COD data in many LMICs are obtained from clinical studies or verbal autopsies. Evidence has shown that there is discordance between clinical diagnoses and postmortem diagnoses, with many missed OIs in clinical diagnoses ⁶ . Postmortem causes of death studies are therefore integral to establishing the correct diagnoses. This study is one of the first systematic reviews of autopsy findings in the pre- and post-ART eras in sub-Saharan Africa (SSA) focusing on specific AIDS-defining illnesses as a cause of death and synthesized quantitatively with meta-analyses. In this study, we review autopsy findings in SSA to observe whether the prevalence of 14 AIDS-defining illnesses changed from the pre-ART era to the post-ART era.

This systematic review and meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines ( Extended data, Supplementary Table 1) ^{8, 9} .

Participants and comparators. Participants were HIV-positive deceased individuals in SSA in the post-ART era who had a complete, partial, or minimally invasive autopsy performed to determine their COD. Comparators were HIV-positive deceased individuals in SSA in the pre-ART era who had a complete, partial, or minimally invasive autopsy done to determine the COD ⁶ . Study populations were categorized into three age groups: adult (15 years or older), child (under 15 years), or unknown (unspecified or mixed age groups).

Interventions. Definitions for complete, partial, and minimally invasive autopsies were taken from Cox et al. ⁶ . A complete autopsy refers to a macro- and microscopic assessment of all thoracic and abdominal organs and the brain. Partial autopsies are defined as the micro- or macro-sampling and examination of a singular organ or multiple organs. Minimally invasive autopsies included guided or unguided percutaneous needle autopsies, as well as investigations using endoscopic or laparoscopic techniques.

Context/setting. The deceased were from any sub-Saharan African country where the death had occurred in a hospital or community setting.

Outcomes. The outcomes were the prevalences of 14 AIDS-defining illnesses in adults and mixed adult and child cases divided into three categories, namely:

Report characteristics. Peer-reviewed studies and gray literature were deemed eligible for inclusion if they: 1) were published between January 1, 1990 and September 30, 2018 inclusive; 2) had full text available in English or French; 3) were conducted within sub-Saharan Africa; 4) were original studies reporting results of complete, partial, or minimally invasive autopsies; 5) listed the year(s) in which the autopsies were conducted; and 6) reported autopsy findings for a minimum of 8 HIV-positive cases.

Original studies reporting verbal autopsy results or only clinical causes of death (without postmortem autopsy findings) were excluded. Sub-studies reporting selected results from a previously published large-scale autopsy study were also excluded. If two or more studies utilized an identical group of participants with overlapping or similar study periods, the study that reported the most complete and clearly articulated pathogen and disease prevalence was retained. Studies that recruited subjects with a particular diagnosis were excluded, if they only presented pathology findings related to that specific disease category. Refer to Figure 1 for the process.

The search strategy was developed by an information specialist at St. Michael’s Hospital Health Sciences Library located in Toronto, Canada, and was run on the following electronic databases: Medline, CINAHL, Evidence Based Medicine, EMBASE, Scopus, and the Web of Science. Search terms for the electronic databases are outlined in Extended data, Supplementary Table 2 ⁹ . This search yielded 1,346 relevant articles up to and including December 31, 2016. In October 2018, the search was updated to include the International AIDS Society conferences, and to extend the review time period up to and including September 30, 2018. All available abstracts from the Conference on Retroviruses and Opportunistic Infections (CROI) were also reviewed for inclusion eligibility.

The titles and abstracts of all articles found were screened by two reviewers for duplicates or relevance. Both reviewers independently conducted the full-text screening and data extraction; if an agreement could not be reached, a third reviewer adjudicated.

A data extraction sheet was developed and piloted by the study authors extracting the following information from the included studies: country, years of data collection, the number of HIV-positive patients, the number of patients that received ART, age category of HIV-positive patients, type of autopsy conducted (complete, partial, or minimally invasive), and the autopsy-determined pathogens and diseases listed as outcomes above ^{10, 11} .

If multiple pathogens or diseases were reported within each of these 14 AIDS-defining illnesses in the original study, the counts were not aggregated; instead, the pathogen or disease with the highest prevalence was recorded in that category unless otherwise specified above, in order to prevent over-reporting the number of patients with that specific pathogen or disease. For example, if a more potent pathogen or disease was reported, it was recorded as the cause of death even if there were other infectious pathogens or diseases. The most potent pathogen or disease was determined to be the disease most likely causing the death ¹² .

If pathogens and diseases were not reported by ART status in the source study, the study was categorized as occurring within the pre- or post-ART era by reviewing the number of individuals who received ART in each study or using World Bank ART country coverage estimates ¹³ . If the number of study subjects who received ART was one or more, the study was classified as taking place within the post-ART era. If the ART status of none of the study subjects were reported, and the World Bank ART coverage estimate was lower than 30% during the year(s) of study data collection, the study was considered to be pre-ART.

Each full-text study and conference abstract was evaluated for reporting quality according to items listed in the STROBE (STrengthening the Reporting of OBservational studies in Epidemiology) statement for reporting observational studies ^{14, 15} . The items on the STROBE checklist include study participant numbers, bias, variables, and analysis. One full point was given for full completion of each item, a half-point was given for partial completion, and zero points were given for poorly explained items or items that were not addressed. Some items were found to be not applicable for all studies, and were marked as such.

To measure whether there is a difference in the prevalence of AIDS-defining illnesses in autopsy samples pre- and post-ART, a random effects meta-analysis of single proportions with binomial exact 95% confidence intervals was conducted for each AIDS-defining illness by age group ^{16, 17} . The Freeman-Tukey double arcsine transformation was used to stabilize the proportions. Heterogeneity was quantified using the I ² statistic for each of the groups of studies ^{18, 19} . All analyses were conducted in Stata version 14.2 using the metaprop command ^{16, 20} . For AIDS-defining illnesses with data from two or more studies in each of the pre- and post-ART eras, forest plots were generated to display the prevalence of 14 AIDS-defining illnesses given as the cause of death at autopsy. Study prevalence estimates were separated by age category (adult and mixed) and stratified by pre- and post-ART eras.

Two funnel plots, one for adult and mixed studies and one for adult studies only, were generated to assess risk of publication bias in each age group.

Figure 1 describes the stepwise process of study selection. A total of 1936 records were found in the original search. Two independent reviewers removed the duplicates, resulting in 1827 studies retained. Titles and abstracts were screened, resulting in 69 articles and conference abstracts. A review of the full-text articles and conference abstracts resulted in 33 articles included in the quantitative synthesis ( Figure 1), including 30 articles ^{7, 12, 21– 48} and 3 conference abstracts ^{49– 51} . Other articles and abstracts were excluded because insufficient autopsies in HIV-positive individuals were performed, the autopsies were not reported by HIV status, or reporting on outcomes was duplicated for the same study population.

Refer to Extended data, Supplementary Table 3 ⁹ for study characteristics of the 33 included publications. There were 16 cross-sectional, 12 prospective cohort, 4 retrospective cohort, and 1 mixed study design. The majority of the studies were conducted in South Africa (9 studies) and the Ivory Coast (4 studies), with the remainder in eastern SSA. Years of study data collection ranged from 1989 to 2014. Of the studies, 28 were hospital-based and the rest were community-based, of which two were conducted in pathology departments and two others in treatment centers at mines in South Africa. Sample sizes ranged from 20 to 3725.

Study participants were individuals who died either in a hospital or community setting and were then transferred to hospital for an autopsy. All participants were HIV-positive and from SSA. Interventions in the studies were complete, partial, or minimally invasive autopsies, with additional interventions including radiology, ELISA, and Western blot HIV testing. Study outcomes were COD prevalence of the 14 AIDS-defining illnesses mentioned above.

The 2014 study by Field et al. was the only article that reported autopsy results by HIV-positive patients receiving ART versus those not on ART, and is reported in our analyses in both pre- and post-ART eras ³⁶ . All other included articles and abstracts were classified as pre- or post-ART according to study criteria.

The 30 full-text studies generally had high reporting quality with respect to the STROBE guidelines for observational studies ( Extended data, Supplementary Table 4a) ^{9, 14} . Introduction sections, including background and objectives, and Results sections were generally complete across all included studies. Due to the nature of most autopsy studies, 24/30 included studies did not report on “outcome data” and so were graded “not applicable” for this item, instead reporting on main results. The Methods and Discussion sections contained much more variability. In particular, definitions were frequently not explicit or were missing for study design (16/30 studies) and included variables (13/30 studies). In the Discussion section, key results and interpretation were complete for 29/30 studies. However, limitations and generalizability of the studies were less well addressed, with 17/30 studies lacking explicit reference to one or both of these areas. In total, 19 of the 30 studies declared a funding source.

Of the three conference abstracts, two had high levels of reporting according to the corresponding STROBE checklist (Supplementary Table 4b) ^{9, 15} . For all three abstracts, study titles and authors were always provided, and results sections, including participant count, main results, and conclusions, were complete. The methods sections of the abstracts were more variable with regards to reporting items, as was clear definition of study objectives.

Refer to the Extended data, Supplementary material Table 5 ⁹ for outcome data of the individual studies.

Meta-analyses were conducted for the adult and mixed age categories for all 14 AIDS-defining illnesses, and selected results are presented here as prevalence estimates with 95% confidence intervals. Nineteen studies conducted autopsies on HIV-positive adults ^{12, 21– 36, 49} and 9 on HIV-positive children ^{37– 45} . A ‘mixed group’ refers to six studies that did not report results by age ^{7, 46– 48, 50, 51} . Only 1 of the 9 eligible child studies was conducted in the post-ART era. As a result, no meta-analysis could be conducted for this age category.

Table 1 shows the estimated overall prevalence of AIDS-defining illnesses when examining the meta-analyses for all deaths according to categories. Figure 2– Figure 7 report on the studies and trends per AIDS-defining illness as reported by 18 studies (pre-ART: 13 studies; post-ART: 6 studies; pre- and post-ART: 1 study).

Infectious diseases. The estimated overall prevalence of TB as a cause of death in adults during the pre-ART era was 27.9% (95% CI 19.9-36.5%), and rose to 40.8% (95% CI 29.6-52.4%) in the post-ART era ( Figure 2). The overall TB prevalence in pre-ART mixed groups was approximately 24.1% (95% CI 11.5-39.3%), and also increased in the post-ART era to 29.5% (95% CI 19.8-40.2%; Figure 3).

The overall prevalence of Pneumocystis pneumonia as a cause of death during the pre-ART era in adults was 8.7% (95% CI 5.7-12.1%), while the overall prevalence in the post-ART era decreased to 2.5% (95% CI 0.9-4.7%; Extended data, Supplementary Figure 1) ⁹ . In adults, the overall prevalence of other causes of pneumonia as a cause of death in the pre-ART era was 24.2% (95% CI 19.2-28.8%), while the overall prevalence in the post-ART era was lower at 21.4% (95% CI 11.2-33.7%; Extended data, Supplementary Figure 2) ⁹ . For the mixed population group, the overall prevalence of other causes of pneumonia as a cause of death in the pre-ART era was 16.3% (95% CI 6.3-29.4%), while the overall prevalence in the post-ART era was lower, at 6.5% (95% CI 1.8-13.4%; Extended data, Supplementary Figure 3) ⁹ .

In adults, the observed overall prevalence of cryptococcal meningitis as a cause of death was 6.8% (95% CI 3.1-11.5%) pre-ART, and 5.8% (95% CI 0.7-14.2%) post-ART ( Extended data, Supplementary Figure 4) ⁹ . In the mixed group, overall prevalence of cryptococcal meningitis in the pre-ART era was 7.6% (95% CI 2.8-14.1%), and increased to 9.3% (95% CI 3.5-17.0%; Extended data, Supplementary Figure 5) ⁹ . The overall prevalence of other meningitis in adults reported in the pre- and post-ART era were 13.8% (95% CI 5.5-25.0%) and 5.2% (95% CI 1.7-10.3%), respectively ( Extended data, Supplementary Figure 6) ⁹ .

The overall cytomegalovirus prevalence in pre-ART adults was 5.9% (95% CI 1.8-11.8%), while the estimated overall prevalence in the post-ART era for adults was 2.9%, (95% CI 0.9-5.7%; Extended data, Supplementary Figure 7) ⁹ .

Liver infection in adult deaths decreased from 13.8% (95% CI 0.6-38.0%) pre-ART to 7.7% (95% CI 1.4-17.6%) post-ART ( Extended data, Supplementary Figure 8) ⁹ . These included HIV co-infections with hepatitis B and/or C, as well as pyogenic abscess.

Cancers. There was minimal increase in estimated difference in overall prevalence for Kaposi’s sarcoma in adults, with pre-ART value 2.9% (95% CI 1.0-5.5%) and post-ART value 4.6% (95% CI 2.3-7.5%) observed ( Figure 4).

For non-Hodgkin’s lymphoma, the overall prevalence in adult deaths in pre-ART was 2.4% (95% CI 1.2-3.8%), and 3.8% (95% CI 0.6-8.9%) in the post-ART era ( Figure 5). For other/unspecified cancers in adult studies, the overall prevalence for pre-ART era was 2.1% (95% CI 1.1-3.4%), and the post-ART era was 3.9% (95% CI 1.8-6.5%; Extended data, Supplementary Figure 9) ⁹ .

Other diseases. The overall prevalence of CVD/cerebrovascular diseases in adults in the pre-ART era was 4.9% (95% CI 1.9-8.9%), and 5.0% (95% CI 2.7-7.9%) in the post-ART era ( Extended data, Supplementary Figure 10) ⁹ ; prevalence of CVD/cerebrovascular diseases was similarly stable in the mixed population from the pre- to post-ART time period ( Extended data, Supplementary Figure 11) ⁹ . Liver disease in adult deaths increased from 9.1% (95% CI 1.8-20.6%) in the pre-ART era to 19.4% (95% CI 12.3-27.7%) in the post-ART era ( Figure 6). These included cirrhosis, steatosis, hepatocellular cancer, and portal thrombosis. For kidney disease, the overall prevalence reported in adults for the pre-ART era was 14.7% (95% CI 2.3-34.5%), and 5.8% (95% CI 0.9-13.6%) in the post-ART era ( Figure 7).

Two funnel plots explore publication bias in the studies for the adult ( Extended data, Supplementary Figure 12) ⁹ and mixed population groups ( Extended data, Supplementary Figure 13) ⁹ reporting AIDS-defining causes of death of HIV-infected individuals. There seems to be no apparent publication bias, i.e. that small studies are only published if they show a significant effect. This makes sense as most of these studies did not explicitly target the effects of ART (pre vs post) themselves.

To our knowledge, this is the first systematic literature review and meta-analysis of AIDS-defining illnesses as diagnosed by autopsy studies in the pre- and post-ART eras in HIV-infected adults and children in SSA. The dearth of autopsy studies in SSA available in the post-ART era makes it challenging to assess differences in the prevalence of AIDS-defining illnesses pre- and post-ART, especially in children.

There was a reduction in most OIs post-ART with the notable exception of TB, which showed a 13% increase in prevalence in adults and a 5% increase in the mixed population group (consisting of adults and children). A systematic review by Gupta et al. showed that, in resource-limited settings, TB prevalence decreased by more than 10% in HIV-infected children but increased in HIV-infected adults post-ART ⁵² . This could account for why the increase in the mixed population is not as high as in the adult population for our review. Studies included in our review contained insufficient data for a child population meta-analysis to confirm this. Another review by Low et al. showed a reduction in all other OIs in the first 12 months of ART, except for TB ⁵³ . While ART improves overall outcomes in patients with HIV and TB co-infection, the mortality rate during the first two months of TB treatment is not reduced by ART ^{13, 54} , and may be driven by other explanations such as delayed initiation of treatment in very advanced cases, or immune reconstitution inflammatory syndrome (IRIS). In the study by Wong et al., TB was the leading cause of death regardless of ART status and was particularly high in subjects dying in the first 3 months of ART ³² . Gupta et al. also conducted additional meta-regression analyses that indicated a positive association between prevalence of TB at autopsy and national population TB prevalence ⁵² . This would be relevant for eight of the studies included in this review which used data from South Africa, where TB prevalence rates are among the highest in the world ⁵⁵ .

Evolving TB diagnostics may also contribute to the increase in TB prevalence in the adult population. During the pre-ART era, TB diagnostics largely relied on sputum samples being tested for the presence of acid-fast bacilli, a procedure with typically very low sensitivity, especially in the context of HIV co-infection ^{56– 59} . More recently, nucleic acid amplification TB diagnostic modalities such as the Xpert MTB/RIF assay were rolled out in many SSA settings during the post-ART era and resulted in significantly higher sensitivity compared to sputum smear microscopy ⁶⁰ . The increase in TB in adults may additionally be linked to accelerated decreases in mortality from other causes of death. As autopsy studies by definition are limited to deceased individuals, changes in specific causes of death are always relative to other causes of death.

The World Health Organization (WHO) has recommended TB/HIV collaborative activities in high HIV prevalence settings to combat death from TB. Integrated TB/HIV centers and programs promote testing for TB in HIV-positive patients who are on ART. However, there are challenges integrating HIV and TB programs, which may be culminating in poor patient outcomes in those with co-infection ⁶¹ .

The study by Low et al. also showed significant decreases in oral candidiasis, PCP, and toxoplasmosis post-ART ⁵³ . We did not look at oral candidiasis, and our toxoplasmosis study numbers were negligible. However, the PCP findings of the study by Low et al. were consistent with the decrease in prevalence indicated by our analysis. Even in the pre-ART era, the WHO recommended cotrimoxazole (CTX) prophylaxis for people infected with HIV to prevent OIs. CTX, a combination of two antimicrobial drugs, is active against a range of bacterial, fungal, and parasitic infections that reduces morbidity and mortality in people living with HIV. CTX prophylaxis and increase in coverage could have contributed to this decrease.

Prevalence of all cancers in the study, including non-Hodgkin’s lymphoma and Kaposi’s sarcoma, increased modestly from the pre-ART era to the post-ART era. Kaposi’s sarcoma remains the second most frequent tumor in HIV-infected people globally and has become the most common cancer in SSA ⁶² . It has also been reported as occurring in patients with well-controlled HIV infection and CD4+ T cell count >200 cells/μl, and patients with Kaposi’s sarcoma on ART typically have a less aggressive presentation when compared to those not receiving ART. In a 2012 review, Semeere et al. looked at the impact of ART on Kaposi’s sarcoma, and found only one population-level study report in an LMIC, which estimated an increase in prevalence from 2007 to 2010 in Malawi compared to earlier periods ⁶³ . However, individual patient-level effectiveness of ART on Kaposi’s sarcoma incidence in LMIC is comparable to high-income countries. Conclusions of this study were that more studies are required in order to produce evidence in LMICs. Non-Hodgkin’s lymphoma incidence tends to be less affected by the use of ART, which could account for the observed increase in our review ⁶⁴ .

In high-income countries where ART has been available for longer, availability of ART markedly improved survival of people living with HIV ⁶⁵ . However, there is a consequent increased risk of developing non-communicable diseases (NCDs), with common causes of death including liver disease, CVD, and non-AIDS malignancies ^{66– 68} . This risk increases with age and can be related to HIV and use of ART ⁶⁹ . It has been estimated that liver disease accounts for 13–18% of all-cause mortality in people infected with HIV in the post-ART era ⁶⁸ . The observed increase in liver disease in our review is consistent with this finding. Liver disease is also an independent risk factor for CVD. Our findings in this review were that CVD/cerebrovascular diseases showed negligible change in prevalence. This is inconsistent with findings of post-ART populations in high-income countries where CVD including heart failure in HIV-infected people is one of the leading causes of death, and is predicted to increase globally in the next 15 years ^{70, 71} . In most LMICs, NCDs are managed episodically, which results in patients being at risk for long-term complications and death ⁶⁹ . In high-income countries where NCD patients have access to appropriate long-term care and treatment, there is a reduction in morbidity and mortality ⁷² . As a result, improved NCD data in ageing HIV-infected individuals receiving ART is needed to inform cost-effective solutions for health systems in LMICs to create diagnostic and treatment processes inclusive of both HIV and NCDs.

In our study, we found a notable decrease in kidney disease incidence (almost three times lower) in the post-ART era. The reason for this could possibly be because most deaths in the included studies were hospital-based and there could have been other underlying causes of death. It is known that the risk of acute and chronic kidney disease remains higher in people infected with HIV when compared to the general population ⁷³ . Acute kidney disease is associated with an increased risk of heart failure, CVD, and end-stage renal disease, which ultimately leads to mortality. However, widespread highly effective ART has attenuated HIV-associated nephropathy as a form of chronic kidney disease (CKD), characterizing CKD in people infected with HIV as being related to diabetes or hypertension ⁷³ . Also worth mentioning is that partial autopsies and minimally invasive tissue samples do not always sample kidney tissue. As usage of these two techniques increases in the absence of complete autopsies, mortality due to kidney diseases may be diagnosed less frequently. More research is warranted to further explore the relationship between HIV infection and kidney disease in the post-ART era.

It is worth noting that, over the last decade, academic journals have begun to improve reporting quality of studies by requesting checklists such as STROBE along with new submissions. Many of the studies included in this review predate reporting quality guidelines like the STROBE checklist that are frequently used today. It is therefore unsurprising that many of the more recent studies included in this review have higher reporting quality by current standards than do the studies from the 1990s or early 2000s. This is especially clear for particular STROBE checklist items, such as indication of study design in the study title, as well as declaration of funding source.

All data underlying the results are available as part of the article and no additional source data are required.

Open Science Framework: AIDS-defining causes of death from autopsy findings for HIV-positive individuals in sub-Saharan Africa in the pre- and post-ART era: A systematic review and meta-analyses.

https://doi.org/10.17605/OSF.IO/3UR5F ⁹ .

This project contains the following extended data:

Open Science Framework: PRISMA checklist for “AIDS-defining causes of death from autopsy findings for HIV-positive individuals in sub-Saharan Africa in the pre- and post-ART era: A systematic review and meta-analyses. https://doi.org/10.17605/OSF.IO/3UR5F ⁹ .

Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).