Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Design, Study Site, and Rodent Trapping
2.2. Sample Collection
2.3. Identification of Rodents
2.4. Molecular Screening for Mammarenavirus RNA
2.5. Metagenomic Detection of Mammarenaviruses and Helminths
2.6. RNA Extraction, Library Preparation, and Next-Generation Sequencing
2.7. Determination of Luna Virus-Specific mNGS Reads per Million (rPM)
2.8. Quality Control Metrics and Detection of Pathogens
2.9. Phylogenetic Analysis of Detected Mammarenaviruses
2.10. Statistical Analysis
3. Results
3.1. Demographic Characteristics of Captured Animals
3.2. Prevalence of Mammarenaviruses
3.3. Distribution of LUAV in Tissues
3.4. Phylogenetic Analysis of LUAV Sequences
3.5. LUAV–Helminth Co-Infections in M. natalensis
3.6. Risk Factors for the Occurrence of LUAV in M. natalensis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Location | Sex | Age | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
Riverine Habitat | Non-Riverine Habitat | ||||||||||
LSK | KF | LSK | KF | LV | CH | M | F | Adult | Juvenile | ||
Rodents | M. natalensis (n = 182) | 101 | 16 | 0 | 5 | 27 | 33 | 82 | 100 | 169 | 13 |
Gerbilliscus sp. (n = 27) | 9 | 0 | 0 | 16 | 0 | 2 | 11 | 16 | 25 | 2 | |
Saccostomus sp. (n = 18) | 0 | 0 | 0 | 5 | 0 | 13 | 6 | 12 | 13 | 5 | |
Rattus rattus (n = 13) | 0 | 0 | 13 | 0 | 0 | 4 | 9 | 13 | 0 | ||
Mus sp. (n = 1) | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | ||
Arvicanthis sp. (n = 1) | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | ||
Lemiscomys sp. (n = 1) | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | |||
Shrew | Crocidura sp. (n = 7) | 0 | 5 | 0 | 0 | 0 | 2 | 0 | 7 | 6 | 1 |
Total (%) | 133 (53.2) | 117(46.8) | 104 (41.6) | 146 (58.4) | 229 (91.6) | 21 (8.4) |
Category | Characteristic | Prevalence | |
---|---|---|---|
M. natalensis (n = 182) | Habitat | Riverine (n = 117) | 11.1% (13/117) |
Non-riverine (n = 65) | 1.5% (1/65) | ||
Sex | Male (n = 82) | 12.2% (10/82) | |
Female (n = 100) | 4% (4/100) | ||
Age | Juvenile (n = 13) | 23.1% (3/13) | |
Adult (n = 169) | 6.5% (11/169) |
Sex | Sample Type | Number of Samples | Number of Reads Aligning to LUAV Genomes in the NCBI NR/NT Database, per Million Reads | Average Coverage Breadth **/Average Coverage Depth *** |
---|---|---|---|---|
Male | Semen | 4 | 658, 925 | 77.8%/269.3x |
Mixed tissues * | 6 | 27, 130 | 36%/5.1x | |
Foetal tissues | 1 | 16, 399 | 98.9%/50.1x | |
Female | Mixed tissues * | 4 | 11, 114 | 55.9%/2.31x |
Luna Viruses | Reference (Accession Number) | Percent Identity |
---|---|---|
Lusaka-186 Zambia | LSK-1 (AB586645.1) | 91.3 |
Lusaka-185 Zambia | LSK-3 (AB702941.1) | 99.0 |
Lusaka-182 Zambia | LSK-1 (AB586645.1) | 94.4 |
Lusaka-181 Zambia | LSK-3 (AB702941.1) | 99.1 |
Lusaka-174 Zambia | LSK-3 (AB702941.1) | 99.3 |
Lusaka-171 Zambia | LSK-1 (AB586645.1) | 94.6 |
Lusaka-170 Zambia | LSK-3 (AB702941.1) | 99.1 |
Kafue-167 Zambia | LSK-1 (AB586645.1) | 91.8 |
Kafue-164 Zambia | NMW-1 (AB586647.1) | 90.1 |
Lusaka-161 Zambia | LSK-3 (AB702941.1) | 99.7 |
Lusaka-160 Zambia | LSK-3 (AB702941.1) | 98.6 |
Lusaka-155 Zambia | LSK-3 (AB702941.1) | 98.8 |
Lusaka-154 Zambia | LSK-3 (AB702941.1) | 92.3 |
Lusaka-152 Zambia | LSK-3 (AB702941.1) | 99.2 |
Lusaka-147 Zambia | LSK-3 (AB702941.1) | 99.1 |
Helminth Infection Characteristic | Prevalence of Helminths (21/182) | Prevalence of LUAV (7/182) |
---|---|---|
≤1 helminth species (n = 17) | 9.3% (17/182) | 17.4% (3/17) |
>1 helminth species (n = 4) | 2.2% (4/182) | 100% (4/4) |
Cestodes (n = 7) | 3.8% (7/182) | 28.6% (2/7) |
Nematodes (n = 14) | 7.7% (14/182) | 20.5% (5/14) |
Variables | Characteristic | Luna Virus | p-Value | |
---|---|---|---|---|
Negative | Positive | |||
Sex | Male | 71 | 10 | 0.035 * |
Female | 97 | 4 | ||
Nematodes | Negative | 159 | 9 | <0.0001 * |
Positive | 9 | 5 | ||
Cestodes | Negative | 163 | 12 | 0.035 * |
Positive | 5 | 2 | ||
Age | Juvenile | 10 | 3 | 0.031 * |
Adults | 158 | 11 | ||
Habitat | Non-riverine | 64 | 1 | 0.020 * |
Riverine | 104 | 13 | ||
Season | Dry | 88 | 4 | 0.087 * |
Wet | 80 | 10 |
Risk Factor | Level | OR | 95% CI | p-Value * |
---|---|---|---|---|
Age | Juvenile | 9.38 | 1.47–59.85 | 0.018 |
Adult | Ref | |||
Sex | Male | 4.6 | 1.100–18.90 | 0.036 |
Female | Ref | |||
Nematodes | Positive | 15.45 | 3.11–76.70 | 0.001 |
Negative | Ref | |||
Cestodes | Positive | 10.85 | 1.36–86.77 | 0.025 |
Negative | Ref | |||
Season | Rainy | 2.07 | 0.509–8.44 | 0.309 |
Dry | Ref | |||
Habitat | Riverine | 7.94 | 0.85–3.56 | 0.068 |
Non-riverine | Ref |
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Share and Cite
Munjita, S.M.; Moonga, G.; Mukubesa, A.N.; Ndebe, J.; Mubemba, B.; Vanaerschot, M.; Tato, C.; Tembo, J.; Kapata, N.; Chitanga, S.; et al. Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen. Pathogens 2022, 11, 1345. https://doi.org/10.3390/pathogens11111345
Munjita SM, Moonga G, Mukubesa AN, Ndebe J, Mubemba B, Vanaerschot M, Tato C, Tembo J, Kapata N, Chitanga S, et al. Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen. Pathogens. 2022; 11(11):1345. https://doi.org/10.3390/pathogens11111345
Chicago/Turabian StyleMunjita, Samuel Munalula, Given Moonga, Andrew Nalishuwa Mukubesa, Joseph Ndebe, Benjamin Mubemba, Manu Vanaerschot, Cristina Tato, John Tembo, Nathan Kapata, Simbarashe Chitanga, and et al. 2022. "Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen" Pathogens 11, no. 11: 1345. https://doi.org/10.3390/pathogens11111345