Detection in wastewaters, genotypic analysis and microbiome interactions of SARS-CoV-2 in Botswana and South Africa

First described in Wuhan City, China in December 2020, the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the disease it causes (COVID-19) are fast evolving subjects with significant global health concern. In Botswana, 48 confirmed COVID-19 cases resulting in a single fatality have been reported as of 10th June, 2020. Faecal shedding of SARS-CoV-2 RNA from COVID-19 patients has since been reported. For Botswana, where wastewater is occasionally used for agricultural purposes, surveillance of the SARS-CoV-2 virus in this respect is necessary to identify possible risks associated with this phenomenon. Several farms along the Gaborone wastewater system harvest and use these untreated sewage water for irrigation of fresh vegetables. The potential presence, and possible transference on fresh produce, presents renewed public health risks amid the COVID-19 pandemic especially if produce is consumed raw. Furthermore the personnel involved in the handling of these wastewaters present another potential risk. Thus, this study aims to perform molecular surveillance of SARS-CoV-2 and determine the role of wastewater environments in the genetic profile of the virus. In addition, we intend to elucidate microbial biomes associated with wastewater systems and determine their possible role in the evolution of SARS-CoV-2 in Botswana Expected Outputs 1. Provision of the first ever estimate of prevalence of SARS-CoV-2 in sewage water and its environs, in wastewater effluents destined for irrigation and the irrigated crops in Botswana. Detection of the virus in these environments will be significant as they may drive programs and regulations aimed at curbing the potential spread of the virus to wastewater treatment workers, farmworkers who may be exposed to SARS-CoV-2 contaminated water and vegetables and subsequently, the possible spread of the virus to the community by this group of workers. 2. In order to control and manage a disease, an in-depth understanding of the etiologic agent and its local adaptation and evolution is imperative. Therefore, knowledge on the circulating strains of SARS-CoV-2 may aid targeted treatment and consequently control and management of COVID-19 infections in Botswana. This work may provide new insights into the evolution of SARS-CoV-2 in the Botswana environment and its pattern of spread in the community. Data generated on the molecular divergence of SARS-CoV-2 strains in Botswana may aid strategies aimed at targeted treatment and control of circulating strains in Botswana. From a sub-regional perspective, it is important to understand phylogenetic relatedness and metagenomics variations of strains prevailing in Botswana and South Africa. 3. Phylogenetic data will be supplemented with biome interactions obtained from microbiome analysis. We propose to obtain microbiome data from different sanitation water ponds at GVWTP and associated air and environmental surfaces. Additional microbiome data will be obtained from vegetables and bioaerosol samples at horticultural farms irrigated with sewage water. To assess the impact of microbiota on the molecular evolution and/or adaptation of SARS-CoV-2 at these sites, we will measure mutation rates across the biomes studied herein.