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. 2016 Oct 28;8(11):278.
doi: 10.3390/v8110278.

Kaumoebavirus, a New Virus That Clusters with Faustoviruses and Asfarviridae

Leena H Bajrai  1   2 , Samia Benamar  3 , Esam I Azhar  4 , Catherine Robert  5 , Anthony Levasseur  6 , Didier Raoult  7 , Bernard La Scola  8
Affiliations

Kaumoebavirus, a New Virus That Clusters with Faustoviruses and Asfarviridae

Leena H Bajrai et al. Viruses. .

Abstract

In this study, we report the isolation of a new giant virus found in sewage water from the southern area of Jeddah (Saudi Arabia), with morphological and genomic resemblance to Faustoviruses. This new giant virus, named Kaumoebavirus, was obtained from co-culture with Vermamoeba vermiformis, an amoeboid protozoa considered to be of special interest to human health and the environment. This new virus has ~250 nm icosahedral capsids and a 350,731 bp DNA genome length. The genome of Kaumoebavirus has a coding density of 86%, corresponding to 465 genes. Most of these genes (59%) are closely related to genes from members of the proposed order Megavirales, and the best matches to its proteins with other members of the Megavirales are Faustoviruses (43%) and Asfarviruses (23%). Unsurprisingly, phylogenetic reconstruction places Kaumoebavirus as a distant relative of Faustoviruses and Asfarviruses.

Keywords: Asfarviruses; Faustoviruses; Kaumoebavirus; Vermamoeba vermiformis.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Observation of Kaumoebavirus in Vermamoeba vermiformis at selected times of development. Kaumoebavirus particles (black arrow) are phagocytized (A) then observed in the cytoplasm of V. vermiformis mostly packaged in clumps of two to four particles (B). After the eclipse phase, new virions may be observed within the virus factory (C,D). During the early stage of its formation, the virus factory of Kaumoebavirus is not round-shaped but poly-lobed. During the microtome cut, some slice planes showed newly formed viruses in these lobes as clusters of virions (white arrows). At this stage, remnants of phagocytized particles may be observed (black arrow) (C). At a late stage, the virus factory loses its poly-lobed aspect for a large round vacuole aspect and appears completely filled with Kaumoebavirus mature particles (D).
Figure 2
Figure 2
Circular representation of the Kaumoebavirus genome. The circles from the center to the outside show: GC skew (green/purple); GC content (black); open reading frames (ORFs) on the plus and minus strands (blue).
Figure 3
Figure 3
Distribution of the best-matching homologs to Kaumoebavirus proteins (the diagram shows only the 59% of genes with significant BLAST hits). Best-matching homologous proteins were determined using BLASTP (E value < 10−3) against the non-redundant (NR) database at the National Center for Biotechnology Information (NCBI).
Figure 4
Figure 4
Phylogenetic reconstruction based on a concatenated A32-like packaging ATPase and the family B DNA polymerase. Phylogenetic analysis was performed using the maximum likelihood method based on protein sequences from Kaumoebavirus and representative members from the different families of Megavirales order.
Figure 5
Figure 5
Overview of the genomic region in Kaumoebavirus that encodes the major capsid protein and the corresponding match in the Faustovirus E12 mRNA. The sequences coding for the major capsid protein are shown in green. A conserved nuclease found in the capsid region of both Faustoviruses and Kaumoebavirus is colored pink. Regions of Kaumoebavirus annotated as ORFs having a partial similarity with Faustovirus E12 mRNA are colored purple; only the parts with high similarity to Faustovirus E12 mRNA are colored green.
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