First COVID-19 case in Zambia — Comparative phylogenomic analyses of SARS-CoV-2 detected in African countries

Since its first discovery in December 2019 in Wuhan, China, COVID-19, caused by the novel coronavirus SARS-CoV-2, has spread rapidly worldwide. While African countries were relatively spared initially, the initial low incidence of COVID-19 cases was not sustained for long due to continuing travel links between China, Europe and Africa. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 h of the individual entering the country by air travel from a trip to France. Contact tracing showed that SARS-CoV-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. Phylogenomic analysis of the patient’s SARS-CoV-2 strain showed that it belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of SARS-CoV-2 lineages across Africa

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The prevalence and socio-economic determinants of HIV among teenagers aged 15–18 years who were participating in a mobile testing population based survey in 2013–2014 in Zambia

Abstract Background The objective of the study was to estimate the prevalence of HIV among teenagers in Zambia and determine whether age, sex, setting, educational level, marital and socioeconomic status were associated with being HIV positive. Methods A cross sectional population based survey of the prevalence of HIV among teenagers aged 15–18 years old who were also participants in a national Tuberculosis (TB) prevalence survey. Consenting teenagers were counselled and tested for HIV. The HIV prevalence was estimated using a logistic regression model. Associations of social demographic characteristics with HIV were determined using univariate and multivariate. Results The study involved 6,395 teenagers aged 15–18 years where 2,532 declined HIV testing, 44 tested positive and 3,806 tested negative. The HIV prevalence was estimated to be 1.1 % (95 % CI 0.71-1.60); in females the HIV prevalence was 1.6 % (95 % CI 0.99-2.20) whereas in males it was 0.58 % (95 % CI 0.10-1.10). The prevalence of HIV was twice as high among the urban (1.90 %; 95 % CI 0.99-2.90) than the rural teenagers (0.89 %; 95 % CI 0.46-1.30), and being divorced or widowed was associated with higher risk of HIV regardless of residence. The risk of HIV was lower among students or those who were in school compared to those who were unemployed and not in school. Conclusion HIV prevalence among teenagers was lower than the overall national level prevalence. The patterns of HIV risk among the young population will require further monitoring in order to identify appropriate tools for intervention

Decliners of provider-initiated HIV testing and counselling: Characteristics of participants who refused HIV testing in a population survey in Zambia

Objective: To assess the prevalence of HIV infection, to highlight HIV-testing refusal rates among participants in a population-based tuberculosis survey and to assess the implication for programme implementation. Methods: This cross-sectional study on the characteristics of participants who refused HIV testing was conducted in a national survey in Zambia. All eligible participants were aged above 15 years and included in the analysis. Results: Out of the 44 791 tuberculosis survey participants, 14 164 (31.6%) refused to participate in HIV testing. The unemployed, rural dwellers, married, and those aged 15–24 years were associated with higher refusal rates. Conclusions: Strategies to improve HIV testing acceptance are necessary. Qualitative research is recommended to understand the reasons for testing refusals so that remedial interventions can be implemented

The adult prevalence of HIV in Zambia: results from a population based mobile testing survey conducted in 2013-2014

To estimate the adult prevalence of HIV among the adult population in Zambia and determine whether demographic characteristics were associated with being HIV positive. A cross sectional population based survey to asses HIV status among participants aged 15 years and above in a national tuberculosis prevalence survey. Counselling was offered to participants who tested for HIV. The prevalence was estimated using a logistic regression model. Univariate and multivariate associations of social demographic characteristics with HIV were determined. Of the 46,099 individuals who were eligible to participate in the survey, 44,761 (97.1 %) underwent pre-test counselling for HIV; out of which 30,605 (68.4 %) consented to be tested and 30, 584 (99.9 %) were tested. HIV prevalence was estimated to be 6.6 % (95 % CI 5.8-7.4); with females having a higher prevalence than males 7.7 % (95 % CI 6.8-8.7) versus 5.2 % (95 % CI 4.4-5.9). HIV prevalence was higher among urban (9.8 %; 95 % CI 8.8-10.7) than rural residents (5.0 %; 95 % CI 4.3-5.8). The risk of HIV was double among urban dwellers than among their rural counterparts. Being divorced or widowed was associated with a threefold higher risk of being HIV positive than being never married. The risk of being HIV positive was four times higher among those with tuberculosis than those without tuberculosis. HIV prevalence was lower than previously estimated in the country. The burden of HIV showed sociodemographic disparities signifying a need to target key populations or epidemic drivers. Mobile testing for HIV on a national scale in the context of TB prevalence surveys could be explored further in other setting

Outcomes of multidrug-resistant tuberculosis in Zambia: a cohort analysis

PURPOSE The purpose of this study was to establish a baseline for measuring the impact of the programmatic management of drug-resistant TB program by following up on outcomes of all patients diagnosed with multidrug-resistant tuberculosis in Zambia between 2012 and 2014. METHODS A cohort study of all the MDR-TB patients diagnosed at the national TB reference laboratory from across Zambia. MDR-TB was diagnosed by culture and DST, whereas outcome data were collected in 2015 by patient record checks and home visits. RESULTS The total number of patients diagnosed was 258. Of those, 110 (42.6%) patients were traceable for this study. There were 67 survivor participants (60.9%); 43 (39.1%) were deceased. Out of the 110 patients who were traced, only 71 (64.5%) were started on second-line treatment. Twenty-nine (40.8%) patients were declared cured and 16.9% were still on treatment; 8.4% had failed treatment. The survival rate was 20.2 per 100 person-years of follow-up. Taking ARVs was associated with a decreased risk of dying (hazard ratio 0.12, p = 0.002). Sex, age, marital status and treatment category were not important predictors of survival in MDR-TB patients. CONCLUSIONS More than half of the patients diagnosed with MDR-TB were lost to follow-up before second-line treatment was initiated

The Prevalence of Tuberculosis in Zambia: Results from the First National TB Prevalence Survey, 2013-2014.

BACKGROUND:Tuberculosis in Zambia is a major public health problem, however the country does not have reliable baseline data on the TB prevalence for impact measurement; therefore it was among the priority countries identified by the World Health Organization to conduct a national TB prevalence survey. OBJECTIVE:To estimate the prevalence of tuberculosis among the adult Zambian population aged 15 years and above, in 2013-2014. METHODS:A cross-sectional population-based survey was conducted in 66 clusters across all the 10 provinces of Zambia. Eligible participants aged 15 years and above were screened for TB symptoms, had a chest x-ray (CXR) performed and were offered an HIV test. Participants with TB symptoms and/or CXR abnormality underwent an in-depth interview and submitted one spot- and one morning sputum sample for smear microscopy and liquid culture. Digital data collection methods were used throughout the process. RESULTS:Of the 98,458 individuals who were enumerated, 54,830 (55.7%) were eligible to participate, and 46,099 (84.1%) participated. Of those who participated, 45,633/46,099 (99%) were screened by both symptom assessment and chest x-ray, while 466/46,099 (1.01%) were screened by interview only. 6,708 (14.6%) were eligible to submit sputum and 6,154/6,708 (91.7%) of them submitted at least one specimen for examination. MTB cases identified were 265/6,123 (4.3%). The estimated national adult prevalence of smear, culture and bacteriologically confirmed TB was 319/100,000 (232-406/100,000); 568/100,000 (440-697/100,000); and 638/100,000 (502-774/100,000) population, respectively. The risk of having TB was five times higher in the HIV positive than HIV negative individuals. The TB prevalence for all forms was estimated to be 455 /100,000 population for all age groups. CONCLUSION:The prevalence of tuberculosis in Zambia was higher than previously estimated. Innovative approaches are required to accelerate the control of TB