SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis.

BACKGROUND: SARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccinescaused by inequitable distribution. OBJECTIVE: To monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health. METHODS: Here we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples weresequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed. RESULTS: The Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acidsubstitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previousinfection or vaccination. CONCLUSION: There were nine lineages circulating in Zimbabwe during the second wave. The B.1.351 was dominant, accounting for >75%.There were over 3 000 mutations on the diagnostic genes and lineage B.1.351, contributing almost two-thirds of the mutations. The S-genehad the most mutations and the E-gene was the least mutated.

TB prevalence in Zimbabwe: a national cross-sectional survey, 2014.

BACKGROUND: We conducted the first national TB prevalence survey to provide accurate estimates of bacteriologically confirmed pulmonary TB disease among adults aged ≥15 years in 2014.METHODS: A TB symptoms screen and chest X-ray (CXR) were used to identify presumptive TB cases who submitted two sputum samples for smear microscopy, liquid and solid culture. Bacteriological confirmation included acid-fast bacilli smear positivity confirmed using Xpert® MTB/RIF and/or culture. Prevalence estimates were calculated using random effects logistic regression with multiple imputations and inverse probability weighting.RESULTS: Of 43,478 eligible participants, 33,736 (78%) were screened; of these 5,820 (17%) presumptive cases were identified. There were 107 (1.9%) bacteriologically confirmed TB cases, of which 23 (21%) were smear-positive. The adjusted prevalences of smear-positive and bacteriologically confirmed TB disease were respectively 82/100,000 population (95% CI 47-118/100,000) and 344/100,000 (95% CI 268-420/100,000), with an overall all-ages, all-forms TB prevalence of 275/100,000 population (95% CI 217-334/100,000). TB prevalence was higher in males, and age groups 35-44 and ≥65 years. CXR identified 93/107 (87%) cases vs. 39/107 (36%) using the symptom screen.CONCLUSION: Zimbabwe TB disease prevalence has decreased relative to prior estimates, possibly due to increased antiretroviral therapy coverage and successful national TB control strategies. Continued investments in TB diagnostics for improved case detection are required.

A feasibility study using time-driven activity-based costing as a management tool for provider cost estimation: lessons from the national TB control program in Zimbabwe in 2018.

BACKGROUND: Insufficient cost data and limited capacity constrains the understanding of the actual resources required for effective TB control. This study used process maps and time-driven activity-based costing to document TB service delivery processes. The analysis identified the resources required to sustain TB services in Zimbabwe, as well as several opportunities for more effective and efficient use of available resources. METHODS: A multi-disciplinary team applied time-driven activity-based costing (TDABC) to develop process maps and measure the cost of clinical pathways used for Drug Susceptible TB (DS-TB) at urban polyclinics, rural district and provincial hospitals, and community based targeted screening for TB (Tas4TB). The team performed interviews and observations to collect data on the time taken by health care worker-patient pairs at every stage of the treatment pathway. The personnel's practical capacity and capacity cost rates were calculated on five cost domains. An MS Excel model calculated diagnostic and treatment costs. FINDINGS: Twenty-five stages were identified in the TB care pathway across all health facilities except for community targeted screening for TB. Considerable variations were observed among the facilities in how health care professionals performed client registration, taking of vital signs, treatment follow-up, dispensing medicines and processing samples. The average cost per patient for the entire DS-TB care was USD324 with diagnosis costing USD69 and treatment costing USD255. The average cost for diagnosis and treatment was higher in clinics than in hospitals (USD392 versus USD256). Nurses in clinics were 1.6 time more expensive than in hospitals. The main cost components were personnel (USD130) and laboratory (USD119). Diagnostic cost in Tas4TB was twice that of health facility setting (USD153 vs USD69), with major cost drivers being demand creation (USD89) and sputum specimen transportation (USD5 vs USD3). CONCLUSION: TDABC is a feasible and effective costing and management tool in low-resource settings. The TDABC process maps and treatment costs revealed several opportunities for innovative improvements in the NTP under public health programme settings. Re-engineering laboratory testing processes and synchronising TB treatment follow-up with antiretroviral treatments could produce better and more uniform TB treatments at significantly lower cost in Zimbabwe.

The disconnect between a national tuberculosis drug resistance survey and treatment outcomes: a lost opportunity.

We linked results from the Fourth Botswana National Drug Resistance Survey (DRS), 2007-2008, to patient records from the national Electronic Tuberculosis Registry to determine treatment outcomes. Of 915 new patients, 651 (71%) had treatment data available. Completion or cure was achieved for 10/15 (67%, 95%CI 42-85) with isoniazid monoresistance, (6/16, 38%, 95%CI 18-61) with multidrug resistance, while 73% (391/537, 95%CI 69-76) were susceptible to first-line drugs. The analysis was limited because of unavailable treatment records and undocumented outcomes. Prospective analyses following DRSs should be considered to ensure adequate outcome data.

Increase in anti-tuberculosis drug resistance in Botswana: results from the fourth National Drug Resistance Survey.

SETTING: Although approximately 0.5 million cases of multidrug-resistant tuberculosis (MDR-TB) occur globally each year, surveillance data are limited. Botswana is one of the few high TB burden countries to have carried out multiple anti-tuberculosis drug resistance surveys (in 1995-1996, 1999 and 2002). OBJECTIVE: In 2007-2008, we conducted the fourth national survey of anti-tuberculosis drug resistance in Botswana to assess anti-tuberculosis drug resistance, including trends over time. In the previous survey, 0.8% (95%CI 0.4-1.5) of new patients and 10.4% (95%CI 5.6-17.3) of previously treated patients had MDR-TB. DESIGN: During the survey period, eligible specimens from all new sputum-smear positive TB patients and from all TB patients with history of previous anti-tuberculosis treatment underwent mycobacterial culture and anti-tuberculosis drug susceptibility testing (DST). RESULTS: Of 924 new TB patients and 137 with previous anti-tuberculosis treatment with DST results, respectively 23 (2.5%, 95%CI 1.6-3.7) and 9 (6.6%, 95%CI 3.3-11.7) had MDR-TB. The proportion of new TB patients with MDR-TB has tripled in Botswana since the previous survey. CONCLUSION: Combatting drug-resistant TB will require the scale-up of MDR-TB diagnosis and treatment to prevent the transmission of MDR-TB and strengthening of general TB control to prevent the emergence of resistance.

Lessons learned during tuberculosis screening in public medical clinics in Francistown, Botswana.

In Botswana, where one quarter of the adult population is infected with the human immunodeficiency virus and the annual tuberculosis (TB) incidence is among the highest globally, intensified TB case finding is needed in health care facilities to detect and treat TB cases early and prevent transmission. During August-December 2009, TB screening was implemented among adults at patient intake in five clinics in Francistown. Among 11 779 TB screenings at intake, 926 were positive. Nineteen patients were diagnosed with TB. Routine TB screening at intake was operationally feasible, but had low yield. Innovative case-finding strategies are needed in Botswana.

Factors associated with occupational injuries at a beverage manufacturing company in Harare, Zimbabwe--2008.

OBJECTIVE: A beverage manufacturing company reported 59.3% increase in occupational injuries between 2006 and 2007. Factors associated with occupational injuries at this company in Harare were characterized, described the injuries, identified the hazards and control measures in place. DESIGN: An analytical cross sectional study was conducted. SETTING: Two plants of a beverage manufacturing company in Harare. SUBJECTS: We interviewed randomly selected workers at the 2 plants of the company MAIN OUTCOME MEASURES: Prevalence of occupational injuries, Factors associated with injury, occupational hazards, control measures RESULTS: Of 392 workers interviewed, 53.3% reported having had a work-related injury. Twenty-six percent had not reported the injuries. Independent risk factors were: working in packaging department OR = 3.64 (95% CI: 2.25-5.88), having sleep disorder OR = 2.26 (95% CI: 1.21-4.22) and 7 day working week without rest OR = 1.88 (95% CI: 1.01-3.47). Hazards identified were noise, broken bottles, unguarded machines and coal dust. High risk areas were automated. Common injuries were cuts/lacerations (70.8%) and the most affected parts being the fingers 27.3% (57/209) and the hands 17.2% (36/209). Most injuries (74.8%) occurred in the packaging department due to breaking bottles. CONCLUSION: Prevalence of occupational injuries is high. We recommended regular machinery maintenance to minimize bottle breakages, reduction in working time and supply of adequate personal protective clothing.

HIV status disclosure among people living with HIV/AIDS at FASO, Mutare, Zimbabwe.

OBJECTIVE: To examine the prevalence, patterns and reasons for disclosure of HIV status among people living with HIV/AIDS. DESIGN: Adescriptive cross sectional survey. SETTING: FamilyAIDS Support Organisation (FASO), Mutare, Zimbabwe. SUBJECTS: A random selection of members of FASO attending clinic or meetings. OUTCOME MEASURES: Disclosure of HIV seropositivity to sexual partner, to one or more family members, to health care workers and to the wider public. RESULTS: There was 79%, 72% and 70% disclosure to the family, health workers and to sexual partners respectively. While public disclosure was 23%, more people wanted to disclose but did not get an opportunity. Main reasons for disclosure to family were to obtain psychosocial and material support; to the public it was to give HIV/AIDS a face; and to the sexual partner it was to have safer sex. Knowing one's HIV status for a year or longer was significantly associated with disclosure to family, sexual partner and the public. Females were significantly more likely to disclose to family members compared to males (p=0.004). People in abusive relationships were significantly less likely to disclose to sexual partners (OR=0.17, p=0.039). CONCLUSION: Though disclosure rates were generally high, attention must be given to the small number of people engaging in high-risk behaviour, and disclosure counseling needs to be enhanced. Domestic violence hindered disclosure and we advise that it must be prevented.

Behavioural factors associated with cutaneous anthrax in Musadzi area of Gokwe North, Zimbabwe.

OBJECTIVES: To determine behaviour factors for contracting human cutaneous anthrax among residents of Musadzi area. DESIGN: We conducted a matched case-control study for age, sex, and village. SETTING: A rural community in Musadzi area of Gokwe North district. SUBJECTS: We interviewed 35 cases and 35 controls. A case was defined as any resident/visitor of Musadzi, diagnosed with anthrax between 9 September and 10 November 2004. A control was any resident who had not been diagnosed with anthrax and had no lesions suggestive ofanthrax on day of the interview. MAIN OUTCOME MEASURES: Behaviour factors associated with contracting anthrax. RESULTS: In September 2004, cattle were reported to be dying in Musadzi area. Bacillus anthracis was positively identified in a blood smear from some of the carcasses. The attack rate among humans was 5%. Risk factors associated with contracting anthrax were: skinning of animals that had died from unknown causes AOR=3.8 (95% CI:1.3-10.7); preparation of the meat for cooking (AOR=3.1 (95% CI:1.16-8-4); preparation of the meat for drying AOR=2.7 (95% CI: 1.0081-7.4); belonging to a religious or ethnic sect that allow handling of meat from animals that had died from unknown causes (AOR=5.2 (95% CI: 1.8-14.8). CONCLUSION: The human anthrax outbreak was secondary to an anthrax epizootic occurring in cattle. The Ministry of Health activated the local zoonotic committee, carried out anthrax awareness campaigns, supervised the destruction of carcasses, disinfected potentially contaminated sites and introduced a participatory health education tool on anthrax. The veterinary department quarantined and vaccinated cattle.

Treatment outcomes of patients on antiretrovirals after six months of treatment, Khami Clinic, Bulawayo, Zimbabwe.

OBJECTIVE: To describe treatment outcomes of patients on anti-retrovirals at six months of treatment. STUDY DESIGN: We conducted pre-intervention post intervention surveys using a pretest-post test design. SETTING: Khami Municipal Clinic, Bulawayo. SUBJECTS: We interviewed consecutive patients eligible to receive antiretroviral drugs (ARVs). All patients had a history of TB treatment and a CD4 count less than 200 cells/mm. MAIN OUTCOME MEASURES: Mean change in CD4 count, weight, body mass index, and Karnofsky performance measured before and at six months ofantiretroviral treatment. RESULTS: 72 subjects were interviewed at baseline, their median age was 38 years (Q1, 32 years, Q3, 43 years). Of these, 17 (24%) died before six months of treatment. Three (4%) defaulted treatment follow up. A total of 52 respondents were alive and interviewed at six months though only 50, had repeat CD4 counts at six months. Among the 50 survivors, the mean CD4 count at six months was significantly higher than at baseline (p = 0.0003). There was a 4.2 point statistical significant increase in the mean weight from baseline (p = 0.0005). Similarly, the mean Body Mass Index (BMI) significantly increased by 1.5 kg/m2 from baseline, (p = 0.001). The mean Karnofsky performance increased from 89% at baseline to 95% at six months (p = 0004). The researchers noted that patients on TB treatment were being deferred antiretroviral therapy until they completed TB treatment. CONCLUSION: The Khami project bears testimony that even in a resource poor setting; treatment of HIV/AIDS with antiretroviral drugs is feasible. We recommend early treatment initiation for those on TB treatment in line with national guidelines.

Occupational injuries among workers in the cleansing section of the City Council's Health Services Department--Bulawayo, Zimbabwe, 2001-2002.

INTRODUCTION: During 2001-2002, a total of 97 occupational injuries occurred among workers in the cleansing section of the Bulawayo, Zimbabwe, City Council's Health Services Department. This report describes a study that was conducted to describe the nature of these injuries and determine the associated risk factors. METHODS: A retrospective, descriptive cross-sectional survey was conducted concerning occupational injuries incurred by workers in the cleansing section during 2001-2002. A total of 153 workers who had been in the section as of January 1, 2001, and 23 senior managers and section supervisors were interviewed, the occupational injury register was reviewed, and a walk-through survey was conducted to estimate risk factors. RESULTS: The occupational injury register indicated that during the study period, 62 workers sustained 67 injuries, including one that was fatal. Of these 67 injuries, 27 (40%) involved workers who sustained cuts inside a box-type refuse removal truck, and 11 (16%) involved workers who had sprained ankles and wrists as a result of improper lifting. Workers aged 18-25 years were more likely to incur an injury than workers aged >25 years. Working as a bin loader and not having received preemployment training were associated with injuries. None of the bin loaders had received preemployment training. Hazards identified during the walk-through survey included use of small jacks in workshops, contact with biologic and chemical materials on trucks and landfill sites, and poor use of protective clothing. Supervisors cited worker negligence as the main cause of injury, whereas 72 (84%) workers cited lack of adequate protective clothing as a source of injury, and eleven (7%) workers cited use of inappropriate equipment. CONCLUSION: On the basis of the modifiable risk factors for injury identified in this study, the Bulawayo City Council drafted a new health and safety training manual. New recruits now receive training before starting work on refuse collection trucks.

Malaria and HIV co-infection: available evidence, gaps and possible interventions.

OBJECTIVES: To review the evidence of association between malaria and HIV/AIDS co-infection for purposes of developing strategies for malaria control. DESIGN: Desktop review of literature. SETTING: Harare, Zimbabwe. MAIN OUTCOME MEASURES: Response to treatment, development of severe malaria, malarial immunological response in HIV/AIDS positive people and incidence of malaria in HIV/AIDS positive individuals. RESULTS: HIV-1 infection increases the incidence of Plasmodium falciparum parasitaemia and is associated with the development of severe malaria, commonly anaemia, cerebral malaria and high parasite density (OR = 2.56; 95% CI = 1.53 to 4.29; p < 0.001). The efficacy of chloroquine and sulphadoxine-pyrimethamine in reducing placental malaria in HIV-1 positive pregnant women was impaired compared to HIV-1 negative pregnant women. However, the situation in non-gravid HIV-1 positive people as regards efficacy of chloroquine and sulphadoxine-pyrimethamine prophylaxis is not known. Also not known is the relationship between malaria parasitaemia without symptoms and HIV-1 infection, the results of which may provide useful information regarding malaria control and prevention in HIV-1 positive people. CONCLUSIONS: HIV-1 positive people staying in malaria endemic areas are at risk of developing severe malaria. Malaria prevention using insecticide-treated bednets and indoor residual house spraying may be the best available options for these people. Chloroquine and sulphadoxine-pyrimethamine prophylaxis require further studies to verify their efficacy, in the presence of HIV-1/AIDS infection.

Mercury poisoning: prevalence, knowledge and frequency of gold panning and doing retort among alluvial gold panners in Chiweshe and Tafuna communal lands in Zimbabwe.

OBJECTIVES: To estimate the prevalence of mercury poisoning, to estimate the knowledge level that mercury can be a poison, and to establish the frequency of gold panning and doing retorts. DESIGN: Cross sectional study. SETTING: Chiweshe and Tafuna communal lands. SUBJECTS: Gold panners. MAIN OUTCOME MEASURE: Mercury levels in blood and urine. RESULTS: Totals of 23 respondents from Chiweshe and 43 respondents from Tafuna were recruited. Four out of 43 respondents in Tafuna and seven out of 23 respondents in Chiweshe had levels of mercury greater than 0.05 mg/L in blood (p = 0.040). Out of 43 respondents in Tafuna, four (9.3%) had levels of mercury of more than 0.01 mg/L in urine. Totals of 18 out of 37 and seven out of 22 respondents from Tafuna and Chiweshe, respectively, did not know that mercury could be a poison. Altogether, 35 (56.5%) out of 62 respondents were full time gold panners. Significantly more respondents in Chiweshe (14/19) than in Tafuna (8/29) did less than four retorts per month (p = 0.005). Respondents who did four or more retorts per month were 3.21 (95% CI 1.06 to 9.72) times more likely to have had raised levels of mercury in their blood compared with persons who did less than four retorts per month. CONCLUSION: Mercury poisoning among gold panners in Chiweshe and Tafuna communal lands is of public health importance. Panners should be educated on the possibilities of mercury being a poison. A low cost and safe technology to separating mercury from the amalgam should be introduced to the panners.

Association of HIV infection with the development of severe and complicated malaria cases at a rural hospital in Zimbabwe.

OBJECTIVE: To determine the association between HIV infection and progression of Plasmodium falciparum malaria illness in Hurungwe district, Zimbabwe. DESIGN: Prospective cohort. SETTING: Hurungwe Rural Hospital in Mashonaland West Province, Zimbabwe. SUBJECTS: Blood slide positive P. falciparum malaria patients. MAIN OUTCOME MEASURES: Development of severe and complicated malaria. RESULTS: A total of 659 clinical malaria cases were investigated and 237 (36.0%) confirmed cases entered the study. The total HIV positive malaria patients were 82 (34.6%) of confirmed cases or 12.4% of the total clinical cases. The case fatality rate was 5.9% (14 deaths) in the confirmed cases and 11 of these deaths were HIV positive. The commonly reported complications were high parasite count of 2% or more (38.5%), anaemia (29.0%), cerebral malaria (23.1%), low blood pressure (8.3%) and renal failure (1.2%). The HIV positive cases which developed severe and complicated malaria were 72, 30.4% of the sample studied or 55.8% of the total severe and complicated cases. The mode of transport to the nearest health centre was the only confounding factor identified during the analysis. After adjusting for this confounding factor, the risk of developing severe and complicated malaria was 2.35 (95% CI 1.85 to 2.98) times more in the HIV positive malaria patients than in HIV negative patients. CONCLUSION: We conclude that HIV infection is significantly associated with the development of severe and complicated malaria. There is need for future studies to determine whether HIV positive malaria patients require different management protocol from HIV negative malaria patients.