor A, Nuta C, Adu E, et al. Prevalence of HIV-1 drug resistance among patients failing first-line ART in Monrovia, Liberia: a cross-sectional study. J Antimicrob Chemother. 2015;70(6):1881–4. Epub February 18, 2015. doi: 10.1093/jac/dkv030 [DOI] [PubMed] [Google Scholar]
  • 9.Nyenswah TG, Kateh F, Bawo L, Massaquoi M, Gbanyan M, Fallah M, et al. Ebola and Its Control in Liberia, 2014–2015. Emerg Infect Dis. 2016;22(2):169–77. Epub 2016/01/27. doi: 10.3201/eid2202.151456 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.UNAIDS. UNAIDS Country Factsheet: Liberia [wbesite]. USA: UNAIDS; 2019. [updated 2019; cited 2019 August 29, 2019]. https://www.unaids.org/en/regionscountries/countries/liberia. [Google Scholar]
  • 11.National AIDS Commission Liberia. Annual Report January-December 2016. NAC Website: February 2017.
  • 12.Kennedy SB, Bolay F, Kieh M, Grandits G, Badio M, Ballou R, et al. Phase 2 Placebo-Controlled Trial of Two Vaccines to Prevent Ebola in Liberia. New England Journal of Medicine. 2017;377(15):1438–47. doi: 10.1056/NEJMoa1614067 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Sneller MC, Reilly C, Badio M, Bishop RJ, Eghrari AO, Moses SJ, et al. A Longitudinal Study of Ebola Sequelae in Liberia. The New England Journal of Medicine. 2019;380(10):924–34. Epub 2019/03/12. doi: 10.1056/NEJMoa1805435 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Diagnostics S. SD BIOLINE HIV/Syphilis Duo (06FK30, 06FK35) leaflet. In: Standard Diagnostic I, editor. Package insert. South Korean: Standard Diagnostic; 2013. [Google Scholar]
  • 15.Taremwa IM, Twelwanike A, Mwambi B, Atuhairwe C. Laboratory assessment of SD Bioline HIV/Syphilis Duo Kit among pregnant women attending antenatal clinic Mayuge Health Center III, East central Uganda. BMC Research Notes. 2019;12(1):238. doi: 10.1186/s13104-019-4272-6 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Omoding D, Katawera V, Siedner M, Boum Y. Evaluation of the SD BIOLINE HIV/syphilis Duo assay at a rural health center in Southwestern Uganda. BMC Research Notes. 2014;7(1):746. doi: 10.1186/1756-0500-7-746 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Liberia Ministry of Health. 2nd EditionNational Standard Therapeutic Guidelines and Essential Medicines List Liberia 2017. Liberia: Ministry of Health; 2017. [Google Scholar]
  • 18.Liang K-Y, Zeger SL. Longitudinal data analysis using generalized linear models. Biometrika. 1986;73(1):13–22. [Google Scholar]
  • 19.Cox DR. Regression Models and Life-Tables. Journal of the Royal Statistical Society: Series B (Methodological). 1972;34(2):187–202. 10.1111/j.2517-6161.1972.tb00899.x. [DOI] [Google Scholar]
  • 20.Hess KR. Assessing time-by-covariate interactions in proportional hazards regression models using cubic spline functions. Statistics in Medicine. 1994;13(10):1045–62. 10.1002/sim.4780131007 [DOI] [PubMed] [Google Scholar]
  • 21.Schoenfeld D. Partial residuals for the proportional hazards regression model. Biometrika. 1982;69(1):239–41. [Google Scholar]
  • 22.WHO-Liberia. WHO Annual Report 2018. Liberia: WHO Liberia Country Office, 2019 2018.
  • 23.UNAIDS. UNAIDS Data 2018. UNAIDS Website: Joint United Nations Program on HIV/AIDS (UNIAIDS), 2019 2018.
  • 24.USAID. International Data & Economic Analysis: Liberia Country Dashboard: USAID; 2019 [updated March 2019; cited 2019 September 22, 2019]. https://idea.usaid.gov/cd/liberia/health.
  • 25.Medicins sans Frontieres. Out of Focus: How Millions of People and West and Central Africa are being left out of the global HIV response. Medicins san Frontiers, 2016 April 2016.
  • 26.Kempton J, Hill A, Levi JA, Heath K, Pozniak A. Most new HIV infections, vertical transmissions and AIDS-related deaths occur in lower-prevalence countries. J Virus Erad. 2019;5(2):92–101. . [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Martí‐Carvajal AJ, Solà I, Peña‐Martí GE, Comunián‐Carrasco G. Treatment for anemia in people with AIDS. Cochrane Database of Systematic Reviews. 2011;(10). doi: 10.1002/14651858.CD004776.pub3 [DOI] [PubMed] [Google Scholar]
  • 28.Obirikorang C, Yeboah FA. Blood haemoglobin measurement as a predictive indicator for the progression of HIV/AIDS in resource-limited setting. J Biomed Sci. 2009;16(1):102-. doi: 10.1186/1423-0127-16-102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Woldeamanuel GG, Wondimu DH. Prevalence of anemia before and after initiation of antiretroviral therapy among HIV infected patients at Black Lion Specialized Hospital, Addis Ababa, Ethiopia: a cross-sectional study. BMC Hematology. 2018;18(1):7. doi: 10.1186/s12878-018-0099-y [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Dusingize JC, Hoover DR, Shi Q, Mutimura E, Rudakemwa E, Ndacyayisenga V, et al. Association of Abnormal Liver Function Parameters with HIV Serostatus and CD4 Count in Antiretroviral-Naive Rwandan Women. AIDS Res Hum Retroviruses. 2015;31(7):723–30. Epub 2015/05/01. doi: 10.1089/AID.2014.0170 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Hamza M, Adamu SA, Maifada Y, Musa B, Nalado AM, Mijinyawa MS, et al. Prevalence and risk factors for hepatotoxicity among patients with HIV/AIDS on highly active antiretroviral therapy in North-Western Nigeria. Sub-Saharan African Journal of Medicine. 2014;1(4):175–84. doi: 10.4103/2384-5147.144727 [DOI] [Google Scholar]
  • 32.Nunez M. Hepatotoxicity of antiretrovirals: incidence, mechanisms and management. J Hepatol. 2006;44(1 Suppl):S132–9. Epub 2005/12/21. doi: 10.1016/j.jhep.2005.11.027 . [DOI] [PubMed] [Google Scholar]
  • 33.Pol S, Lebray P, Vallet-Pichard A. HIV infection and hepatic enzyme abnormalities: intricacies of the pathogenic mechanisms. Clin Infect Dis. 2004;38Suppl 2:S65–72. Epub 2004/02/27. doi: 10.1086/381499 . [DOI] [PubMed] [Google Scholar]

Decision Letter 0

Graciela Andrei

11 Jun 2021

PONE-D-21-03663

High mortality among HIV-infected individuals in a post-Ebola epidemic setting

PLOS ONE

Dear Dr. Reilly,

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.

==============================

  • Please take into account all the pertinent comments from the reviewers to improve the language, presentation of the data, and conclusions of the manuscript.

==============================

Please submit your revised manuscript by Jul 25 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Graciela Andrei

Academic Editor

PLOS ONE

Journal Requirements:

When submitting your revision, we need you to address these additional requirements.

1. 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

2. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

3. Please ensure you have included the registration number for the clinical trial referenced in the manuscript.

4. Thank you for including your ethics statement:  "All protocols received approval from the NIAID Institutional Review Board and the National Research Ethics Board of Liberia.

All participants provided informed consent or consent was provided by caregivers and assents were obtained in accordance with international clinical research ethical norms.".  

Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information.

Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”).

For additional information about PLOS ONE ethical requirements for human subjects research, please refer to http://journals.plos.org/plosone/s/submission-guidelines#loc-human-subjects-research.

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

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

[Note: HTML markup is below. Please do not edit.]

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The statistical methods appear to be high quality, though I've made a few suggestions to improve the language and reporting. The authors are a bit too zealous or cavalier in their conclusions. These are trial data and it's not normally a good assumption that people in a trial will be or behave the same as those outside a trial. I believe these are interesting analyses, but I think more caution should be taken regarding the conclusions and the discussion should be more measured.

1. (Statistical Methods section) Please provide citations for all statistical methods, preferably methodological over software.

2. (line 145) I'm curious why you chose an independence correlation structure over other structures that, potentially, would modeling the correlation between observations over time better.

3. (lines 143, 149, …) Is it the HIV status at baseline? In PREVAIL I, my understanding is HIV testing was only done at baseline. It might be a good idea to make this clear in this section.

4. (lines 151-2) I didn't understand what "covariate-time interaction terms" are. Time is part of the outcome, so I wasn't sure how interactions between covariates and time were included in the linear predictor. Do you mean time-dependent covariates?

5. (lines 294-6) I found this statement a little hard to accept. Maybe for PREVAIL I since the inclusion criteria are pretty minimal. Though, it's noted mostly men enrolled. For PREVAIL III, the sampling appears to be more specialized, so I'm not sure I am willing to go along with the statement that the pooling of these two cohorts is similar to the general population.

6. (line 345) The conclusions drawn and a good portion of the discussion hinge on the belief that the results are comparable to nationwide estimates and, for lack of a better term, "represent" the general population. It's confusing that now the authors are claiming the results from this study about HIV/AIDS should be interpreted with caution.

7. (Figures 1&2) Please include confidence bands on the survival estimates.

Reviewer #2: Your manuscript is well written, and the topic adressed is relevant, especially for resource-limited countries that very rarely conduct longitudinal studies to estimate HIV incidence. You just need to review a few things.

1. Abstract

The paragraph from line 23 to line 26 better justifies the results of this study. However, it is not very much in harmony with the title of the study. In addition, the elements mentioned in this paragraph do not appear very clearly in the general introduction of the body of this manuscrit. As the abstract is the synthesis of the body of the manuscrit, in my opinion, there should be no element in the abstract that isn't in the body of the article. I suggest that you harmonise the justification that appears in the abstract of the study with that which appears in the general introduction to the body of the manuscrit.

2. Introduction

- You have provided enough information on the weaknesses in access to HIV health care services; however, there is little information on the overall organisation of HIV health care services in Liberia. It would be important for you to briefly describe the current organisation of HIV health care provision in Liberia. This would better support the weaknesses that you were willing to address in your manuscript.

- From Line 72 to Line 73 you have mentionned that "Thousands of patients living with HIV were lost to follow-up during and after the Ebola outbreak, with significant declines reported in access to HIV counselling, testing and treatments", but there are not enough statistics to support the claims about the decline in the use of health services during and after the Ebola epidemic. In addition, it would be important for you to report on the proportion of the lost to follow-up patients among the persons which are living with HIV in treatment centres in Liberia.

- The justification for your study that you mention in lines 77 to 81 seems to me to be a bit global, not too specific. It isn't very specific to the title of your manuscript. I suggest you improve this part.

- The objectives of your study go beyond mortality (you talk about prevalence, incidence and mortality). However, the title of your study focuses only on mortality. In my opinion, there is a need to adapt the title of your study

3. Methods

- In lines 124 to 125 you indicate that blood tests were taken from participants who returned for a clinical visit. This was done to test for HIV and Syphilis. In my opinion, it is important to clarify the nature of the tests used and the algorithm for HIV testing and syphilis testing. It is also important to explain a bit more how the management of HIV or syphilis positive cases was carried out.

- In line 116, you mention "1,144 Ebola survivors and 2,784 controls" without explaining the criteria for matching controls to cases. I suggest that you provide more details.

- Were there any lost to follow-up cases who returned to the cohort? If so, I suggest you report this in the methodology; and say how the data for these cases was managed?

4. Results

No comment

5. Discussion

The result: "We found an overall prevalence of 3.2% and an annual incidence of 3.3 per thousand per year" mentioned here, in lines 191 and 192, is not very explicit in the result chapter. In my opinion, these statistics should be mentioned in the result chapter in lines 171 to 179.

**********

6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Niouma Nestor LENO

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2021 Sep 10;16(9):e0257049. doi: 10.1371/journal.pone.0257049.r002

Author response to Decision Letter 0


16 Jul 2021

Response to Reviewers

PONE-D-21-03663

High mortality among HIV-infected individuals in a post-Ebola epidemic setting

PLOS ONE

Journal Requirements: When submitting your revision, we need you to address these additional requirements.

1. 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 [journals.plos.org]

We have checked our manuscript for conformance to these style requirements and believe we are compliant.

2. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

We have revised the reference list to include citations for the statistical methods at the request of one of the reviewers.

3. Please ensure you have included the registration number for the clinical trial referenced in the manuscript.

We now include the clinical trials.gov identifier in the manuscript (page 5 line 104).

4. Thank you for including your ethics statement: "All protocols received approval from the NIAID Institutional Review Board and the National Research Ethics Board of Liberia. All participants provided informed consent or consent was provided by caregivers and assents were obtained in accordance with international clinical research ethical norms.".

Please provide additional details regarding participant consent. In the ethics statement in the Methods and online submission information, please ensure that you have specified what type you obtained (for instance, written or verbal, and if verbal, how it was documented and witnessed). If your study included minors, state whether you obtained consent from parents or guardians. If the need for consent was waived by the ethics committee, please include this information.

We have modified our description of the consent process to describe the type: “All participants provided written informed consent or written informed consent was provided by parents or guardians and written assents were obtained in accordance with international clinical research ethical norms.” This is on page 5 lines 99-102.

Once you have amended this/these statement(s) in the Methods section of the manuscript, please add the same text to the “Ethics Statement” field of the submission form (via “Edit Submission”).

For additional information about PLOS ONE ethical requirements for human subjects research, please refer to

http://journals.plos.org/plosone/s/submission-guidelines#loc-human-subjects-research [journals.plos.org].

5. We note that the grant information you provided in the “Funding Information” and “Financial Disclosure” sections do not match. 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.

We have addressed this in the resubmission.

Reviewer #1: The statistical methods appear to be high quality, though I've made a few suggestions to improve the language and reporting. The authors are a bit too zealous or cavalier in their conclusions. These are trial data and it's not normally a good assumption that people in a trial will be or behave the same as those outside a trial. I believe these are interesting analyses, but I think more caution should be taken regarding the conclusions and the discussion should be more measured.

1. (Statistical Methods section) Please provide citations for all statistical methods, preferably methodological over software.

Thank you for reviewing our manuscript. As suggested, we have added 4 references to the statistical methods section (page 8).

2. (line 145) I'm curious why you chose an independence correlation structure over other structures that, potentially, would modeling the correlation between observations over time better.

We used an independence correlation structure because it is relatively robust to the true correlation structure. While there may be some loss of efficiency, there is less of a danger of a major loss of efficiency compared to using an incorrect correlation structure that deviates from independence. This is demonstrated in the Liang and Zeger paper now referenced in this section.

3. (lines 143, 149,) Is it the HIV status at baseline? In PREVAIL I, my understanding is HIV testing was only done at baseline. It might be a good idea to make this clear in this section.

We agree and have modified the text to be more explicit about baseline and incident HIV status (page 7-8 line 159-160).

4. (lines 151-2) I didn't understand what "covariate-time interaction terms" are. Time is part of the outcome, so I wasn't sure how interactions between covariates and time were included in the linear predictor. Do you mean time-dependent covariates?

Thank you for making this point. The unspecified baseline hazard function in the Cox model is potentially (and generally assumed to be) dependent on time. By including terms that depend on time and the covariate, one can evaluate if the impact of the covariate acts in a manner that is consistent with the proportional hazards assumption. We have provided a reference (i.e., Hess) that describes how to do this using cubic splines (page 8 line 170).

5. (lines 294-6) I found this statement a little hard to accept. Maybe for PREVAIL I since the inclusion criteria are pretty minimal. Though, it's noted mostly men enrolled. For PREVAIL III, the sampling appears to be more specialized, so I'm not sure I am willing to go along with the statement that the pooling of these two cohorts is similar to the general population.

You raise an important point. We agree that the broad inclusion criteria of PREVAIL I make it likely that those study participants were likely similar to the community from which they came, with the exception that men were over-represented. For this reason, we have been careful to stratify or control for gender in the summaries we compute. The entry criteria for PREVAIL III were either being an Ebola survivor or having a contact who is an Ebola survivor. The contacts were drawn from the same communities, and mostly from the same families, as Ebola survivors so the survivors and contacts should be similar to one another with regard to many features, including HIV risk factors. Thus, the similarity of PREVAIL III participants to the larger community largely comes down to the similarity of Ebola survivors to the larger population. There are likely individual characteristics that make it more or less likely that one will contract and survive an Ebola infection. These are likely related to occupation and overall health status and potentially includes HIV infection (and so HIV risk factors). This would make the population of PREVAIL III participants less likely to be HIV positive, so there is some potential for underestimation of prevalence and incidence of HIV. However, we don’t think this would alter the nature of the association between HIV status and other factors explored (e.g., d-dimer). We have altered the discussion to make these points (pages 17-18 lines 330-338).

6. (line 345) The conclusions drawn and a good portion of the discussion hinge on the belief that the results are comparable to nationwide estimates and, for lack of a better term, "represent" the general population. It's confusing that now the authors are claiming the results from this study about HIV/AIDS should be interpreted with caution.

We apologize for the confusion. The advice to interpret the results with caution at the referenced point in the manuscript is based on the fact that this is a secondary analysis of data generated to address different sets of questions than those investigated here. It is not based on concerns about the ability of these data to represent the general population. As noted in this reviewer’s previous comments and our response, there is some concern regarding the “representativeness” of these cohorts and as noted we now note this and provide some supporting arguments for this point.

7. (Figures 1&2) Please include confidence bands on the survival estimates.

This is a good suggestion and we have included these in the resubmission.

Reviewer #2: Your manuscript is well written, and the topic adressed is relevant, especially for resource-limited countries that very rarely conduct longitudinal studies to estimate HIV incidence. You just need to review a few things.

1. Abstract

The paragraph from line 23 to line 26 better justifies the results of this study. However, it is not very much in harmony with the title of the study. In addition, the elements mentioned in this paragraph do not appear very clearly in the general introduction of the body of this manuscrit. As the abstract is the synthesis of the body of the manuscrit, in my opinion, there should be no element in the abstract that isn't in the body of the article. I suggest that you harmonise the justification that appears in the abstract of the study with that which appears in the general introduction to the body of the manuscrit.

Thank you for reviewing our manuscript and making this valuable point. We have expanded the introduction to ensure these points are incorporated (page 4-5 lines 85-92).

2. Introduction

- You have provided enough information on the weaknesses in access to HIV health care services; however, there is little information on the overall organisation of HIV health care services in Liberia. It would be important for you to briefly describe the current organisation of HIV health care provision in Liberia. This would better support the weaknesses that you were willing to address in your manuscript.

Thank you for this comment. Although a description of the overall organization of HIV care services in Liberia would be quite challenging to summarize briefly, we have made some revisions to the Introduction that now includes efforts made by the Liberian government to better organize services for people living with HIV infection (page 3 lines 63-67).

- From Line 72 to Line 73 you have mentionned that "Thousands of patients living with HIV were lost to follow-up during and after the Ebola outbreak, with significant declines reported in access to HIV counselling, testing and treatments", but there are not enough statistics to support the claims about the decline in the use of health services during and after the Ebola epidemic. In addition, it would be important for you to report on the proportion of the lost to follow-up patients among the persons which are living with HIV in treatment centres in Liberia.

The reviewer makes a fair point here. We have scaled this back some in the Introduction to account for the lack of robust numbers. As such, reporting the proportion of persons living with HIV who were lost to follow up in treatment centers in Liberia is not something that can be reliably done beyond what is presented in the cited references. These changes are on page 4 lines 75-78.

- The justification for your study that you mention in lines 77 to 81 seems to me to be a bit global, not too specific. It isn't very specific to the title of your manuscript. I suggest you improve this part.

Our goal was to summarize the status of persons living with HIV in Liberia during and shortly after the 2014 Ebola epidemic with data obtained from 2 studies of Ebola. In the portion of the manuscript referenced here, we note that this was motivated by a lack of HIV services and accurate reporting resulting from the breakdown in the health care system due to the Ebola epidemic. We have altered the title to better reflect the results presented in this manuscript. We have also updated the 90-90-90 goal to the current 2030 95-95-95 goal.

- The objectives of your study go beyond mortality (you talk about prevalence, incidence and mortality). However, the title of your study focuses only on mortality. In my opinion, there is a need to adapt the title of your study

This is a good point and we have modified the title to better reflect the content of the manuscript. Thanks for this suggestion.

3. Methods

- In lines 124 to 125 you indicate that blood tests were taken from participants who returned for a clinical visit. This was done to test for HIV and Syphilis. In my opinion, it is important to clarify the nature of the tests used and the algorithm for HIV testing and syphilis testing. It is also important to explain a bit more how the management of HIV or syphilis positive cases was carried out.

We agree and we now provide this information. The additional information has been presented on page 6-7 lines 133-139 and page 7 lines 145-149.

- In line 116, you mention "1,144 Ebola survivors and 2,784 controls" without explaining the criteria for matching controls to cases. I suggest that you provide more details.

We provided a description of how cases and controls were matched: “To qualify as a contact, one needed to be selected by a survivor as someone who had close contact with the survivor during the survivor’s acute illness or had sexual contact after acute illness.” This is now on page 6 lines 127-129.

- Were there any lost to follow-up cases who returned to the cohort? If so, I suggest you report this in the methodology; and say how the data for these cases was managed?

Some participants missed visits, but they were not withdrawn from the study due to missed visits.

4. Results

No comment

5. Discussion

The result: "We found an overall prevalence of 3.2% and an annual incidence of 3.3 per thousand per year" mentioned here, in lines 191 and 192, is not very explicit in the result chapter. In my opinion, these statistics should be mentioned in the result chapter in lines 171 to 179.

We now include the prevalence estimate in the text at the location suggested by the reviewer. The incidence estimate is given on page 11 lines 216-218 in the results section, not just in the discussion.

Attachment

Submitted filename: Response to Reviewers.docx

Decision Letter 1

Graciela Andrei

23 Aug 2021

The impact of the 2014 Ebola epidemic on HIV disease burden and outcomes in Liberia West Africa

PONE-D-21-03663R1

Dear Dr. Reilly,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. 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.

Kind regards,

Graciela Andrei

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: (No Response)

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: After reading the entire new version of your manuscript, I find that it has taken into account almost all of my previous comments.

From my side, it's okay for publication.

Thank you

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Niouma Nestor LENO

Acceptance letter

Graciela Andrei

2 Sep 2021

PONE-D-21-03663R1

The impact of the 2014 Ebola epidemic on HIV disease burden and outcomes in Liberia West Africa

Dear Dr. Reilly:

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.

If we can help with anything else, please email us at plosone@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Graciela Andrei

Academic Editor

PLOS ONE

Associated Data

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

    Supplementary Materials

    Attachment

    Submitted filename: Response to Reviewers.docx

    Data Availability Statement

    All relevant data are uploaded to Figshare and publicly accessible via the following DOI: 10.6084/m9.figshare.16441671.


    Articles from PLoS ONE are provided here courtesy of PLOS

    RESOURCES