Modeling COVID-19 daily cases in Senegal using a generalized Waring regression model

The rapid spread of the COVID-19 pandemic has triggered substantial economic and social disruptions worldwide. The number of infection-induced deaths in Senegal in particular and West Africa in general are minimal when compared with the rest of the world. We use count regression (statistical) models such as the generalized Waring regression model to forecast the daily confirmed COVID-19 cases in Senegal. The generalized Waring regression model has an advantage over other models such as the negative binomial regression model because it considers factors that cannot be observed or measured, but that are known to affect the number of daily COVID-19 cases. Results from this study reveal that the generalized Waring regression model fits the data better than most of the usual count regression models, and could better explain some of the intrinsic characteristics of the disease dynamics.

Stigma and healthcare access among men who have sex with men and transgender women who have sex with men in Senegal

Objectives:

Cisgender gay, bisexual, and other men who have sex with men and transgender women experience HIV incidence disparities in Senegal. These analyses determined how depression and different stigma mechanisms related to sexual behavior are associated with healthcare access, sexually transmitted infection testing, and HIV testing among cisgender gay, bisexual, and other men who have sex with men and transgender women across three cities in western Senegal.

Methods:

Logistic regression assessed the relationship of three stigma scales (stigma from family and friends, anticipated healthcare stigma, and general social stigma) and depression with these outcomes.

Results:

Depression and stigma were not associated with healthcare access, sexually transmitted infection testing, or HIV testing. However, individuals who had disclosed their sexual identity to a medical provider were more likely to test for HIV.

Conclusions:

Sexual behavior stigma experienced by cisgender gay, bisexual, and other men who have sex with men and trans women in Senegal may not limit access to routine healthcare, but may limit disclosure of sexual orientation and practices, limiting access to appropriate HIV prevention services.

Long-term Experience and Outcomes of Programmatic Antiretroviral Therapy for Human Immunodeficiency Virus Type 2 Infection in Senegal, West Africa

BACKGROUND

Programmatic treatment outcome data for people living with human immunodeficiency virus type 2 (HIV-2) in West Africa, where the virus is most prevalent, are scarce.

METHODS

Adults with HIV-2 initiating or receiving antiretroviral therapy (ART) through the Senegalese national AIDS program were invited to participate in this prospective, longitudinal observational cohort study. We analyzed HIV-2 viral loads, CD4 cell counts, antiretroviral drug resistance, loss to follow-up, and mortality. We also examined changes in treatment guidelines over time and assessed progress toward the Joint United Nations Programme on HIV/AIDS (UNAIDS) 90-90-90 targets for HIV-2.

RESULTS

We enrolled 291 participants at 2 sites for 926.0 person-years of follow-up over 13 years. Median follow-up time was 2.2 years per participant. There were 21 deaths reported (7.2%), and 117 individuals (40.2%) were lost to follow-up, including 43 (14.7%) who had an initial visit but never returned for follow-up. CD4 counts and HIV-2 viral suppression (< 50 copies/mL) at enrollment increased over calendar time. Over the study period, 76.7% of plasma viral loads for participants receiving ART were suppressed, and median CD4 gain was 84 cells/μL in participants' first 2 years on study. Since the UNAIDS 90-90-90 strategy was published, 88.1% of viral loads were suppressed. Fifteen percent of patients experienced virologic failure with no known resistance mutations, while 56% had evidence of multiclass drug resistance.

CONCLUSIONS

Participants in the Senegalese national AIDS program are initiating ART earlier in the course of disease, and more modern therapeutic regimens have improved outcomes among those receiving therapy. Despite these achievements, HIV-2 treatment remains suboptimal, and significant challenges to improving care remain.

Intersectional stigmas and HIV-related outcomes among a cohort of key populations enrolled in stigma mitigation interventions in Senegal

OBJECTIVES

The current study aims to assess longitudinal differences in stigma and HIV outcomes among key populations at risk for and living with HIV.

DESIGN

Key populations enrolled into two parallel prospective cohorts; one for female sex workers and one for sexual and gender minorities (SGMs). Participants were recruited from three urban areas in Senegal; were followed for 24 months; and had the option to participate in an integrated stigma mitigation intervention.

METHODS

Participants included individuals both at risk for and living with HIV. Sociobehavioral questionnaires and biological HIV testing were administered every 3-4 months. Longitudinal analyses used nonparametric Chi-squared test for trends and multivariable logistic regression with generalized estimating equations.

RESULTS

183 SGM and 192 sex workers were enrolled. Among SGM participants, 39.9% were living with HIV at baseline and incidence over 24 months was 3.21/100 person-years. Among sex workers, 36.6% were living with HIV at baseline and incidence was 1.32/100 person-years. Among SGM, perceived healthcare stigma (P < 0.001), anticipated healthcare stigma (P < 0.001), and perceived friend stigma (P = 0.047) reduced, but differed by HIV status for perceived [adjusted odds ratio (aOR): 3.51; 95% confidence interval (CI): 1.75, 7.06] and anticipated healthcare stigmas (aOR: 2.85; 95% CI: 1.06-7.67). Among sex workers perceived healthcare stigma (P = 0.043) and perceived friend stigma (P = 0.006) reduced. Viral suppression increased among SGM (P = 0.028) and was associated with perceived (aOR: 2.87; 95% CI: 1.39-5.55) and enacted healthcare stigma (aOR: 0.42; 95% CI: 0.18-0.99).

CONCLUSION

Overall, there were decreases in stigmas observed but clear differences in stigma patterns by HIV status. These data highlight the need to consider specific strategies to address multiple intersecting stigmas as a means of improving HIV-related prevention and treatment outcomes among key populations with diverse identities.

Phylodynamic analysis of HIV-1 subtypes B, C and CRF 02_AG in Senegal

Surveillance of HIV epidemics in key populations and in developing countries is often challenging due to sparse, incomplete, or low-quality data. Analysis of HIV sequence data can provide an alternative source of information about epidemic history, population structure, and transmission patterns. To understand HIV-1 dynamics and transmission patterns in Senegal, we carried out model-based phylodynamic analyses using the structured-coalescent approach using HIV-1 sequence data from three different subgroups: reproductive aged males and females from the adult Senegalese population and men who have sex with other men (MSM). We fitted these phylodynamic analyses to time-scaled phylogenetic trees individually for subtypes C and CRF 02_AG, and for the combined data for subtypes B, C and CRF 02_AG. In general, the combined analysis showed a decreasing proportion of effective number of infections among all reproductive aged adults relative to MSM. However, we observed a nearly time-invariant distribution for subtype CRF 02_AG and an increasing trend for subtype C on the proportion of effective number of infections. The population attributable fraction also differed between analyses: subtype CRF 02_AG showed little contribution from MSM, while for subtype C and combined analyses this contribution was much higher. Despite observed differences, results suggested that the combination of high assortativity among MSM and the unmet HIV prevention and treatment needs represent a significant component of the HIV epidemic in Senegal.

Use and Acceptability of HIV Self-Testing Among First-Time Testers at Risk for HIV in Senegal

HIV Self-Testing (HIVST) aims to increase HIV testing coverage and can facilitate reaching the UNAIDS 90-90-90 targets. In Senegal, key populations bear a disproportionate burden of HIV and report limited uptake of HIV testing given pervasive stigma and criminalization. In these contexts, HIVST may represent a complementary approach to reach populations reporting barriers to engagement with existing and routine HIV testing services. In this study, 1839 HIVST kits were distributed in Senegal, with 1149 individuals participating in a pre-test questionnaire and 817 participating in a post-test questionnaire. Overall, 46.9% (536/1144) were first-time testers and 26.2% (300/1144) had tested within the last year; 94.3% (768/814) reported using the HIVST, and 2.9% (19/651) reported a reactive result which was associated with first-time testers (p = 0.024). HIVST represents an approach that reached first-time testers and those who had not tested recently. Implementation indicators suggest the importance of leveraging existing community structures and programs for distribution.

A note on tests for relevant differences with extremely large sample sizes

A well-known problem in classical two-tailed hypothesis testing is that P-values go to zero when the sample size goes to infinity, irrespectively of the effect size. This pitfall can make the testing of data consisting of large sample sizes potentially unreliable. In this note, we propose to test for relevant differences to overcome this issue. We illustrate the proposed test a on real data set of about 40 million privately insured patients.

Estimating the contribution of key populations towards the spread of HIV in Dakar, Senegal

INTRODUCTION

Key populations including female sex workers (FSW) and men who have sex with men (MSM) bear a disproportionate burden of HIV. However, the role of focusing prevention efforts on these groups for reducing a country's HIV epidemic is debated. We estimate the extent to which HIV transmission among FSW and MSM contributes to overall HIV transmission in Dakar, Senegal, using a dynamic assessment of the population attributable fraction (PAF).

METHODS

A dynamic transmission model of HIV among FSW, their clients, MSM and the lower-risk adult population was parameterized and calibrated within a Bayesian framework using setting-specific demographic, behavioural, HIV epidemiological and antiretroviral treatment (ART) coverage data for 1985 to 2015. We used the model to estimate the 10-year PAF of commercial sex between FSW and their clients, and sex between men, to overall HIV transmission (defined as the percentage of new infections prevented when these modes of transmission are removed). In addition, we estimated the prevention benefits associated with historical increases in condom use and ART uptake, and impact of further increases in prevention and treatment.

RESULTS

The model projections suggest that unprotected sex between men contributed to 42% (2.5 to 97.5th percentile range 24 to 59%) of transmissions between 1995 and 2005, increasing to 64% (37 to 79%) from 2015 to 2025. The 10-year PAF of commercial sex is smaller, diminishing from 21% (7 to 39%) in 1995 to 14% (5 to 35%) in 2015. Without ART, 49% (32 to 71%) more HIV infections would have occurred since 2000, when ART was initiated, whereas without condom use since 1985, 67% (27 to 179%) more HIV infections would have occurred, and the overall HIV prevalence would have been 60% (29 to 211%) greater than what it is now. Further large decreases in HIV incidence (68%) can be achieved by scaling up ART in MSM to 74% coverage and reducing their susceptibility to HIV by two-thirds through any prevention modality.

CONCLUSIONS

Unprotected sex between men may be an important contributor to HIV transmission in Dakar, due to suboptimal coverage of evidence-informed interventions. Although existing interventions have effectively reduced HIV transmission among adults, it is crucial that further strategies address the unmet need among MSM.