A simplified approach for producing Tier 2 enteric-methane emission factors based on East African smallholder farm data

Context: Accurate reporting of livestock greenhouse-gas (GHG) emissions is important in developing effective mitigation strategies, but the cost and labour requirements associated with on-farm data collection often prevent this effort in low- and middle-income countries. Aim: The aim of this study was to investigate the precision and accuracy of simplified activity data collection protocols in African smallholder livestock farms for country-specific enteric-methane emission factors. Method: Activity data such as live weight (LW), feed quality, milk yield, and milk composition were collected from 257 smallholder farms, with a total herd of 1035 heads of cattle in Nandi and Bomet counties in western Kenya. The data collection protocol was then altered by substituting the actual LW measurements with algorithm LW (ALG), feed quality (FQ) data being sourced from the Feedipedia database, reducing the need for daily milk yield records to a single seasonal milk measurement (MiY), and by using a default energy content of milk (MiE). Daily methane production (DMP) was calculated using these simplified protocols and the estimates under individual and combined protocols were compared with values derived from the published (PUBL) estimation protocol. Key results: Employing the algorithm LW showed good agreement in DMP, with only a small negative bias (7%) and almost no change in variance. Calculating DMP on the basis of Feedipedia FQ, by contrast, resulted in a 27% increase in variation and a 27% positive bias for DMP compared with PUBL. The substitutions of milk (MiY and MiE) showed a modest change in variance and almost no bias in DMP. Conclusion: It is feasible to use a simplified data collection protocol by using algorithm LW, default energy content of milk value, seasonal single milk yield data, but full sampling and analysis of feed resources is required to produce reliable Tier 2 enteric-methane emission factors. Implications: Reducing enteric methane emissions from the livestock is a promising pathway to reduce the effects of climate change, and, hence, the need to produce accurate emission estimates as a benchmark to measure the effectiveness of mitigation options. However, it is expensive to produce accurate emission estimates, especially in developing countries; hence, it is important and feasible to simplify on-farm data collection

A simplified approach for producing Tier 2 enteric methane emission factors based on East African smallholder farm data

Context: Accurate livestock greenhouse gas (GHG) emissions reporting is important in developing effective mitigation strategies, but the cost and labor requirements associated with on-farm data collection often prevent this effort in low-and-middle-income countries. Aim: The aim of this study was to investigate the precision and accuracy of simplified activity data collection protocols in African smallholder livestock farms for country-specific enteric methane emission factors. Method: Activity data such as live weight (LW), feed quality, milk yield, and milk composition were collected from 257 smallholder farms with a total herd of 1,035 heads of cattle in Nandi and Bomet counties in Western Kenya. The data collection protocol was then altered by substituting actual LW measurements with algorithm LW (ALG), feed quality (FQ) data sourced from the Feedipedia database, reducing the need for daily milk yield records to a single seasonal milk measurement (MiY), and using a default energy content of milk (MiE). Daily methane production (DMP) was calculated using these simplified protocols and the estimates under individual and combined protocols were compared with values derived from the published (PUBL) estimation protocol. Key results: Employing the algorithm LW showed good agreement in DMP with only a small negative bias (7%) and almost no change in variance. Calculating DMP based on Feedipedia FQ, by contrast, resulted in a 27% increase in variation and a 27% positive bias for DMP compared to PUBL. The substitutions of milk (MiY and MiE) showed a modest change in variance and almost no bias in DMP. Conclusion: It is feasible to use a simplified data collection protocol by using algorithm LW, default energy content of milk value, seasonal single milk yield data, but full sampling and analysis of feed resources is required to produce reliable Tier 2 enteric methane emission factors. Implications: Reducing enteric methane emissions from the livestock is a promising pathway to reduce the effects of climate change hence the need to produce accurate emissions estimates as benchmark to measure the effectiveness of mitigation options. However, it is expensive to produce accurate emission estimates especially in developing countries, hence important and feasible to simplify on-farm data collection

Farm-level emission intensities of smallholder cattle (Bos indicus; B. indicus–B. taurus crosses) production systems in highlands and semi-arid regions

Ruminants are central to the economic and nutritional life of much of sub-Saharan Africa, but cattle are now blamed for having a disproportionately large negative environmental impact through emissions of greenhouse gas (GHG). However, the mechanism underlying excessive emissions occurring only on some farms is imperfectly understood. Reliable estimates of emissions themselves are frequently lacking due to a paucity of reliable data. Employing individual animal records obtained at regular farm visits, this study quantified farm-level emission intensities (EIs) of greenhouse gases of smallholder farms in three counties in Western Kenya. CP was chosen as the functional unit to capture the outputs of both milk and meat. The results showed that milk is responsible for 80–85% of total CP output. Farm EI ranged widely from 20 to >1 000 kg CO$_{2}$-eq/kg CP. Median EIs were 60 (Nandi), 71 (Bomet), and 90 (Nyando) kg CO$_{2}$-eq/kg. Although median EIs referenced to milk alone (2.3 kg CO$_{2}$-eq/kg milk) were almost twice that reported for Europe, up to 50% of farms had EIs comparable to the mean Pan-European EIs. Enteric methane (CH$_{4}$) contributed >95% of emissions and manure ∼4%, with negligible emissions attributed to inputs to the production system. Collecting data from individual animals on smallholder farms enabled the demonstration of extremely heterogeneous EI status among similar geographical spaces and provides clear indicators on how low EI status may be achieved in these environments. Contrary to common belief, our data show that industrial-style intensification is not required to achieve low EI. Enteric CH$_{4}$ production overwhelmingly drives farm emissions in these systems and as this is strongly collinear with nutrition and intake, an effort will be required to achieve an “efficient frontier” between feed intake, productivity, and GHG emissions

Securing Africa’s health sovereignty : why investing in science and innovation matters

This paper aims at provoking broad-based dialogues and debates on ways and means of securing Africa’s health sovereignty. It argues that health sovereignty is about the realization of specific national constitutional and policy objectives on citizens’ access to and enjoyment of good health, resilient to COVID-19 and related disease pandemics. The paper also emphasizes the urgency of African countries fulfilling their commitments under global and regional declarations on health research. Investing in research, knowledge and innovation is critical to fight and win the war against COVID-19 and other diseases that undermine economic productivity and competitiveness of African countries. There is also a need for venture capitalists to demonstrate bankable ideas emanating from the science academies and funded by National Science Foundations. The base teachings at school level need to significantly invest in the “African philosophy” to create a shift in mind-set from the “grab and own without use mentality that is currently predominant on the continent. The paper recommends that executive, political and science leadership are needed to strengthen national health research and innovation systems through improved evidence-based policy implementation. With these thrusts working effectively together, rather than in silos, will afford the African continent to emerge victoriously in the combat against COVID-19 and other disease burdens

HIV viremia is associated with compromised SARS-CoV-2 Beta variant neutralization

Background:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may be associated with worse clinical outcomes in people with human immunodeficiency virus (HIV) (PWH). We report anti–SARS-CoV-2 antibody responses in patients hospitalized with coronavirus disease 2019 in Durban, South Africa, during the second SARS-CoV-2 infection wave dominated by the Beta (B.1.351) variant.Methods:Thirty-four participants with confirmed SARS-CoV-2 infection were followed up with weekly blood sampling to examine antibody levels and neutralization potency against SARS-CoV-2 variants. Participants included 18 PWH, of whom 11 were HIV viremic.Results:SARS-CoV-2–specific antibody concentrations were generally lower in viremic PWH than in virologically suppressed PWH and HIV-negative participants, and neutralization of the Beta variant was 4.9-fold lower in viremic PWH. Most HIV-negative participants and antiretroviral therapy–suppressed PWH also neutralized the Delta (B.1.617.2) variant, whereas the majority of viremic PWH did not. CD4 cell counts Conclusions:HIV viremia was associated with reduced Beta variant neutralization. This highlights the importance of HIV suppression in maintaining an effective SARS-CoV-2 neutralization response

HIV transmission dynamics and population-wide drug resistance in rural South Africa

Despite expanded antiretroviral therapy (ART) in South Africa, HIV-1 transmission persists. Integrase strand transfer inhibitors (INSTI) and long-acting injectables offer potential for superior viral suppression, but pre-existing drug resistance could threaten their effectiveness. In a community-based study in rural KwaZulu-Natal, prior to widespread INSTI usage, we enroled 18,025 individuals to characterise HIV-1 drug resistance and transmission networks to inform public health strategies. HIV testing and reflex viral load quantification were performed, with deep sequencing (20% variant threshold) used to detect resistance mutations. Phylogenetic and geospatial analyses characterised transmission clusters. One-third of participants were HIV-positive, with 21.7% having detectable viral loads; 62.1% of those with detectable viral loads were ART-naïve. Resistance to older reverse transcriptase (RT)-targeting drugs was found, but INSTI resistance remained low (<1%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, particularly to rilpivirine (RPV) even in ART-naïve individuals, was concerning. Twenty percent of sequenced individuals belonged to transmission clusters, with geographic analysis highlighting higher clustering in peripheral and rural areas. Our findings suggest promise for INSTI-based strategies in this setting but underscore the need for RPV resistance screening before implementing long-acting cabotegravir (CAB) + RPV. The significant clustering emphasises the importance of geographically targeted interventions to effectively curb HIV-1 transmission

Testing of commercial inoculants to enhance P uptake and grain yield of promiscuous soybean in Kenya

The aim of this study was to assess the potential of commercial mycorrhizal inoculants and a rhizobial inoculant to improve soybean yield in Kenya. A promiscuous soybean variety was grown in a greenhouse pot study with two representative soils amended with either water-soluble mineral P or rock P to assess product performance. The performance of selected mycorrhizal inoculants combined with a rhizobial inoculant (Legumefix) was then assessed with farmer groups in three agroecological zones using a small-plot, randomized complete block design to assess soybean root colonization by mycorrhiza, nodulation, and plant biomass production in comparison to rhizobial inoculant alone or with water-soluble mineral P. Greenhouse results showed highly significant root colonization by commercial mycorrhizal inoculant alone (p < 0.001) and in interaction with soil type (p < 0.0001) and P source (p < 0.0001). However, no significant effect was shown in plant P uptake, biomass production, or leaf chlorophyll index. In field conditions, the e ects of mycorrhizal and rhizobial inoculants in combination or alone were highly context-specific and may induce either a significant increase or decrease in root mycorrhizal colonization and nodule formation. Mycorrhizal and rhizobial inoculants in combination or alone had limited effect on plant P uptake, biomass production, leaf chlorophyll index, and grain yield. Though some mycorrhizal inoculants induced significant root colonization by mycorrhizal inoculants, this did not lead to higher soybean yield, even in soils with limited P content. Our results are further evidence that inoculant type, soil type, and P source are critical factors to evaluate commercial inoculants on a context-specific basis. However, our results highlight the need for the identification of additional targeting criteria, as inoculant type, soil type, and P source alone were not enough to be predictive of the response. Without the identification of predictive criteria for improved targeting, the economic use of such inoculants will remain elusive

CD8 T cell response and evolutionary pressure to HIV-1 cryptic epitopes derived from antisense transcription

Retroviruses pack multiple genes into relatively small genomes by encoding several genes in the same genomic region with overlapping reading frames. Both sense and antisense HIV-1 transcripts contain open reading frames for known functional proteins as well as numerous alternative reading frames (ARFs). At least some ARFs have the potential to encode proteins of unknown function, and their antigenic properties can be considered as cryptic epitopes (CEs). To examine the extent of active immune response to virally encoded CEs, we analyzed human leukocyte antigen class I–associated polymorphisms in HIV-1 gag, pol, and nef genes from a large cohort of South Africans with chronic infection. In all, 391 CEs and 168 conventional epitopes were predicted, with the majority (307; 79%) of CEs derived from antisense transcripts. In further evaluation of CD8 T cell responses to a subset of the predicted CEs in patients with primary or chronic infection, both sense- and antisense-encoded CEs were immunogenic at both stages of infection. In addition, CEs often mutated during the first year of infection, which was consistent with immune selection for escape variants. These findings indicate that the HIV-1 genome might encode and deploy a large potential repertoire of unconventional epitopes to enhance vaccine-induced antiviral immunity