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ARS Home » Research » Research Project #444704

Research Project: Characterization of Emerging Zoonotic Threats

Location: Zoonotic and Emerging Disease Research

Project Number: 3022-32000-027-008-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 22, 2023
End Date: Aug 21, 2028

Investigate the prevalence of emerging zoonotic threats in Nigeria, a country that is home to over 200 million people. The growing urbanization of the area has led to decreased pastures and increases in human and animal contact. Moreover, Nigeria is a hub with cattle migrations from Cameroon, Niger, Burkina Faso and Chad. The border is considered porous with an estimated 1500 unofficial border crossings. In Nigeria, evidence suggests that large animals such cattle, donkeys and camels are mainly brought in through Borno, Sokoto, Katsina, Adamawa, and Taraba states from Eastern and central African countries. Movement and trade of animals along these borders provide a route by which numerous pathogens can come together. Coupled with the inefficient quarantine and screening of incoming animals, people and animals can be exposed to zoonotic and transboundary pathogens, in an environment where novel pathogens can quickly amplify and spread internationally posing health risks. Generally, Nigeria’s surveillance system remains suboptimal in its capacity to monitor and track animal transboundary diseases and emerging zoonotic pathogens. Till date there is no genomic surveillance system to monitor diseases or track their genetic variations, evolution and spread of endemic and emerging pathogens. Thus there is paucity of information for public health intervention and for the development of diagnosis, therapy and vaccines. Most significantly, the true geographic distribution and risk of emerging zoonotic pathogens is unknown primarily due lack of surveillance or systematic investigations in most countries in the subregion including West Africa. This presents significant public health and animal health risk regionally and internationally. Meanwhile the presence of competent vectors (arthropods), hosts ( wild and domestic animals) and suitable weather and climate conditions in West Africa provide strong indication that pathogenic organisms may be circulating in Nigeria or West Africa. We hypothesize that given the porous boundaries, the ecosystem and the conducive environmental conditions in West Africa, many unknown and re-emerging pathogens are circulating and are maintained in animals, environment and arthropod vector populations in Nigeria. Outbreaks of Ebola, Lassa Fever and Mpox have however helped reinforce one of the strongest public health responses in the region. ACEGID, Redeemer's University has become a hub for sequencing and a referral center for many surrounding countries. We plan therefore to leverage the existing Next generation sequencing, metagenomics and Bioinformatics capacity available at ACEGID, Redeemer’s University, Ede, to unravel the presence and the extent of genetic diversity of a few emerging zoonotic pathogens in Southern Nigeria.

Aim 1. Active disease genomic surveillance of animal weak or recumbent or dead animals Employ shotgun next-generation sequencing using the illumina platform to identify and describe emerging pathogens from weak, recumbent or dead animals sampled at major animal markets from 3 study sites in southwest Nigeria, specifically in Ogun, Oyo and Osun states. A total of 300 animals with a history of unexplained deaths, or found weak and recumbent will be sampled, i.e., 5-10 mls of blood, oral swabs, and rectal swabs will be collected. The animals to be sampled will include cattle, small ruminants and pigs. Additionally, 300 arthropod (ticks) vectors will be collected from sampled animals. The samples collected will be processed and preserved in DNA/RNA shield or Trizol before storage at -80°c until analyzed. Meta data including geospatial locations, clinical presentations and other information available will be collected. From the 300 animals and 300 ticks (pooled to make 50 samples), a total of 200 suspect samples of interest (150 from animals/50 from ticks) will be sequenced. Prior to sequencing each sample’s nucleic acid will be extracted using QIAGEN RNA extraction kit. Library preparation and sequencing using the viral metagenomic protocol on Illumina platform described by Hameed et al., 2020 will be carried out. Aim 2: Serologic investigation of prospective and historic samples From the findings recorded from sequenced data in the first aim, zoonotic pathogens suspected to be Crimean Congo Hemorrhagic fever virus (CCHFV), West Nile virus, Orthopox virus, Lassa virus, and Dengue virus will be selected for serologic investigation, if antigen targets are already commercially available for the serologic investigation of 100 historic samples stored at ACEGID and 200 prospective plasma samples. We will use the luminex multiplex platform for the IgG and/or IgM detection of the above selected zoonotic pathogens using the same commercially available multiplex kit. Aim 3: Characterization of historical samples From the serologically positive historical samples (preferably IgM positive), 50 will be selected for shotgun sequencing using the Illumina platform as described above. Sequences generated will be submitted to the GenBank. They will enable us to describe the viruses, their genetic variations. We will perform comparative genomic analysis of the sequences generated from the project from samples across animal species (including ticks) and study locations. We will also evaluate our generated sequences against the reference genomes in GenBank. Diversity will also be looked at vis a vis the origin of the animals and other metadata. Bayesian molecular timeline phylogenetic analysis will be done to determine the dynamic of the viruses found.