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. 2023 Oct 12:14:1258810.
doi: 10.3389/fmicb.2023.1258810. eCollection 2023.

Metagenomics analysis reveals presence of the Merida-like virus in Georgia

Jennifer M Potter-Birriel  1 , Adam R Pollio  1 , Brian D Knott  2 , Tamar Chunashvili  2 , Christian K Fung  1 , Matthew A Conte  1 , Drew D Reinbold-Wasson  2 , Jun Hang  1
Affiliations

Metagenomics analysis reveals presence of the Merida-like virus in Georgia

Jennifer M Potter-Birriel et al. Front Microbiol. .

Abstract

Arbovirus surveillance is fundamental for the discovery of novel viruses and prevention of febrile vector-borne illnesses. Vector-borne pathogens can rapidly expand and adapt in new geographic and environmental conditions. In this study, metagenomic surveillance was conducted to identify novel viruses in the Country of Georgia. A total of 521 mosquitoes were captured near a military training facility and pooled from species Culex pipiens (Linnaeus) (87%) and Aedes albopictus (Skuse) (13%). We decided to further analyze the Culex pipiens mosquitoes, due to the more extensive number of samples collected. Our approach was to utilize an unbiased total RNA-seq for pathogen discovery in order to explore the mosquito virome. The viral reads from this analysis were mostly aligned to Insect-specific viruses from two main families, the Iflaviridae; a positive-stranded RNA virus and the Rhabdoviridae; a negative- and single-stranded RNA virus. Our pathogen discovery analysis revealed viral reads aligning to the Merida-like virus Turkey (MERDLVT) strain among the Rhabdoviridae. To further validate this result, we conducted a BLAST sequence comparison analysis of our samples with the MERDLVT strain. Our positive samples aligned to the MERDLVT strain with 96-100% sequence identity and 99.7-100% sequence coverage. A bootstrapped maximum-likelihood phylogenetic tree was used to evaluate the evolutionary relationships among these positive pooled specimens with the (MERDLVT) strain. The Georgia samples clustered most closely with two strains from Turkey, the Merida-like virus KE-2017a isolate 139-1-21 and the Merida-like virus Turkey isolate P431. Collectively, these results show the presence of the MERDLVT strain in Georgia.

Keywords: Culex pipiens; Merida like-virus; NGS; mosquito; pathogen discovery; vector control.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision.

Figures

Figure 1
Figure 1
Mosquito collections in the Country of Georgia. (A) A map containing the location for each collection site, in the Senaki area. Each dot represents the collection site, 2018 (blue) and 2019 (red). (B) Species of mosquitoes captured in Georgia. Chart illustrates the percentage of the two species of mosquitoes captured, the Culex pipiens 87% and the Aedes albopictus 13%. (C) The vector count of Culex pipiens mosquitoes captured per year, 2018 (N = 219) and 2019 (N = 235).
Figure 2
Figure 2
Distribution of the total reads per sample and taxonomy kingdom. (A) The total reads per sample were queried to the NCBI database using CZ ID and STAR. The mapped Super kingdom data is shown Bacteria 1,430,993 (14%), Eukaryote 445,670 (4%) and Virus 8,775,711 (82%). (B) Comparison of sequencing reads that were aligned to viruses per sample.
Figure 3
Figure 3
Heat Map analysis shows virus diversity in collected samples. The heat map was set to NT rPM > =10 which only shows viruses with at least 10 reads per million. Samples are divided by collection date. The most abundant viruses aligned to insect-specific viruses including: the Culex Iflavi-like virus 4, Merida-like virus KE-2017a and the Merida-like virus Turkey.
Figure 4
Figure 4
Maximum likelihood tree of rhabdovirus family including Merida virus and Merida-like virus samples. Merida virus genomes from Georgia samples are highlighted in red and closely related MERDLVT samples are highlighted in blue. Node confidence values represent ultrafast bootstrap replicate support.
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References

    1. Agboli E., Leggewie M., Altinli M., Schnettler E. (2019). Mosquito-specific viruses-transmission and interaction. Viruses 11:873. doi: 10.3390/v11090873 - DOI - PMC - PubMed
    1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403–410. doi: 10.1016/S0022-2836(05)80360-2 - DOI - PubMed
    1. Boisvert S., Raymond F., Godzaridis E., Laviolette F., Corbeil J. (2012). Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol. 13:R122. doi: 10.1186/gb-2012-13-12-r122 - DOI - PMC - PubMed
    1. Bolling B. G., Olea-Popelka F. J., Eisen L., Moore C. G., Blair C. D. (2012). Transmission dynamics of an insect-specific flavivirus in a naturally infected Culex pipiens laboratory colony and effects of co-infection on vector competence for West Nile virus. Virology 427, 90–97. doi: 10.1016/j.virol.2012.02.016 - DOI - PMC - PubMed
    1. Brettin T., Davis J. J., Disz T., Edwards R. A., Gerdes S., Olsen G. J., et al. . (2015). RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 5:8365. doi: 10.1038/srep08365 - DOI - PMC - PubMed