An analysis of the COVID-19 laboratory dataset at AiBST Laboratory in Harare, Zimbabwe, 2020.

INTRODUCTION: coronavirus disease 2019 (COVID-19) has become a major public health problem and has spread rapidly around the globe since its first identification in Wuhan, China, in December 2019. Zimbabwe reported its first case on the 20th March 2020, and since then the disease has spread to almost every part of the country. Laboratory testing is important in controlling this pandemic. However, few studies have focused on assessing trends of SARS-CoV-2 laboratory data. We described SARS-CoV-2 data from African Institute of Biomedical Science and Technology (AiBST) Laboratory in Harare, Zimbabwe. METHODS: a retrospective record review of secondary SARS-CoV-2 data from AiBST Laboratory in Harare between May to September 2020 was done. Epi Info TM 7.2.2.6 was used to generate frequencies, proportions and conduct bivariate analysis. RESULTS: a total of 6,535 SARS-CoV-2 laboratory records were analysed. The median age of the patients was 36 years and 55% (3594/6535) were males. There was an increase in average analytical turn-around time (TAT) of SARS-CoV-2 results from May to August 2020. Analytical and preanalytical TAT remained above 2 days from August to September. Males were 1.18 times at risk of being SARS-CoV-2 infected than females (p<0.05). The risk of being SARS-CoV-2 infected increased with age from 1.06 in the 11-20 age group to 1.45 in the 41-50 age group. CONCLUSION: COVID-19 poses a greater threat to the older age groups and to men. The delayed TAT of SARS-CoV-2 results limits the efforts to control the pandemic. Decentralization of testing to provincial and district level would help improve result TAT.

Comparison of Real-Q 2019-nCoV and DaAn Gene 2019-nCoV polymerase chain reaction assays for the detection of SARS-CoV-2.

BACKGROUND: Various nucleic acid amplification assays for the diagnosis of SARS-CoV-2 infection have been developed, and there is a need to assess their test performance relative to one another. The aim of this study was to compare the performance characteristics of the Biosewoom Real-Q 2019-nCoV assay targeting the E and RdRP genes to DaAn Gene 2019-nCoV kit targeting the N gene and ORF1ab in the diagnosis of SARS-CoV-2. METHODS: We performed a diagnostic comparison study by testing nasopharyngeal samples for SARS-CoV-2 using the two reverse transcription polymerase chain reaction (RT-PCR) assays. Assay agreement was assessed by overall percent agreement, negative percent agreement, positive percent agreement, and Cohen's kappa coefficient. RESULTS: A total of 48 nasopharyngeal samples were tested using the two assays. One sample was invalid, and three showed inconclusive results with Real-Q; hence, 44 were included for the comparative analysis. Overall, percent agreement between the assays was 93.2% (95% CI 81.3%-98.6%), Positive percent agreement (PPA) was 86.4% (95% CI 65.1%-97.1%) and negative percent agreement (NPA) was 100% (95% CI 84.6%-100%). The kappa coefficient was 0.86 (95% CI 0.72-1.01). Three samples (6.8%) were positive with DaAn gene kit and negative with Real-Q. The fluorescence intensity for Real-Q reporter dyes was low. CONCLUSION: The two kits showed high levels of concordance in their detection of SARS-CoV-2 despite having different gene targets. The Biosewoom kit can be improved through addressing the fluorescence intensity of the target dyes, and feedback was given to the manufacturer.

Comprehensive occupational health services for healthcare workers in Zimbabwe during the SARS-CoV-2 pandemic.

BACKGROUND: Healthcare workers are disproportionately affected by COVID-19. In low- and middle- income countries, they may be particularly impacted by underfunded health systems, lack of personal protective equipment, challenging working conditions and barriers in accessing personal healthcare. METHODS: In this cross-sectional study, occupational health screening was implemented at the largest public sector medical centre in Harare, Zimbabwe, during the "first wave" of the country's COVID-19 epidemic. Clients were voluntarily screened for symptoms of COVID-19, and if present, offered a SARS-CoV-2 nucleic acid detection assay. In addition, measurement of height, weight, blood pressure and HbA1c, HIV and TB testing, and mental health screening using the Shona Symptom Questionnaire (SSQ-14) were offered. An interviewer-administered questionnaire ascertained client knowledge and experiences related to COVID-19. RESULTS: Between 27th July and 30th October 2020, 951 healthcare workers accessed the service; 210 (22%) were tested for SARS-CoV-2, of whom 12 (5.7%) tested positive. Clients reported high levels of concern about COVID-19 which declined with time, and faced barriers including lack of resources for infection prevention and control. There was a high prevalence of largely undiagnosed non-communicable disease: 61% were overweight or obese, 34% had a blood pressure of 140/90mmHg or above, 10% had an HbA1c diagnostic of diabetes, and 7% had an SSQ-14 score consistent with a common mental disorder. Overall 8% were HIV-positive, with 97% previously diagnosed and on treatment. CONCLUSIONS: Cases of SARS-CoV-2 in healthcare workers mirrored the national epidemic curve. Implementation of comprehensive occupational health services during a pandemic was feasible, and uptake was high. Other comorbidities were highly prevalent, which may be risk factors for severe COVID-19 but are also important independent causes of morbidity and mortality. Healthcare workers are critical to combatting COVID-19; it is essential to support their physical and psychological wellbeing during the pandemic and beyond.

Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data.

BACKGROUND: Advances in SARS-CoV-2 sequencing have enabled identification of new variants, tracking of its evolution, and monitoring of its spread. We aimed to use whole genome sequencing to describe the molecular epidemiology of the SARS-CoV-2 outbreak and to inform the implementation of effective public health interventions for control in Zimbabwe. METHODS: We performed a retrospective study of nasopharyngeal samples collected from nine laboratories in Zimbabwe between March 20 and Oct 16, 2020. Samples were taken as a result of quarantine procedures for international arrivals or to test for infection in people who were symptomatic or close contacts of positive cases. Samples that had a cycle threshold of less than 30 in the diagnostic PCR test were processed for sequencing. We began our analysis in July, 2020 (120 days since the first case), with a follow-up in October, 2020 (at 210 days since the first case). The phylogenetic relationship of the genome sequences within Zimbabwe and global samples was established using maximum likelihood and Bayesian methods. FINDINGS: Of 92 299 nasopharyngeal samples collected during the study period, 8099 were PCR-positive and 328 were available for sequencing, with 156 passing sequence quality control. 83 (53%) of 156 were from female participants. At least 26 independent introductions of SARS-CoV-2 into Zimbabwe in the first 210 days were associated with 12 global lineages. 151 (97%) of 156 had the Asp614Gly mutation in the spike protein. Most cases, 93 (60%), were imported from outside Zimbabwe. Community transmission was reported 6 days after the onset of the outbreak. INTERPRETATION: Initial public health interventions delayed onset of SARS-CoV-2 community transmission after the introduction of the virus from international and regional migration in Zimbabwe. Global whole genome sequence data are essential to reveal major routes of spread and guide intervention strategies. FUNDING: WHO, Africa CDC, Biotechnology and Biological Sciences Research Council, Medical Research Council, National Institute for Health Research, and Genome Research Limited.

Using the Water and Sanitation for Health Facility Improvement Tool (WASH FIT) in Zimbabwe: A Cross-Sectional Study of Water, Sanitation and Hygiene Services in 50 COVID-19 Isolation Facilities.

The availability of water, sanitation and hygiene (WASH) services is a key prerequisite for quality care and infection prevention and control in health care facilities (HCFs). In 2020, the COVID-19 pandemic highlighted the importance and urgency of enhancing WASH coverage to reduce the risk of COVID-19 transmission and other healthcare-associated infections. As a part of COVID-19 preparedness and response interventions, the Government of Zimbabwe, the United Nations Children's Fund (UNICEF), and civil society organizations conducted WASH assessments in 50 HCFs designated as COVID-19 isolation facilities. Assessments were based on the Water and Sanitation for Health Facility Improvement Tool (WASH FIT), a multi-step framework to inform the continuous monitoring and improvement of WASH services. The WASH FIT assessments revealed that one in four HCFs did not have adequate services across the domains of water, sanitation, health care waste, hand hygiene, facility environment, cleanliness and disinfection, and management. The sanitation domain had the largest proportion of health care facilities with poor service coverage (42%). Some of the recommendations from this assessment include the provision of sufficient water for all users, Menstrual Hygiene Management (MHM)- and disability-friendly sanitation facilities, handwashing facilities, waste collection services, energy for incineration or waste treatment facilities, cleaning supplies, and financial resources for HCFs. WASH FIT may be a useful tool to inform WASH interventions during the COVID-19 pandemic and beyond.

Use of geographic information systems web mapping application to support active case search to guide public health and social measures in the context of COVID-19 in Zimbabwe: a preliminary report to guide replication of methods in similar resource settings.

INTRODUCTION: the new coronavirus (COVID-19) that emerged from Wuhan, Hubei Province of China in December 2019, causing severe acute respiratory syndrome (SARS) has fast spread across the entire globe, with most countries struggling to slow and reduce the spread of the virus through rapid screening, testing, isolation, case management, contact tracing, implementing social distancing and lockdowns. This has been shown to be a major factor in countries that have been successful in containing COVID-19 transmission. Early detection of cases is important, and the use of geospatial technology can support to detect and easily identify potential hotspots that will require timely response. The use of spatial analysis with geographic information systems (GIS) had proved to be effective in providing timely and effective solutions in supporting epidemic response and pandemics over the years. It has developed and evolved rapidly with a complete technological tool for representing data, model construction, visualization and platform construction among others. METHODS: we conducted a geospatial analysis to develop a web mapping application using ArcMap and ArcGIS online to guide and support active case search of potential COVID-19 cases, within 500m radius of COVID-19 confirmed cases to improve detection and testing of suspected cases. RESULTS: the web mapping application tool guides the active case search teams in the field, with clear boundaries on the houses to be visited within 500-meter radius of confirmed positive cases, to conduct active case search of all cases of severe acute respiratory illnesses (SARI), acute respiratory illnesses (ARI), pneumonia etc, to detect and test for COVID-19 towards containing the pandemic. CONCLUSION: the use of GIS and spatial statistical tools have become an important and valuable tool in decision-making and, more importantly, guiding health care professional and other stakeholders in the response being carried out in a more coherent and easy manner. It has proven to be effective in supporting the active case search process to rapidly detect, test and isolate cases during the process, towards containing the COVID-19 pandemic.