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Research Project: Rift Valley Fever Pathogenesis, Epidemiology, and Control Measures

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Title: SARS-CoV-2 strain dominance in an adult white-tailed deer co-infection experiment

item MCDOWELL, CHESTER - Kansas State University
item MEEKINS, DAVID - Kansas State University
item COOL, KONNER - Kansas State University
item TRUJILLO, JESSIE - Kansas State University
item GAUDREAULT, NATASHA - Kansas State University
item BALARAMAN, VELMURUGAN - Kansas State University
item MOROZOV, IGOR - Kansas State University
item Wilson, William
item GARCIA-SASTRE, ADOLFO - The Icahn School Of Medicine At Mount Sinai
item RICHT, JUERGEN - Kansas State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/22/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Objective: The zoonotic betacoronavirus SARS-CoV-2 has spread rapidly around the world resulting in a global public health crisis. Early in the pandemic, the genetic lineage A of SARS-CoV-2 dominated. However, as the virus continues to circulate, variants of concern (VOCs), characterized by increased fitness and transmissibility, have emerged. The lineage B alpha VOC, (B.1.1.7 or UK variant) emerged in the fall of 2020, and has rapidly become a dominant variant. Additional beta, gamma, and delta VOCs emerged in mid to late 2020 in South Africa, Brazil, and India, respectively. A thorough understanding of potential wildlife reservoirs is needed for developing effective control strategies for SARS-CoV-2. White-tailed deer (Odocoileus virginianus) fawns have been shown to be susceptible to SARS-CoV-2. To investigate the role of an emerging VOC in this host, we conducted a competition experiment whereby adult white-tailed deer (WTD) were co-infected with lineage A (USA-WA1/2020) and lineage B alpha variant (B.1.1.7-like; USA/CA_CDC_5545/2020) SARS-CoV-2 isolates. Methods: Nasal/oropharyngeal swabs and respiratory tissues from adult WTD, which were co-infected intranasally and orally, were evaluated using next generation sequencing (NGS) and BLAST-based analysis, and the percentages of the individual lineage A and B viruses were determined at multiple time points post-infection. NGS results were confirmed using lineage A and B-specific RT-qPCR assays targeting a non-conserved region within the spike gene. Results: The SARS-CoV-2 lineage B alpha variant quickly became the dominant virus in WTD following co-infection with lineage A and B viruses. The lineage A strain was only recovered at early time points in small quantities. Additionally, our preliminary data shows that the RT-qPCR assays were capable of differentiating both SARS-CoV-2 lineages. Conclusion: The SARS-CoV-2 lineage B alpha variant has improved fitness compared to the lineage A virus in adult WTD. The RT-qPCR assays could potentially be used in epidemiological surveillance for VOCs in human and animal populations.