Health Policy Alternatives, Inc.

ABSTRACTPublic health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed.In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.

Supermarkets are traditionally viewed by development economists, policymakers, and practitioners as the rich world’s place to shop. The three regions discussed here have the great majority of the poor on the planet. But supermarkets are no longer just niche players for rich consumers in the capital cities of the countries in these regions. The rapid rise of supermarkets in these regions in the past 5-10 years has transformed agrifood markets – at different rates and depths across regions and countries. Many of those transformations present great challenges – even exclusion – for small farms, processing and distribution firms, but also potentially great opportunities. Development models, policy and programs need to adapt to this radical change.This brief article describes this transformation of agrifood systems in Africa, Asia (excluding Japan), and Latin America. First, we describe the traditional retail and wholesale system in the midst of which emerged modern food retailing and its procurement system. Second, we discuss the determinants of and patterns in the diffusion of supermarkets in the three regions. Third, we discuss the evolution of procurement systems of those supermarkets, and consequences for agrifood systems. At the end, we hint at emerging implications for farms and firms in the region.