Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. Enrichment of RNA Virome
2.3. Next Generation Sequencing
2.4. Data Analysis
3. Results
3.1. Abundance of Viral Contigs
3.2. Taxonomic Classification of Viral Contigs
3.3. Frequency of Virus Detection and Abundance by Host Specificity
3.4. Distribution and Abundance of Mammalian Enteric RNA Viruses
3.5. Gut Virome Composition and Changes over Time for Each Study Participant
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | Collection Time | Total Assembled Contigs | Viral Contigs | Percentage Viral Contigs |
---|---|---|---|---|
A1 | 6 weeks | 5549 | 68 | 1.2 |
A2 | 10 weeks | 6255 | 28 | 0.4 |
A3 | 36 weeks | 9805 | 489 | 5.0 |
Total | 21,609 | 585 | 2.7% | |
B1 | 10 weeks | 12,445 | 2504 | 20.1 |
B2 | 14 weeks | 15,184 | 7064 | 46.5 |
B3 | 24 weeks | 5636 | 138 | 2.4 |
Total | 33,265 | 9706 | 29.2% | |
C1 | 6 weeks | 4368 | 87 | 2.0 |
C2 | 14 weeks | 8637 | 60 | 0.7 |
C3 | 20 weeks | 3638 | 67 | 1.8 |
Total | 16,643 | 214 | 1.3% | |
D1 | 6 weeks | 7405 | 36 | 0.5 |
D2 | 14 weeks | 7357 | 37 | 0.5 |
D3 | 20 weeks | 5906 | 70 | 1.2 |
Total | 20,668 | 143 | 0.7% | |
Overall | 92,185 | 10,648 | 11.6% |
Virus Family | Picornaviridae | Reoviridae | Astroviridae | Retroviridae | Caliciviridae | Flaviviridae | Poxviridae | Virgaviridae | Rhabdoviridae | Siphoviridae | Amalgaviridae | PartitiviridaE | Totiviridae | Peribunyaviridae | Unclassified picornavirales | Unclassified | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SAMPLE NUMBER | Sample ID | Sample Collection Time (Weeks) | Total Number of Contigs | Contigs Assigned to Viruses | Coxsackievirus A, B | Enterovirus A, B, C, D | Echovirus E | Poliovirus 1, 2, 3 | Parechovirus 1, 3, 8, 17, 19 | Rhinovirus A, B, C | Swine vesicular disease virus | Bat picornavirus | Marmot sapelovirus | Rotavirus A | Astrovirus | Mamastrovirus | Human endogenous retrovirus | Equine infectious anaemia virus | Norovirus GI, GII.4 | Hepatitis GB virus B | Vaccinia virus | Pepper mild mottle virus | Wheat rosette stunt virus | Geobacillus virus | Zygosaccharomyces bailli Z virus | Botryosphoeria dothidea virus | Scheffersomyces segobiensis virus | Shuangao insect virus | Apodemus agrarius picornavirus | Niniventer confucianus picornavirus | Hubei partiti-like virus | Giant panda associated partiti-like virus |
Genomic Structure | (+)ssRNA | dsRNA | (+)ssRNA | RNA | (+)ssRNA | (+)ssRNA | (+)ssRNA | dsDNA | (+)ssRNA | (−)ssRNA | dsDNA | dsRNA | dsRNA | dsRNA | (−)ssRNA | (+)ssRNA | (+)ssRNA | RNA | RNA | |||||||||||||
A1 | 4450 | 6 | 5549 | 68 | 2 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 58 | 0 | 0 | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 5 | 0 | 0 | 0 | 0 | 0 |
A2 | 6618 | 10 | 6255 | 28 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 27 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
A3 | 8908 | 36 | 9805 | 489 | 84 | 34 | 309 | 0 | 0 | 0 | 2 | 0 | 0 | 59 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
B1 | 8903 | 10 | 12,445 | 2504 | 1386 | 146 | 5 | 914 | 0 | 0 | 0 | 0 | 0 | 51 | 2 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
B2 | 8941 | 14 | 15,184 | 7064 | 3953 | 549 | 22 | 2333 | 0 | 88 | 3 | 1 | 1 | 90 | 9 | 1 | 0 | 1 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 1 | 1 | 0 | 1 |
B3 | 10,287 | 24 | 5636 | 138 | 2 | 1 | 0 | 4 | 94 | 0 | 0 | 0 | 0 | 20 | 0 | 0 | 0 | 0 | 4 | 6 | 1 | 1 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 1 | 0 |
C1 | 8824 | 6 | 4368 | 87 | 5 | 4 | 20 | 1 | 0 | 0 | 0 | 0 | 0 | 52 | 0 | 0 | 0 | 0 | 0 | 3 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 |
C2 | 10,127 | 14 | 8637 | 60 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 57 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
C3 | 10,233 | 20 | 3638 | 67 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 43 | 0 | 0 | 0 | 17 | 0 | 2 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
D1 | 8355 | 6 | 7405 | 36 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 32 | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
D2 | 8910 | 14 | 7357 | 37 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 37 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
D3 | 10,098 | 20 | 5906 | 70 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 67 | 0 | 0 | 2 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
TOTAL VIRUS CONTIGS | 10,648 | 5435 | 735 | 357 | 3253 | 94 | 90 | 5 | 1 | 1 | 593 | 11 | 1 | 3 | 19 | 4 | 21 | 1 | 1 | 1 | 1 | 1 | 1 | 10 | 1 | 1 | 1 | 1 | 1 |
Sample Number | Collection Time | (+)ssRNA Viruses | (−)ssRNA Viruses | dsRNA Viruses | DNA Viruses | Unclassified RNA Viruses | Total (Different Viral Genomes) |
---|---|---|---|---|---|---|---|
A1 | 6 weeks | 3 | - | 2 | - | - | 5 |
A2 | 10 weeks | 1 | - | 1 | - | - | 2 |
A3 | 36 weeks | 5 | - | 1 | - | - | 6 |
B1 | 10 weeks | 5 | - | 1 | - | - | 6 |
B2 | 14 weeks | 13 | 1 | 2 | - | 1 | 17 |
B3 | 24 weeks | 8 | - | 2 | 1 | 1 | 12 |
C1 | 6 weeks | 5 | - | 2 | - | - | 7 |
C2 | 14 weeks | 2 | - | 1 | - | - | 3 |
C3 | 20 weeks | 5 | 1 | 2 | - | - | 8 |
D1 | 6 weeks | 1 | - | 1 | 1 | 1 | 4 |
D2 | 14 weeks | - | - | 1 | - | - | 1 |
D3 | 20 weeks | 1 | - | 1 | - | 1 | 3 |
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Mogotsi, M.T.; Mwangi, P.N.; Bester, P.A.; Mphahlele, M.J.; Seheri, M.L.; O’Neill, H.G.; Nyaga, M.M. Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses. Viruses 2020, 12, 1260. https://doi.org/10.3390/v12111260
Mogotsi MT, Mwangi PN, Bester PA, Mphahlele MJ, Seheri ML, O’Neill HG, Nyaga MM. Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses. Viruses. 2020; 12(11):1260. https://doi.org/10.3390/v12111260
Chicago/Turabian StyleMogotsi, Milton T., Peter N. Mwangi, Phillip A. Bester, M. Jeffrey Mphahlele, Mapaseka L. Seheri, Hester G. O’Neill, and Martin M. Nyaga. 2020. "Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses" Viruses 12, no. 11: 1260. https://doi.org/10.3390/v12111260