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.

Prevalence, risk factors and treatment outcomes of isoniazid resistant TB in Bulawayo city, Zimbabwe: A cohort study.

INTRODUCTION: The isoniazid-resistant TB poses a threat to TB control efforts. Zimbabwe, one of the high TB burden countries, has not explored the burden of isoniazid resistant TB. Hence among all bacteriologically-confirmed TB patients diagnosed in Bulawayo City during March 2017 and December 2018, we aimed to assess the proportion with isoniazid resistant TB and associated factors. Also, we aimed to describe the TB treatment outcomes. METHODOLOGY: A cohort study involving routinely collected data by the National TB Reference Laboratory (NTBRL) in Bulawayo City and National TB programme of Zimbabwe. The percentage with 95% confidence interval (CI) was used to express the proportion with isoniazid-resistant TB. The modified Poisson regression was used to assess the association of demographic and clinical characteristics with isoniazid mono-resistant TB. RESULTS: Of 2160 bacteriologically-confirmed TB patients, 1612 (74.6%) had their sputum received at the NTBRL and 743 (46.1%) had culture growth. Among those with culture growth, 34 (4.6%, 95% CI: 3.5-6.7) had isoniazid mono-resistant TB, 25 (3.3%, 95% CI: 2.2-4.9) had MDR-TB. Thus, 59 (7.9%, 95% CI: 6.1-10.1) had isoniazid-resistant TB. Children < 15 years had a higher prevalence of isoniazid mono-resistant TB (aPR= 3.93; 95% CI: 1.24-12.45). Among those with rifampicin sensitive TB, patients with isoniazid-sensitive TB had higher favourable treatment outcomes compared to those with isoniazid-resistant TB (86.3% versus 75.5%, p = 0.039). CONCLUSIONS: The prevalence of isoniazid-resistant TB was low compared to neighbouring countries with high burden of TB-HIV. However, Zimbabwe should consider reviewing treatment guidelines for isoniazid mono-resistant TB due to the observed poor treatment outcomes.

Diagnostic performance and usability of the VISITECT CD4 semi-quantitative test for advanced HIV disease screening.

BACKGROUND: In sub-Saharan Africa, a third of people starting antiretroviral therapy and majority of patients returning to HIV-care after disengagement, present with advanced HIV disease (ADH), and are at high risk of mortality. Simplified and more affordable point-of-care (POC) diagnostics are required to increase access to prompt CD4 cell count screening for ambulatory and asymptomatic patients. The Visitect CD4 Lateral Flow Assay (LFA) is a disposable POC test, providing a visually interpreted result of above or below 200 CD4cells/mm3. This study evaluated the diagnostic performance of this index test. METHODS: Consenting patients above 18years of age and eligible for CD4 testing were enrolled in Nsanje district hospital (Malawi), Gutu mission hospital (Zimbabwe) and Centre hopitalier de Kabinda (DRC). A total of 708 venous blood samples were tested in the index test and in the BD FACSCount assay (reference test method) in the laboratories (Phase 1) to determine diagnostic accuracy. A total of 433 finger-prick (FP) samples were tested on the index test at POC by clinicians (Phase 2) and a self-completed questionnaire was administered to all testers to explore usability of the index test. RESULTS: Among 708 patients, 67.2% were female and median CD4 was 297cells/mm3. The sensitivity of the Visitect CD4 LFA using venous blood in the laboratory was 95.0% [95% CI: 91.3-97.5] and specificity was 81.9% [95% CI: 78.2-85.2%]. Using FP samples, the sensitivity of the Visitect CD4 LFA was 98.3% [95% CI: 95.0-99.6] and specificity was 77.2% [95% CI: 71.6-82.2%]. Usability of the Visitect CD4 LFA was high across the study sites with 97% successfully completed tests. Due to the required specific multiple incubation and procedural steps during the Visitect CD4 LFA testing, few health workers (7/26) were not confident to manage testing whilst multi-tasking in their clinical work. CONCLUSIONS: Visitect CD4 LFA is a promising test for decentralized CD4 screening in resource-limited settings, without access to CD4 testing and and it can trigger prompt management of patients with AHD. Lay health cadres should be considered to conduct Visitect CD4 LFA testing in PHCs as well as coordinating all other POC quality assurance.

Common causes of EID sample rejection in Zimbabwe and how to mitigate them.

Early infant diagnosis (EID) of HIV provides an opportunity for early HIV detection and access to appropriate Antiretroviral treatment (ART). Dried Blood Spot (DBS) samples are used for EID of exposed infants, born to HIV-positive mothers. However, DBS rejection rates in Zimbabwe have been exceeding the target of less than 2% per month set by the National Microbiology Reference Laboratory (NMRL), in Harare. The aim of this study was to determine the DBS sample rejection rate, the reasons for rejection and the possible associations between rejection and level of health facility where the samples were collected. This is an analytical cross-sectional study using routine DBS sample data from the NMRL in Harare, Zimbabwe, between January and December 2017.A total of 34 950 DBS samples were received at the NMRL. Of these, 1291(4%) were rejected. Reasons for rejection were insufficient specimen volume (72%), missing request form (11%), missing sample (6%), cross-contamination (6%), mismatch of information (4%) and clotted sample (1%). Samples collected from clinics/rural health facilities were five times more likely to be rejected compared to those from a central hospital. Rejection rates were above the set target of <2%. The reasons for rejection were 'pre-analytical' errors including labelling errors, missing or inconsistent data, and insufficient blood collected. Samples collected at primary healthcare facilities had higher rejection rates.

Distribution of rotavirus genotypes associated with acute diarrhoea in Zimbabwean children less than five years old before and after rotavirus vaccine introduction.

BACKGROUND: Sentinel surveillance for diarrhoea is important to monitor changes in rotavirus epidemiological trends and circulating genotypes among children under 5 years before and after vaccine introduction. The Zimbabwe Ministry of Health and Child Care introduced rotavirus vaccine in national immunization program in May 2014. METHODS: Active hospital-based surveillance for diarrhoea was conducted at 3 sentinel sites from 2008 to 2016. Children aged less than 5 years, who presented with acute gastroenteritis as a primary illness and who were admitted to a hospital ward or treated at the emergency unit, were enrolled and had a stool specimen collected and tested for rotavirus by enzyme immunoassay (EIA). Genotyping of positive stools was performed using reverse-transcription polymerase chain reaction and genotyping assays. Pre-vaccine introduction, 10% of all positive stool specimens were genotyped and all adequate positive stools were genotyped post-vaccine introduction. RESULTS: During the pre-vaccine period, a total of 6491 acute gastroenteritis stools were collected, of which 3016 (46%) tested positive for rotavirus and 312 (10%) of the rotavirus positive stools were genotyped. During the post-vaccine period, a total of 3750 acute gastroenteritis stools were collected, of which 937 (25%) tested positive for rotavirus and 784 (84%) were genotyped. During the pre-vaccine introduction the most frequent genotype was G9P[8] (21%) followed by G2P[4] (12%), G1P[8] (6%), G2P[6] (5%), G12P[6] (4%), G9P[6] (3%) and G8P[4] (3%). G1P[8] (30%) was most dominant two years after vaccine introduction followed by G9P[6] (20%), G2P[4] (15%), G9P[8] (11%) and G1P[6] (4%). CONCLUSION: The decline in positivity rate is an indication of early vaccine impact. Diversity of circulating strains underscores the importance of continued monitoring and strain surveillance after vaccine introduction.

Multicountry Validation of SAMBA - A Novel Molecular Point-of-Care Test for HIV-1 Detection in Resource-Limited Setting.

INTRODUCTION: Early diagnosis of HIV-1 infection and the prompt initiation of antiretroviral therapy are critical to achieving a reduction in the morbidity and mortality of infected infants. The Simple AMplification-Based Assay (SAMBA) HIV-1 Qual Whole Blood Test was developed specifically for early infant diagnosis and prevention of mother-to-child transmission programs implemented at the point-of-care in resource-limited settings. METHODS: We have evaluated the performance of this test run on the SAMBA I semiautomated platform with fresh whole blood specimens collected from 202 adults and 745 infants in Kenya, Uganda, and Zimbabwe. Results were compared with those obtained with the Roche COBAS AmpliPrep/COBAS TaqMan (CAP/CTM) HIV-1 assay as performed with fresh whole blood or dried blood spots of the same subjects, and discrepancies were resolved with alternative assays. RESULTS: The performance of the SAMBA and CAP/CTM assays evaluated at 5 laboratories in the 3 countries was similar for both adult and infant samples. The clinical sensitivity, specificity, positive predictive value, and negative predictive value for the SAMBA test were 100%, 99.2%, 98.7%, and 100%, respectively, with adult samples, and 98.5%, 99.8%, 99.7%, and 98.8%, respectively, with infant samples. DISCUSSION: Our data suggest that the SAMBA HIV-1 Qual Whole Blood Test would be effective for early diagnosis of HIV-1 infection in infants at point-of-care settings in sub-Saharan Africa.

Trends of rubella incidence during a 5-year period of case based surveillance in Zimbabwe.

BACKGROUND: Rubella is a disease of public health significance owing to its adverse effects during pregnancy and on pregnancy outcomes. Women who contract rubella virus during pregnancy may experience complications such as foetal death or give birth to babies born with congenital rubella syndrome. Vaccination against rubella is the most effective and economical approach to control the disease, and to avoid the long term effects and high costs of care for children with congenital rubella syndrome as well as to prevent death from complications. Zimbabwe commenced rubella surveillance in 1999, despite lacking a rubella vaccine in the national Expanded Programme on Immunization, as per the World Health Organization recommendation to establish a surveillance system to estimate the disease burden before introduction of a rubella vaccine. The purpose of this analysis is to describe the disease trends and population demographics of rubella cases that were identified through the Zimbabwe national measles and rubella case-based surveillance system during a 5-year period between 2007 and 2011. METHODS: Data from the Zimbabwe National Measles Laboratory for the 5-year study period were analysed for age, sex, district of origin, seasonality, and rubella IgM serostatus. RESULTS: A total of 3428 serum samples from cases of suspected measles in all administrative districts of the country were received by the laboratory during this period. Cases included 51% males and 49% females. Of these, 2999 were tested for measles IgM of which 697 (23.2%) were positive. Of the 2302 measles IgM-negative samples, 865 (37.6%) were rubella IgM-positive. Ninety-eight percent of confirmed rubella cases were children younger than 15 years of age. Most infections occurred during the dry season. CONCLUSIONS: The national case-based surveillance revealed the disease burden and trends of rubella in Zimbabwe. These data add to the evidence for introducing rubella-containing vaccine into the national immunization programme.

Maximising mentorship: variations in laboratory mentorship models implemented in Zimbabwe

Background: Laboratory mentorship has proven to be an effective tool in building capacity and assisting laboratories in establishing quality management systems. The Zimbabwean Ministry of Health and Child Welfare implemented four mentorship models in 19 laboratories in conjunction with the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme.Objectives: This study outlines how the different models were implemented; cost involved per model and results achieved.Methods: Eleven of the laboratories had been trained previously in SLMTA (Cohort I). They were assigned to one of three mentorship models based on programmatic considerations: Laboratory Manager Mentorship (Model 1; four laboratories); One Week per Month Mentorship (Model 2; four laboratories); and Cyclical Embedded Mentorship (Model 3; three laboratories). The remaining eight laboratories (Cohort II) were enrolled in Cyclical Embedded Mentorship incorporated with SLMTA training (Model 4). Progress was evaluated using a standardised audit checklist.Results: At SLMTA baseline; Model 1-3 laboratories had a median score of 30%. After SLMTA; at mentorship baseline; they had a median score of 54%. At the post-mentorship audit they reached a median score of 75%. Each of the three mentorship models for Cohort I had similar median improvements from pre- to post-mentorship (17 percentage points for Model 1; 23 for Model 2 and 25 for Model 3; p 0.10 for each comparison). The eight Model 4 laboratories had a median baseline score of 24%; after mentorship; their median score increased to 63%. Median improvements from pre-SLMTA to post-mentorship were similar for all four models.Conclusion: Several mentorship models can be considered by countries depending on the available resources for their accreditation implementation plan

Does provision of point-of-care CD4 technology and early knowledge of CD4 levels affect early initiation and retention on antiretroviral treatment in HIV-positive pregnant women in the context of Option B+ for PMTCT?

Evidence for Elimination (E4E) is a collaborative project established in 2012 as part of the INSPIRE (INtegrating and Scaling up PMTCT through Implementation REsearch) initiative. E4E is a cluster-randomized trial with 2 arms; Standard of care and "POC Plus" [in which point-of-care (POC) CD4 devices and related counseling support are provided]; aimed at improving retention-in-care of HIV-infected pregnant women and mothers. In November 2013, Zimbabwe adopted Option B+ for HIV-positive pregnant women under which antiretroviral treatment eligibility is no longer based on CD4 count. However, Ministry of Health and Child Care guidelines still require baseline and 6-monthly CD4 testing for treatment monitoring, until viral load testing becomes widely available. Considering the current limited capacity for viral-load testing, the significant investments in CD4 testing already made and the historical reliance on CD4 by health care workers for determining eligibility for antiretroviral treatment, E4E seeks to compare the impact of the provision of POC CD4 technology and early knowledge of CD4 levels on retention-in-care at 12 months, with the current standard of routine, laboratory-based CD4 testing. The study also compares rates of initiation and time-to-initiation between the 2 arms and according to level of maternal CD4 count, the cost of retaining HIV-positive pregnant women in care and the acceptability and feasibility of POC CD4 in the context of Option B+. Outcome measures are derived from routine health systems data. E4E will provide data on POC CD4 testing and retention-in-care associated with Option B+ and serve as an early learning platform to inform implementation of Option B+ in Zimbabwe.

Epidemiologic and genotypic characteristics of rotavirus strains detected in children less than 5 years of age with gastroenteritis treated at 3 pediatric hospitals in Zimbabwe during 2008-2011.

BACKGROUND: In anticipation of rotavirus vaccine introduction, the Zimbabwe Ministry of Health initiated rotavirus surveillance in 2008 to describe the rotavirus epidemiological trends and circulating genotypes among children <5 years of age. METHODS: Active hospital-based surveillance for diarrhea was conducted at 3 sentinel sites from January 2008 to December 2011. Children aged <5 years, who presented with acute gastroenteritis as a primary illness and who were admitted to a hospital ward or treated at the emergency unit, were enrolled in the surveillance program and had a stool specimen collected and tested for rotavirus by enzyme immunoassay. Genotyping of a sample of positive specimens was performed using reverse-transcription polymerase chain reaction. RESULTS: A total of 3728 faecal samples were collected and tested during the 4 year surveillance period and 1804 (48.5%) tested rotavirus positive. The highest prevalence of rotavirus diarrhea was found during the dry, cool season. Rotavirus positivity peaked in children 3-17 months of age with almost 80% of cases. Compared with rotavirus-negative cases, rotavirus-positive cases were more likely to be dehydrated (26% vs. 14%, P ≤ 0.001) and have vomiting (77% vs. 57%, P ≤ 0.001) and less likely to have fever (17% vs. 24%, P = 0.03). G9P[8] (43.3%), G1P[8] (11.8%), G2P[4] (8.7%), G2P[6] (8.7%) and G12P[6] (8.7%) were the most common genotypes detected. DISCUSSION: Rotavirus causes a significant disease burden among children <5 years of age in Zimbabwe. This active surveillance system can serve as a platform to monitor the impact of rotavirus vaccine on disease burden following vaccine introduction.

Maximising mentorship: Variations in laboratory mentorship models implemented in Zimbabwe.

BACKGROUND: Laboratory mentorship has proven to be an effective tool in building capacity and assisting laboratories in establishing quality management systems. The Zimbabwean Ministry of Health and Child Welfare implemented four mentorship models in 19 laboratories in conjunction with the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme. OBJECTIVES: This study outlines how the different models were implemented, cost involved per model and results achieved. METHODS: Eleven of the laboratories had been trained previously in SLMTA (Cohort I). They were assigned to one of three mentorship models based on programmatic considerations: Laboratory Manager Mentorship (Model 1, four laboratories); One Week per Month Mentorship (Model 2, four laboratories); and Cyclical Embedded Mentorship (Model 3, three laboratories). The remaining eight laboratories (Cohort II) were enrolled in Cyclical Embedded Mentorship incorporated with SLMTA training (Model 4). Progress was evaluated using a standardised audit checklist. RESULTS: At SLMTA baseline, Model 1-3 laboratories had a median score of 30%. After SLMTA, at mentorship baseline, they had a median score of 54%. At the post-mentorship audit they reached a median score of 75%. Each of the three mentorship models for Cohort I had similar median improvements from pre- to post-mentorship (17 percentage points for Model 1, 23 for Model 2 and 25 for Model 3; p > 0.10 for each comparison). The eight Model 4 laboratories had a median baseline score of 24%; after mentorship, their median score increased to 63%. Median improvements from pre-SLMTA to post-mentorship were similar for all four models. CONCLUSION: Several mentorship models can be considered by countries depending on the available resources for their accreditation implementation plan.

Weighing the costs: Implementing the SLMTA programme in Zimbabwe using internal versus external facilitators.

BACKGROUND: In 2010, the Zimbabwe Ministry of Health and Child Welfare (MoHCW) adopted the Strengthening Laboratory Management Toward Accreditation (SLMTA) programme as a tool for laboratory quality systems strengthening. OBJECTIVES: To evaluate the financial costs of SLMTA implementation using two models (external facilitators; and internal local or MoHCW facilitators) from the perspective of the implementing partner and to estimate resources needed to scale up the programme nationally in all 10 provinces. METHODS: The average expenditure per laboratory was calculated based on accounting records; calculations included implementing partner expenses but excluded in-kind contributions and salaries of local facilitators and trainees. We also estimated theoretical financial costs, keeping all contextual variables constant across the two models. Resource needs for future national expansion were estimated based on a two-phase implementation plan, in which 12 laboratories in each of five provinces would implement SLMTA per phase; for the internal facilitator model, 20 facilitators would be trained at the beginning of each phase. RESULTS: The average expenditure to implement SLMTA in 11 laboratories using external facilitators was approximately US$5800 per laboratory; expenditure in 19 laboratories using internal facilitators was approximately $6000 per laboratory. The theoretical financial cost of implementing a 12-laboratory SLMTA cohort keeping all contextual variables constant would be approximately $58 000 using external facilitators; or $15 000 using internal facilitators, plus $86 000 to train 20 facilitators. The financial cost for subsequent SLMTA cohorts using the previously-trained internal facilitators would be approximately $15 000, yielding a break-even point of 2 cohorts, at $116 000 for either model. Estimated resources required for national implementation in 120 laboratories would therefore be $580 000 using external facilitators ($58 000 per province) and $322 000 using internal facilitators ($86 000 for facilitator training in each of two phases plus $15 000 for SLMTA implementation in each province). CONCLUSION: Investing in training of internal facilitators will result in substantial savings over the scale-up of the programme. Our study provides information to assist policy makers to develop strategic plans for investing in laboratory strengthening.

Evaluation of the PIMA point-of-care CD4 analyzer in VCT clinics in Zimbabwe.

Point-of-care (POC) CD4 testing was implemented at a stand-alone HIV voluntary testing and counseling centre in Harare, Zimbabwe. To validate the use of this new technology, paired blood samples were collected from 165 patients either by a nurse or a laboratory technician and tested using POC and conventional laboratory CD4 machines. Finger prick (capillary) blood was collected directly into the PIMA POC CD4 Analyzer cartridges and tested immediately, whereas venous blood collected into evacuated tubes was used for CD4 enumeration on a Becton Dickinson FACSCalibur. There was no significant difference in mean absolute CD4 counts between the POC PIMA and Becton Dickinson FACSCalibur platforms (+7.6 cells/microL; P = 0.72). Additionally, there was no significant difference in CD4 counts between the platforms when run by either a nurse (+18.0 cells/microL; P = 0.49), or a laboratory technicians (-3.1 cells/microL; P = 0.93). This study demonstrates that POC CD4 testing can be conducted in a voluntary testing and counseling setting for staging HIV-positive clients. Both nurses and laboratory technicians performed the test accurately, thereby increasing the human resources available for POC CD4 testing. By producing same-day results, POC CD4 facilitates immediate decision-making, patient management and referral and may help improve patient care and retention. POC CD4 may also alleviate testing burdens at traditional central CD4 laboratories, hence improving test access in both rural and urban environments.