Access and benefit sharing policies for climate resilient seed systems: matching global commitments with national realities.

This synthesis paper provides a summary of main findings on climate resilient seed systems and access and benefit sharing of case studies from Uganda, Rwanda, Zambia and Zimbabwe. This study analyses what is actually happening at the national and subnational levels in terms of climate change, its impacts on particular crops, what experiences countries have had to date in terms of accessing, using and sharing benefits derived from genetic resources for climate change adaptation, and what kinds of ABS policy initiatives or reforms could help those countries to make better use of genetic diversity for climate change adaptation in the future. This study is designed to analyze how these different ‘threads’ come together at national and subnational level in the four countries. Findings from these studies indicate that countries are already facing climate change which is affecting farmers and shaping their needs in terms of suitably adapted seed. As a result, the countries are embracing (inter and intra specific) crop diversification as a means to adapt to climate changes. This depends upon accessibility, availability and use of inter and intra specific crop genetic diversity from local, national and international sources. The proportion of PGRFA in the countries’ national genebanks that is potentially adaptable to that country’s changing climate is decreasing over time (as climates change more). National level research and the development of new varieties is also not sufficient to meet these demands. Countries are therefore becoming more interdependent. There are also significant constraints on ability to access, use and share benefits associated with materials in other countries as a result of the lack of on-line accession level documentation (and linked implementation of ITPGRFA and Nagoya Protocol) and lack of proper polices, legislation and guidelines on ABS. The study therefore recommends that international partnerships and programmes are important mechanisms for the exchanges of genetic resources into and out of the four countries for agricultural research and development especially at regional level and that the ITPGRFA and Nagoya Protocol are not self-executing agreements but need to be proactively implemented. In addition, considerable investment in capacity building is necessary for stakeholders – including farmers – to be able to exchange genetic resources in a way that makes seed systems more resilient

Access and benefit-sharing policies for climate-resilient seed systems.

The synthesis report is part of a series of papers on Integrated Seed Sector Development (ISSD) in Africa’s thematic working group on Matching national realities with global commitments. The thematic working group addressed the main question on how African governments implement their global commitments while fostering a viable pluralistic sector. The main hypothesis was that making these commitments more coherent with the practices and realities of farmers and creating an enabling environment for strengthening multiple seed systems will increase farmers’ access to quality seed. Three main topics were discussed under this theme: access and benefit sharing for climate resilient seed systems; national and regional seed laws that support the development of a robust, integrated seed sector that supports smallholder farmers' needs; and creating room for informal and intermediary seed systems in a UPOV '91 informed Plant Variety Protection system. This study provides an overview of climate related changes in past, present and future and the challenges to access to and exchange of genetic resources for climate change adaptation through different access and benefit sharing regimes in 4 countries – Zambia, Zimbabwe, Rwanda and Uganda. Findings from the studies indicate that most African countries face challenges in accessing required PGR for climate change adaptation because they do not have online accession-level documentation; they have not fully implemented international commitments related to ABS and national and regional seed laws hamper the flow of seeds and genetic resources. As a way forward the paper proposes capacity development for mutually supportive implementation of the ITPGRFA, Nagoya protocol and seed laws in ways which reflect the reality and diversity of different seed systems

Close kinship within multiple-genotype malaria parasite infections

Malaria infections containing multiple parasite genotypes are ubiquitous in nature, and play a central role in models of recombination, intra-host dynamics, virulence, sex ratio, immunity and drug resistance evolution in Plasmodium. While these multiple infections (MIs) are often assumed to result from superinfection (bites from multiple infected mosquitoes), we know remarkably little about their composition or generation. We isolated 336 parasite clones from eight patients from Malawi (high transmission) and six from Thailand (low transmission) by dilution cloning. These were genotyped using 384 single-nucleotide polymorphisms, revealing 22 independent haplotypes in Malawi (2–6 per MI) and 15 in Thailand (2–5 per MI). Surprisingly, all six patients from Thailand and six of eight from Malawi contained related haplotypes, and haplotypes were more similar within- than between-infections. These results argue against a simple superinfection model. Instead, the observed kinship patterns may be explained by inoculation of multiple related haploid sporozoites from single mosquito bites, by immune suppression of parasite subpopulations within infections, and serial transmission of related parasites between people. That relatedness is maintained in endemic areas in the face of repeated bites from infected mosquitoes has profound implications for understanding malaria transmission, immunity and intra-host dynamics of co-infecting parasite genotypes

"I have failed to separate my HIV from this pain": the challenge of managing chronic pain among people with HIV

Pain is a highly prevalent and burdensome symptom among people with HIV (PWH). This study aims to identify how the experience of living with HIV and chronic pain influences pain beliefs, health-seeking and pain management. Thirty-nine purposively sampled PWH with chronic pain (sample characteristics = 61% women, 79% Black, Asian and minority ethnic groups, 18% men who have sex with men, 45-54 median age category) participated in focus groups in London. Focus groups were co-facilitated with community members. Transcripts wereanalysed using a thematic approach. Findings revealed that HIV stigma, fractured care pathways, and general practitioners' lack of HIV training are barriers to supported pain management. Unaddressed pain results in poorer mental health and reduced quality of life, which has important clinical implications for HIV treatment adherence. Creating HIV-specific pain resources, activating social networks, and pain self-management techniques are potential solutions. Person-centred assessment and HIV training is needed to help clinicians identify PWH with chronic pain. Clear guidelines need to be developed to identify which health service providers are responsible for chronic pain management in PWH. This study generated a refined version of the Fear Avoidance Model that introduces a dimension of HIV-specific behaviours that impact PWHs seeking chronic pain management

Leveraging routine viral load testing to integrate diabetes screening among patients on antiretroviral therapy in Malawi

Background People living with HIV are at an increased risk of diabetes mellitus due to HIV infection and exposure to antiretroviral therapy (ART). Despite this, integrated diabetes screening has not been implemented commonly in African HIV clinics. Our objective was to explore the feasibility of integrating diabetes screening into existing routine HIV viral load (VL) monitoring and to determine a group of HIV patients that benefit from a targeted screening for diabetes. Methods A mixed methods study was conducted from January to July 2018 among patients on ART aged≥18 y and healthcare workers at an urban HIV clinic in Zomba Central Hospital, Malawi. Patients who were due for routine VL monitoring underwent a finger-prick for simultaneous point-of-care glucose measurement and dried blood spot sampling for a VL test. Diabetes was diagnosed according to WHO criteria. We collected demographic and medical history information using an interviewer-administered questionnaire and electronic medical records. We conducted focus group discussions among healthcare workers about their experience and perceptions regarding the integrated diabetes screening program. Results Of patients undergoing routine VL monitoring, 1316 of 1385 (95%) had simultaneous screening for diabetes during the study period. The median age was 44 y (IQR: 38–53); 61% were female; 28% overweight or obese; and median ART duration was 83 mo (IQR: 48–115). At baseline, median CD4 count was 199 cells/mm3 (IQR: 102–277) and 50% were in WHO clinical stages I or II; 45% were previously exposed to stavudine and 88% were virologically suppressed (<1000 copies/mL). Diabetes prevalence was 31/1316 (2.4%). Diabetes diagnosis was associated with age ≥40 y (adjusted OR [aOR] 7.44; 95% CI: 1.74 to 31.80), being overweight and/or obese (aOR 2.46; 95% CI: 1.13 to 5.38) and being on a protease inhibitor-based ART regimen (aOR 5.78; 95% CI: 2.30 to 14.50). Healthcare workers appreciated integrated diabetes screening but also reported challenges including increased waiting time, additional workload and inadequate communication of results to patients. Conclusions Integrating diabetes screening with routine VL monitoring (every 2 y) seems feasible and was valued by healthcare workers. The additional cost of adding diabetes screening into VL clinics requires further study and could benefit from a targeted approach prioritizing patients aged ≥40 y, being overweight/obese and on protease inhibitor-based regimens

Admissions to a Low-Resource Neonatal Unit in Malawi Using a Mobile App and Dashboard: A 1-Year Digital Perinatal Outcome Audit

Introduction: Understanding the extent and cause of high neonatal deaths rates in Sub-Saharan Africa is a challenge, especially in the presence of poor-quality and inaccurate data. The NeoTree digital data capture and quality improvement system has been live at Kamuzu Central Hospital, Neonatal Unit, Malawi, since April 2019. Objective: To describe patterns of admissions and outcomes in babies admitted to a Malawian neonatal unit over a 1-year period via a prototype data dashboard. Methods: Data were collected prospectively at the point of care, using the NeoTree app, which includes digital admission and outcome forms containing embedded clinical decision and management support and education in newborn care according to evidence-based guidelines. Data were exported and visualised using Microsoft Power BI. Descriptive and inferential analysis statistics were executed using R. Results: Data collected via NeoTree were 100% for all mandatory fields and, on average, 96% complete across all fields. Coverage of admissions, discharges, and deaths was 97, 99, and 91%, respectively, when compared with the ward logbook. A total of 2,732 neonates were admitted and 2,413 (88.3%) had an electronic outcome recorded: 1,899 (78.7%) were discharged alive, 12 (0.5%) were referred to another hospital, 10 (0.4%) absconded, and 492 (20%) babies died. The overall case fatality rate (CFR) was 204/1,000 admissions. Babies who were premature, low birth weight, out born, or hypothermic on admission, and had significantly higher CFR. Lead causes of death were prematurity with respiratory distress (n = 252, 51%), neonatal sepsis (n = 116, 23%), and neonatal encephalopathy (n = 80, 16%). The most common perceived modifiable factors in death were inadequate monitoring of vital signs and suboptimal management of sepsis. Two hundred and two (8.1%) neonates were HIV exposed, of whom a third [59 (29.2%)] did not receive prophylactic nevirapine, hence vulnerable to vertical infection. Conclusion: A digital data capture and quality improvement system was successfully deployed in a low resource neonatal unit with high (1 in 5) mortality rates providing and visualising reliable, timely, and complete data describing patterns, risk factors, and modifiable causes of newborn mortality. Key targets for quality improvement were identified. Future research will explore the impact of the NeoTree on quality of care and newborn survival

Indirect impacts of the COVID-19 pandemic at two tertiary neonatal units in Zimbabwe and Malawi: an interrupted time series analysis.

OBJECTIVES: To examine indirect impacts of the COVID-19 pandemic on neonatal care in low-income and middle-income countries. DESIGN: Interrupted time series analysis. SETTING: Two tertiary neonatal units in Harare, Zimbabwe and Lilongwe, Malawi. PARTICIPANTS: We included a total of 6800 neonates who were admitted to either neonatal unit from 1 June 2019 to 25 September 2020 (Zimbabwe: 3450; Malawi: 3350). We applied no specific exclusion criteria. INTERVENTIONS: The first cases of COVID-19 in each country (Zimbabwe: 20 March 2020; Malawi: 3 April 2020). PRIMARY OUTCOME MEASURES: Changes in the number of admissions, gestational age and birth weight, source of admission referrals, prevalence of neonatal encephalopathy, and overall mortality before and after the first cases of COVID-19. RESULTS: Admission numbers in Zimbabwe did not initially change after the first case of COVID-19 but fell by 48% during a nurses' strike (relative risk (RR) 0.52, 95% CI 0.41 to 0.66, p0.05). CONCLUSIONS: The indirect impacts of COVID-19 are context-specific. While our study provides vital evidence to inform health providers and policy-makers, national data are required to ascertain the true impacts of the pandemic on newborn health

Population Structure Shapes Copy Number Variation in Malaria Parasites.

If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in seven countries in Africa, South East Asia and South America using a high-density single-nucleotide polymorphism/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500 bp to 59 kb, as well as 10,107 flanking, biallelic single-nucleotide polymorphisms. Overall, CNVs were rare, small, and skewed toward low frequency variants, consistent with the deleterious model. Relative to African and South East Asian populations, CNVs were significantly more common in South America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g., DNA helicase and three conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen