Novel Sulfolobus Fuselloviruses with Extensive Genomic Variations

Abstract

Fuselloviruses are among the most widespread and best-characterized archaeal viruses. They exhibit remarkable diversity, as the list of members of this family is rapidly growing. However, it has yet to be shown how a fuselloviral genome may undergo variation at the levels of both single nucleotides and sequence stretches. Here, we report the isolation and characterization of four novel spindle-shaped viruses, named Sulfolobus spindle-shaped viruses 19 to 22 (SSV19-22), from a hot spring in the Philippines. SSV19 is a member of the genus Alphafusellovirus, whereas SSV20-22 belong to the genus Betafusellovirus. The genomes of SSV20-SSV22 are identical except for the presence of two large variable regions, as well as numerous sites of single-nucleotide polymorphisms (SNPs) unevenly distributed throughout the genomes and enriched in certain regions, including the gene encoding the putative end filament protein VP4. We show that coinfection of the host with SSV20 and SSV22 led to the formation of an SSV21-like virus, presumably through homologous recombination. In addition, large numbers of SNPs were identified in DNA sequences retrieved by PCR amplification targeting the SSV20-22 vp4 gene from the original enrichment culture, indicating the enormous diversity of SSV20-22-like viruses in the environment. The high variability of VP4 is consistent with its potential role in host recognition and binding by the virus. IMPORTANCE How a virus survives in the arms race with its host is an intriguing question. In this study, we isolated and characterized four novel fuselloviruses, named Sulfolobus spindle-shaped viruses 19 to 22 (SSV19-22). Interestingly, SSV20-22 differ primarily in two genomic regions and are apparently convertible through homologous recombination during coinfection. Moreover, sites of single-nucleotide polymorphism (SNP) were identified throughout the genomes of SSV20-22 and, notably, enriched in certain regions, including the gene encoding the putative end filament protein VP4, which is believed to be involved in host recognition and binding by the virus.

New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae

“…Such recombination‐based mechanism could play an important role in the emergence of new archaeal virus genes lacking homologues in sequence databases, which typically constitute ~75% of the archaeal virus genomes (Krupovic et al ., 2018). Indeed, it has been previously noted that fusellovirus genomes are prone to recombination (Redder et al ., 2009; Pauly et al ., 2019; Zhang et al ., 2020).…”

Extraordinary diversity of viruses in deep‐sea sediments as revealed by metagenomics without prior virion separation

“…After incubation with shaking at 15°C for overnight, the mixture was centrifuged and filtered through a 0.22‐μm‐pore‐size filter. The filtrate was centrifuged at ~100 000 × g for 1 h. The pellets, which contained VLPs, were re‐suspended in SM buffer (10 mM Tris–HCl, pH 7.5, 100 mM NaCl, 10 mM MgSO 4 ), and the VLPs were observed under a transmission electron microscope (TEM, JEM‐1400, JEOL, Japan) as described previously (Wang et al ., 2018; Zhang et al, 2020).…”

Structure and assembly of archaeal viruses

“…By contrast, spindle-shaped viruses, which are among the most widespread groups of archaea-specific viruses (Krupovic et al, 2014), are less fastidious and many viruses of this group have been isolated. Tailless spindle-shaped viruses have been isolated from hyperthermophilic crenarchaea (Goodman and Stedman, 2018;Pauly et al, 2019;Redder et al, 2009;Schleper et al, 1992;Stedman, 2011;Wiedenheft et al, 2004;Zhang et al, 2020a), hyperhalophilic euryarchaea (Bath et al, 2006;Bath and Dyall-Smith, 1998) and ammonia-oxidizing thaumarchaea (Kim et al, 2019), and are classified into the families Fuselloviridae, Halspiviridae and Thaspiviridae, respectively (Figure 1). Morphologically similar viruses have been also isolated from hyperthermophilic marine euryarchaea (Geslin et al, 2003;Gorlas et al, 2012), but remain unclassified.…”