Alphacoronavirus 1

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1. Classification

Alphacoronavirus 1 is classified under the domain Riboviriae or Orthornavirae, phylum Pisuviricotae, class Pisoniviricetes, order Nidovirales, and family Coronaviridae [1]. Alphacoronavirus 1 can be divided into two distinct clades, A and B, based on differences in spike genes. Based on phylogenetics, feline coronavirus (FCoV) and canine coronavirus (CCoV) have evolutionarily similar spike proteins, and can be classified as clade A. A different CCoV strain has a similar spike protein to Transmissible Gastroenteritis Virus (TGEV) in pigs. These two types of Alphacoronavirus 1 are phylogenetically classified as clade B [2]. In addition, clade A contains an additional open reading frame (ORF) that is not found in clade B, further demonstrating that TGEV and CCoV strain II are distinct from CCoV I and FCoV [3].

a. Higher order taxa

Riboviriae or Orthornavirae, Pisuviricotae, Pisoniviricetes, Nidovirales, Coronaviridae

Species

NCBI: [1]

Alphacoronavirus 1”

2. Description and significance

Alphacoronavirus 1 is a species of coronavirus specific to animals such as canines, felines, and swines . Alphacoronavirus 1 was first discovered in the 1940s in pigs in the United States and causes severe intestinal inflammation resulting in vomiting and diarrhea [4]. While it was first detected as gastrointestinal in pigs, more recent studies show that Alphacoronavirus 1 can infect the respiratory and other bodily systems, as well as infect some wild animals phylogenetically-related to cats and dogs [5]. Alphacoronavirus 1 is pathogenic due to a non-structural protein (nsp1) [6]. that is found in other coronaviruses such as SARS-CoV2 [6]. and is a vaccine target for Alphacoronavirus 1 [7].

3. Genome structure

The genome of Alphacoronavirus 1 consists of non-segmented RNA [8]. with eleven open reading frames (ORFs) [9]. Only about a third of the genome encodes for structural or accessory proteins, while the majority of the genome encodes for non-structural proteins [8]. Alphacoronavirus 1 encodes a specific protein that is unique to α and β coronaviruses, called nsp1 [5]. Nsp1 is a part of another polyprotein called the pp1a polyprotein, which is encoded in multiple sites of the genome. These sites also encode a crucial genomic motif for regulating translation in a host cell [5]. Other parts of the genome encode for receptor-binding domains and receptor-binding loops, which play a role in Alphacoronavirus 1 adaptation across host species and evasion of immune responses [10]. These receptor-binding domains and loops can rapidly evolve to form mutant strains [10].

4. Cell structure

Alphacoronavirus 1 is spherical in shape and enveloped [8]. It is approximately 125 nm in diameter and has club-shaped spike proteins that jut out from its surface. Alphacoronavirus 1 is made up of four main structural proteins: spike (S), membrane (M), envelope (E), and nucleocapsid (N) [8]. Alphacoronavirus 1 also exhibits a unique folding structure for the nsp1 protein. The Alphacoronavirus 1 nsp1 β-barrel structure is composed of 6 β-sheets, and is involved in control of biological functions as well as inhibition of host protein synthesis after infection [11]. The 6 β-sheet structure of nsp1 is also conserved in Severe Acute Respiratory Syndrome (SARS-CoV) coronaviruses in humans, suggesting that it plays an important role in coronavirus function [12].

5. Metabolic processes

Alphacoronavirus 1 is an RNA virus, which is often characterized by a high mutation rate that helps them quickly adapt to changes in the environment [10]. Significant RNA structure conservation among Alphacoronavirus 1 strains and among coronavirus genera suggests that there may be co-evolution between replication machinery [13]. Alphacoronavirus 1 infects animal hosts by attaching to aminopeptidase-N (APN) receptors on host cells. Upon entering the cell, Alphacoronavirus 1 uses nsp1 to limit translation of the host cell DNA and begin viral replication [5]. Following assembly, the virions are transported to the surface of the cell and released via exocytosis [8].

6. Ecology

Alphacoronavirus 1 survives best at cold temperatures, leading to more frequent swine epidemics during the winter months [14]. Alphacoronavirus 1 was originally identified in pigs, cats, and dogs [4]. It is most often found in the small intestine of animals, but it has also been observed in the lungs and liver of bats found in urban Brazil [15]. Alphacoronavirus 1 has the ability to jump between species, as it also infects spotted hyenas and jackals [5]. The ability of Alphacoronavirus 1 to jump to other species is determined by its capacity to bind to the receptors of different host cells. This has been shown in host cells that are evolutionarily similar to the virus’s original host, such as how Alphacoronavirus 1 in house cats can infect hyenas [5].

7. Pathology

Alphacoronavirus 1 acts on the host by destroying the nutrient-absorbing cells, known as villus enterocytes, in the small intestine [14]. This results in villous atrophy, where the surface of the wall of the small intestine is flat instead of being full of protruding villi [14]. This decreases the surface area and absorption capability of the small intestine, resulting in malabsorption, osmotic diarrhea, dehydration, and metabolic acidosis [14]. The incubation period is approximately twenty-four hours [14]. Alphacoronavirus 1 species has some variability in types of infection. In TGEV, some Alphacoronavirus 1 strains have a gene for protein number 7 that helps it fight the host cell immune system [16].Protein 7 binds to a catalytic region of a phosphate-removing enzyme, known as phosphatase 1c, in the host cell. When protein 7 binds to phosphatase 1c, it inhibits its ability to fight off viruses [16]. When the gene for protein 7 is removed from TGEV, the host is better able to fight off infection by Alphacoronavirus 1 [16].

8. Current Research

Current research on Alphacoronavirus 1 focuses on the CoV nonstructural protein I (nsp1), which has been shown to play a key role in infection. Recent research used crystallography and x-ray diffraction to show that Alphacoronavirus 1 nsp1 structural features are maintained between different species of the genus Alphacoronavirus [11]. Upon further analysis of the conserved regions of Alphacoronavirus nsp1, it was determined that nsp1 blocks cell growth and immunity. Alphacoronavirus 1 nsp1 blocks activation of STAT1-S727, which functions in the immune response to pathogens [11][17]. In addition to impairing the immune system, Alphacoronavirus 1 nsp1 reduces expression of host genes in order to control replication of its own viral genome. One study created a modified Alphacoronavirus 1 nsp1 without the region coding for reduced host gene expression. When pigs were infected with the mutant Alphacoronavirus 1, infectivity was significantly reduced. All pigs infected with wild type Alphacoronavirus 1 died within 4 days, while the mutant Alphacoronavirus 1 pigs survived. As a result of this finding, Alphacoronavirus nsp1 protein has been identified as a potential target for vaccines [5]. Future directions of research are focused on better understanding the phylogenetic origins of Alphacoronavirus I. Studies aim to analyze the evolution of virulence factors such as nsp1 and factors that permit species jumping to characterize coronavirus mechanisms and risk of transmission to humans [15].

9. References

1. Taxonomy browser (Alphacoronavirus 1). (n.d.). Retrieved from https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=693997

2. Whittaker, G. R., N. M. Andre, and J. K. Millet. 2018. Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species. mSphere 3(1):e00463-17.

3. Decaro, N., V. Mari, G. Elia, G. Lanave, G. Dowgier, M. L. Colaianni, V. Martella, and C. Buonavoglia. 2015. Full-Length Genome Analysis of Canine Coronavirus Type I. Virus Research 210:100–105.

4. Santana-Clavijo, N. S., D. P. Reyes Romero, D. F. Arango Fajardo, A. Velandia Muñoz, S. A. Taniwaki, S. O. de Souza Silva, and P. E. Brandão. 2020. Molecular diversity of Alphacoronavirus 1 in dogs and cats in Colombia. Heliyon 6(7):e04381.

5. Olarte Castillo, X. A., J. F. dos Remedios, F. Heeger, H. Hofer, S. Karl, A. D. Greenwood, and M. L. East. 2021. The virus-host interface: Molecular interactions of Alphacoronavirus-1 variants from wild and domestic hosts with mammalian aminopeptidase N. Molecular Ecology 30(11):2607-2625.

6. Shen, Z., G. Wang, Y. Yang, J. Shi, L. Fang, F. Li, S. Xiao, Z. F. Fu, and G. Peng. 2019. A conserved region of nonstructural protein 1 from alphacoronaviruses inhibits host gene expression and is critical for viral virulence. Journal of Biological Chemistry 294(37):13606-13618.

7. Schubert, K., E. D. Karousis, A. Jomaa, A. Scaiola, B. Echeverria, L. A. Gurzeler, M. Leibundgut, V. Thiel, O. Muhlemann, and N. Ban. 2020. SARS-CoV-2 Nsp1 binds the ribosomal mRNA channel to inhibit translation. Nature Structural & Molecular Biology 27(10):959-966.

8. Fehr, A. R., and S. Perlman. 2015. Coronaviruses: an overview of their replication and pathogenesis. Methods in Molecular Biology 1282:1–23.

9. de Barros, B., C. de Castro, D. Pereira, L. G. Ribeiro, J. Júnior, S. Casseb, G. M. Holanda, A. Cruz, E. Júnior, and J. Mascarenhas. 2019. First Complete Genome Sequence of a Feline Alphacoronavirus 1 Strain from Brazil. Microbiology Resource Announcements 8(10):e01535-18.

10. Wong, A. H. M., A. C. A. Tomlinson, D. Zhou, M. Satkunarajah, K. Chen, C. Sharon, M. Desforges, P. J. Talbot, and J. M. Rini. 2017. Receptor-binding loops in alphacoronavirus adaptation and evolution. Nature Communications 8(1):1735.

11. Shen, Z., Y. Yang, S. Yang, G. Zhang, S. Xiao, Z. F. Fu, and G. Peng. 2020. Structural and biological basis of Alphacoronavirus nsp1 associated with host proliferation and immune evasion. Viruses 12(8):812.

12. Jansson, A. M. 2013. Structure of alphacoronavirus transmissible gastroenteritis virus nsp1 has implications for coronavirus nsp1 function and evolution. Journal of virology 87(5):2949–2955.

13. Madhugiri, R., M. Fricke, M. Marz, and J. Ziebuhr. 2014. RNA structure analysis of alphacoronavirus terminal genome regions. Virus Research 194:76-89.

14. Burrough, E. R. 2021. Porcine Coronaviral Enteritis. Merck Veterinary Manual.

15. Bittar, C., R. R. Guaragna Machado, M. T. Comelis, L. M. Bueno, M. R. Beguelini, E. Morielle-Versute, M. L. Nogueira, and P. Rahal. 2020. Alphacoronavirus detection in lungs, liver, and intestines of bats from Brazil. Microbial Ecology 79(1):203-212.

16. Cruz, J. L., M. Becares, I. Sola, J. C. Oliveros, L. Enjuanes, and S. Zúñiga. 2013. Alphacoronavirus protein 7 modulates host innate immune response. Journal of virology 87(17), 9754–9767.

17. Putz, E. M., D. Gotthardt, and V. Sexl. 2014. STAT1-S727-the license to kill. Oncoimmunology 3(9):e955441.

Edited by Keiddy Curiel, Lauren Guthrie, Rebecca Hyatt, Gabrielle Kim, and David Ruiz, students of Jennifer Bhatnagar for BI 311 General Microbiology, 2021, Boston University.