Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Case History
2.3. Metagenomic Sequencing and Data Analysis
2.4. PCR Analysis for Viral RNA
2.5. Virus Isolation
3. Results
3.1. Postmortem Findings
3.2. Metagenomic Sequencing Findings
3.3. Targeted Viral RNA Detection
3.4. Chameleon Serpentoviruses: Genomic and Phylogenetic Analysis
3.5. Chameleon Orthoreoviruses: Genomic and Phylogenetic Analysis
3.6. Virus Isolation
4. Discussion
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample and Seq Run | Total Reads (A) | Remove Low Quality Reads (B) | Collapse to Unique Reads (C) | Host Filter (D) | VCSV Reads | VCOrV Reads | |
---|---|---|---|---|---|---|---|
Shotgun RNA Sequencing | VC1 | 6.4 × 106 | 5.7 × 106 (89%) | 1 × 106 (15%) | 0.5 × 106 (8%) | 914 | 0 |
VC2 | 1.5 × 106 | 1.4 × 106 (91%) | 0.3 × 106 (19%) | 0.1 × 106 (9%) | 0 | 0 | |
VC3 | 1.1 × 106 | 1 × 106 (92%) | 0.2 × 106 (20%) | 0.1 × 106 (10%) | 212 | 0 | |
dsRNA Sequencing | VC1 | 16.9 × 106 | 15.7 × 106 (93%) | 2.7 × 106 (16%) | 2.6 × 106 (15%) | 901 | 39 |
VC2 | 42.7 × 106 | 38.5 × 106 (90%) | 6.6 × 106 (16%) | 6 × 106 (14%) | 11 | 2921 | |
VC3 | 13.1 × 106 | 11.4 × 106 (87%) | 3.1 × 106 (24%) | 3 × 106 (23%) | 11,881 | 11 |
Species | ID | Sex | Age | Sample Type | Sample Tissue | Analysis | VCSV | VCOrV |
---|---|---|---|---|---|---|---|---|
Veiled chameleon (Chameleo calyptratus) | VC1 | M | Juvenile | PM | LLK | MGS, PCR | + | + |
VC2 | F | Juvenile | PM | LLK | MGS, PCR | + | + | |
VC3 | M | Juvenile | PM | LTOM | MGS, PCR | + | + | |
VC4 | M | Adult | AM, PM | OS, LT | PCR | + | - * | |
VC5 | F | Adult | AM | OS | PCR | - | - * | |
VC6 | F | Subadult | AM, PM | OS, LT | PCR | + | - * | |
VC7 | F | Juvenile | AM, PM | OS, LT | PCR | + | - * | |
VC8 | F | Juvenile | AM, PM | OS, LT | PCR | + | - * | |
VC9 | F | Juvenile | AM, PM | OS, LT | PCR | + | - * | |
Central bearded dragon (Pogona vitticeps) | BD1 | F | Adult | AM | OS | PCR | - | NT |
BD2 | F | Adult | AM | OS | PCR | - | NT | |
BD3 | M | Adult | AM | OS | PCR | - | NT | |
BD4 | F | Adult | AM | OS | PCR | - | NT | |
BD5 | M | Adult | AM | OS | PCR | - | NT | |
BD6 | F | Adult | AM | OS | PCR | - | NT | |
Common leopard gecko (Eublepharis macularius) | LG1 | U | U | AM | OS | PCR | - | NT |
LG2 | U | U | AM | OS | PCR | - | NT | |
LG3 | U | U | AM | OS | PCR | - | NT | |
Ocelot gecko (Paroedura pictus) | OG1 | U | U | AM | OS | PCR | - | NT |
OG2 | U | U | AM | OS | PCR | - | NT | |
OG3 | U | U | AM | OS | PCR | - | NT |
Segment | Gene | Size (bp) | Protein Size (aa) | GenBank Accession |
---|---|---|---|---|
L1 | Lambda (λ) A | 4000 | 1131 | MT997161 |
L2 | Lambda (λ) C | 3685 | 872 | MT997162 |
L3 | Lambda (λ) B (RdRp) | 3795 | 1165 | MT997163 |
M1 | Mu (μ) NS | 2467 | 793 | MT997164 |
M2 | Mu (μ) A | 2289 | 754 | MT997165 |
M3 | Mu (μ) B | 2091 | 613 | MT997166 |
S1 | P14 (fusion), Sigma (σ) C | 1463 | 126,350 | MT997167 |
S2 | Sigma (σ) A | 1260 | 390 | MT997168 |
S3 | Sigma (σ) B | 1252 | 388 | MT997169 |
S4 | Sigma (σ) NS | 1129 | 282 | MT997170 |
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Hoon-Hanks, L.L.; Stöhr, A.C.; Anderson, A.J.; Evans, D.E.; Nevarez, J.G.; Díaz, R.E.; Rodgers, C.P.; Cross, S.T.; Steiner, H.R.; Parker, R.R.; et al. Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease. Viruses 2020, 12, 1329. https://doi.org/10.3390/v12111329
Hoon-Hanks LL, Stöhr AC, Anderson AJ, Evans DE, Nevarez JG, Díaz RE, Rodgers CP, Cross ST, Steiner HR, Parker RR, et al. Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease. Viruses. 2020; 12(11):1329. https://doi.org/10.3390/v12111329
Chicago/Turabian StyleHoon-Hanks, Laura L., Anke C. Stöhr, Amanda J. Anderson, Dawn E. Evans, Javier G. Nevarez, Raúl E. Díaz, Case P. Rodgers, Shaun T. Cross, Halley R. Steiner, Roy R. Parker, and et al. 2020. "Serpentovirus (Nidovirus) and Orthoreovirus Coinfection in Captive Veiled Chameleons (Chamaeleo calyptratus) with Respiratory Disease" Viruses 12, no. 11: 1329. https://doi.org/10.3390/v12111329