Phylogenetic Analysis of Alphacoronaviruses Based on 3c and M Gene Sequences Isolated from Cats with FIP in Romania
Abstract
1. Introduction
2. Materials and Methods
2.1. Samples
2.2. Coronavirus Antibodies
2.3. RNA Extraction from Effusions and Faecal Samples
2.4. RNA Extraction from Organ Samples
2.5. Amplification Using Real-Time RT-qPCR
2.6. Amplification Using RT-PCR
2.7. Sequencing
2.8. Phylogenetic Analysis
3. Results
3.1. Coronavirus Antibodies Titre
3.2. Amplification, Sequencing, and Phylogenetic Analysis
3.3. Results for the 3c Gene
3.4. Results for M Gene
4. Discussion
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Coronavirus Strain | GenBank Accession No | Year of Collection | Host | Source |
---|---|---|---|---|
FIPV332 | HQ738706 | 2009 | cat | [19] |
FECV407 | HQ738725 | 2010 | cat | [19] |
TGEV_NP058427 | NP_058427 | Tissue culture adapted clone of the TGEV Purdue strain | pig | [20] |
CCoV_MK507579 | MK507579 | 2018 | dog | Not available |
EU664100 (FIPV) | EU664100 | 2004 | cat | [13] |
UU19 (FECV-complete genome) | HQ392470 | 2007 | cat | [18] |
Coronavirus Strain | GenBank Accession No | Year of Collection | Host | Source |
---|---|---|---|---|
Feline Coronavirus isolate 26 M | KP143512 | 2013 | cat | [17] |
Feline coronavirus isolate 27C | KP143507 | 2013 | cat | [17] |
Feline coronavirus isolate 28O | KP143508 | 2013 | cat | [17] |
UU19 (FECV-complete genome) | HQ392470 | 2007 | cat | [18] |
Canine coronavirus strain 119/08 | EU924791 | 2008 | dog | [4] |
Cat | M1 | M2 | M3 | M4 | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample | Real-Time-RT-PCR | RT-PCR | Sequencing | real-Time-RT-PCR | RT-PCR | Sequencing | Real-Time-RT-PCR | RT-PCR | Sequencing | Real-Time--RT-PCR | RT-PCR | Sequencing |
ascites | + | - | - | + | + | 471 pb | NA | NA | NA | + | + | 390 pb |
feces | NA | NA | NA | NA | NA | NA | + | + | 727 pb | + | - | - |
heart | NA | NA | NA | + | - | - | + | - | - | NA | NA | NA |
kidney | + | - | - | + | - | - | + | - | - | + | - | - |
large intestine | NA | NA | NA | NA | NA | NA | + | - | - | NA | - | - |
liver | + | - | - | + | - | - | + | - | - | + | - | - |
lung | + | - | - | + | - | - | + | - | - | + | NA | NA |
lymph node | + | + | 430 pb | NA | NA | NA | + | + | 442 pb | + | + | - |
pancreas | NA | NA | NA | NA | NA | NA | + | + | 405 pb | NA | NA | NA |
small intestine | + | - | - | + | + | 432 pb | + | + | - | + | + | - |
spleen | + | - | - | + | - | - | - | - | - | + | NA | NA |
Cat | M1 | M2 | M3 | M4 | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample | Real-Time-RT-PCR | RT-PCR | Sequencing | Real-Time-RT-PCR | RT-PCR | Sequencing | Real-Time-RT-PCR | RT-PCR | Sequencing | Real-Time- RT-PCR | RT-PCR | Sequencing |
ascites | + | + | 374 pb | + | + | 373 pb | NA | NA | NA | + | + | 368 pb |
feces | NA | NA | NA | NA | NA | NA | + | + | 382 pb | + | NA | NA |
heart | NA | NA | NA | + | NA | NA | + | NA | NA | NA | NA | NA |
kidney | + | NA | NA | + | + | - | + | NA | NA | + | NA | NA |
large intestine | NA | NA | NA | NA | NA | NA | + | + | 201 pb | + | NA | NA |
liver | + | NA | NA | + | NA | NA | + | + | 104 pb | + | NA | NA |
lung | + | NA | NA | + | NA | NA | + | + | 200 pb | + | NA | NA |
lymph node | + | + | - | NA | NA | NA | + | + | 189 pb | NA | + | - |
pancreas | NA | NA | NA | NA | NA | NA | + | + | 194 pb | + | NA | NA |
small intestine | + | NA | NA | + | + | 181 pb | + | NA | NA | + | + | 263 pb |
spleen | + | NA | NA | + | NA | NA | - | NA | NA | NA | NA | NA |
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Popovici, I.; Le Poder, S.; Rîmbu, C.-M.; Horhogea, C.-E. Phylogenetic Analysis of Alphacoronaviruses Based on 3c and M Gene Sequences Isolated from Cats with FIP in Romania. Microorganisms 2024, 12, 1557. https://doi.org/10.3390/microorganisms12081557
Popovici I, Le Poder S, Rîmbu C-M, Horhogea C-E. Phylogenetic Analysis of Alphacoronaviruses Based on 3c and M Gene Sequences Isolated from Cats with FIP in Romania. Microorganisms. 2024; 12(8):1557. https://doi.org/10.3390/microorganisms12081557
Chicago/Turabian StylePopovici, Ivona, Sophie Le Poder, Cristina-Mihaela Rîmbu, and Cristina-Elena Horhogea. 2024. "Phylogenetic Analysis of Alphacoronaviruses Based on 3c and M Gene Sequences Isolated from Cats with FIP in Romania" Microorganisms 12, no. 8: 1557. https://doi.org/10.3390/microorganisms12081557
APA StylePopovici, I., Le Poder, S., Rîmbu, C.-M., & Horhogea, C.-E. (2024). Phylogenetic Analysis of Alphacoronaviruses Based on 3c and M Gene Sequences Isolated from Cats with FIP in Romania. Microorganisms, 12(8), 1557. https://doi.org/10.3390/microorganisms12081557