Citation: Fatoba, A.J.; Adeleke, V.T.; Maharaj, L.; Okpeku, M.; Adeniyi, A.A.; Adeleke, M.A. Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease. Viruses 2022, 14, 1456. https:// doi.org/10.3390/v14071456 Academic Editor: Hualan Chen Received: 28 April 2022 Accepted: 24 June 2022 Published: 30 June 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). viruses Article Design of a Multiepitope Vaccine against Chicken Anemia Virus Disease Abiodun Joseph Fatoba 1, * , Victoria T. Adeleke 2 , Leah Maharaj 1 , Moses Okpeku 1 , Adebayo A. Adeniyi 3,4 and Matthew A. Adeleke 1, * 1 Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, P/Bag X54001, Durban 4000, South Africa; leahmaharaj@gmail.com (L.M.); OkpekuM@ukzn.ac.za (M.O.) 2 Department of Chemical Engineering, Mangosuthu University of Technology, Umlazi, Durban 4031, South Africa; vickteni2006@yahoo.com 3 Department of Industrial Chemistry, Federal University, Oye-Ekiti P.O. Box 370111, Nigeria; adebayo.adeniyi@fuoye.edu.ng 4 Department of Chemistry, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa * Correspondence: abiodunfatoba85@gmail.com (A.J.F.); adelekem@ukzn.ac.za (M.A.A.) Abstract: Chicken anemia virus (CAV) causes severe clinical and sub-clinical infection in poultry globally and thus leads to economic losses. The drawbacks of the commercially available vaccines against CAV disease signal the need for a novel, safe, and effective vaccine design. In this study, a multiepitope vaccine (MEV) consisting of T-cell and B-cell epitopes from CAV viral proteins (VP1 and VP2) was computationally constructed with the help of linkers and adjuvant. The 3D model of the MEV construct was refined and validated by different online bioinformatics tools. Molecular docking showed stable interaction of the MEV construct with TLR3, and this was confirmed by Molecular Dynamics Simulation. Codon optimization and in silico cloning of the vaccine in pET-28a (+) vector also showed its potential expression in the E. coli K12 system. The immune simulation also indicated the ability of this vaccine to induce an effective immune response against this virus. Although the vaccine in this study was computationally constructed and still requires further in vivo study to confirm its effectiveness, this study marks a very important step towards designing a potential vaccine against CAV disease. Keywords: chicken anemia virus; disease; immunoinformatics; immune response; multiepitope; viral proteins 1. Introduction Chicken anemia virus (CAV) is a global challenge to the poultry industry as it causes severe anemia, hemorrhages, and immunosuppression in young chickens, leading to considerable economic losses [1,2]. Young chicks less than 3 weeks of age with maternally derived antibodies (MDA) are usually protected from severe clinical symptoms caused by the vertical transmission of this virus [1]. However, sub-clinical infections (such as a high feed conversion ratio and low weight) through the horizontal transmission of this virus remain a challenge in adult chickens, with severe consequences on health and welfare [3–5]. CAV is a relatively small virus with a diameter of 23 nm [6]. It is a non-enveloped, icosahedral, single-stranded DNA virus that is grouped into the genus Gyrovirus and the family Anelloviridae [7]. It consists of three overlapping open reading frames encoding three viral proteins (VPs). VP1 which is the main structural capsid protein, is known to be antigenic, and can induce neutralizing antibodies in hosts [8]. The non-structural protein (VP2), which is involved in phosphatase activity, also functions as a scaffold, which helps in the correct assemblage of VP1 [9]. The co-expression of VP1 and VP2 has been reported to induce virus-neutralizing antibodies in chicken hosts, and as such, they have been regarded Viruses 2022, 14, 1456. https://doi.org/10.3390/v14071456 https://www.mdpi.com/journal/viruses