Family: Nipumfusiviridae

Yimin Ni¹ and Yongjie Wang^1,2,*

The citation for this ICTV Report chapter is the summary to be published as Ni & Wang (2026): ICTV Virus Taxonomy Profile: Nipumfusiviridae 2026, Journal of General Virology (in press).

Corresponding author: Yongjie Wang ([email protected])
Edited by: Mart Krupovic & Evelien Adriaenssens
Posted: January 2026

Summary

The Nipumfusiviridae family comprises DNA viruses predicted to infect marine ammonia-oxidizing archaea of the family Nitrosopumilaceae (Table 1 Nipumfusiviridae). These viruses have been identified exclusively through metagenomic analyses of diverse environments including coastal inlets, intertidal zones, epipelagic waters, open ocean, and terrestrial soils. To date, no members of this family have been isolated or experimentally enriched. The family currently includes four genera (Baiafusivirus, Marefusivirus, Terrafusivirus, and Yangshanfusivirus) encompassing ten species. Structural predictions of the major capsid protein suggest these viruses likely possess spindle-shaped virions. Genomic analyses provide limited insights into their translation and replication mechanisms due to the absence of cultured representatives.

Table 1 Nipumfusiviridae. Characteristics of members of the family Nipumfusiviridae

Virion

Morphology

Based on the analysis of the putative major capsid protein, virions of this virus family are deduced to be spindle-shaped, a morphology only observed for archaeal viruses (Baquero et al., 2020). The putative major capsid protein shares similar glycosylation sites and hydrophilicity proteins encoded by with known spindle-shaped viruses (Ni et al., 2024b). Although there is no evidence of conserved tail structures in the family, the virions are expected to contain terminal appendages implicated in host recognition and binding (Figure 1 Nipumfusiviridae).

Figure 1 Nipumfusiviridae. Comparative genomic analysis of members in the family Nipumfusiviridae. Shared proteins are highlighted by color-coding. Shared proteins of unknown functions are not labeled in the figure. Genomes are aligned relative to the major capsid protein (MCP) of Nitrosopumilaceae spindle-shaped virus NYM1. Arrow directions indicate ORF transcription orientation.

Nucleic acid

The genome is circular dsDNA of 27–38 kbp.

Proteins

The major capsid protein is currently the only reliably predicted structural component. The highly hydrophobic major capsid protein is predicted to have the α-helical hairpin fold (Ni et al., 2024b), characteristic of all previously described spindle-shaped viruses (Han et al., 2022, Wang et al., 2022). Virus genomes do not encode recognizable homologs of the tail or spike proteins found in other spindle-shaped viruses.

Carbohydrates

Glycosylation of the major capsid protein is predicted based on the presence of the N-glycosylation sequon within the conserved region known to be glycosylated in other spindle-shaped viruses (Figure 2 Nipumfusiviridae).

Figure 2 Nipumfusiviridae. Multiple sequence alignment of MCP sequences from Nipumfusiviridae family members. Predicted N-glycosylation sites are highlighted in red. Predicted secondary structure (top ribbon diagram) shows two conserved hydrophobic α-helices. Nitrosopumilaceae spindle-shaped virus NYM1, BK067792; Nitrosopumilaceae spindle-shaped virus NMH1, BK067784; Nitrosopumilaceae spindle-shaped virus NMJ1, BK067785; Nitrosopumilaceae spindle-shaped virus NMC1, BK067789; Nitrosopumilaceae spindle-shaped virus NMM1, BK067790; Nitrosopumilaceae spindle-shaped virus NMP1, BK067782; Nitrosopumilaceae spindle-shaped virus NTM1, BK067788; Nitrosopumilaceae spindle-shaped virus NTT1, BK067791; Nitrosopumilaceae spindle-shaped virus NBC1, BK067786; Nitrosopumilaceae spindle-shaped virus NBD1, BK067787.

Genome organization and replication

Members of the family Nipumfusiviridae possess a circular dsDNA genome of 27–38 kbp encoding 42–82 genes. Genomic analysis reveals that conservation of the replication machinery is limited to an ATPase, potentially implicated in replication (Krupovic et al., 2014). No other conserved replication-associated proteins have been detected, suggesting host-derived complementation. However, some members of the family encode recognizable genome replication proteins (e.g., DNA primase in Nitrosopumilaceae spindle-shaped virus NYM1).

Biology

All currently described representatives have been identified through metagenomics (Ni et al., 2024a, Ni et al., 2024b). There are no isolates available for experimental characterization. Notably, frequent occurrences of zinc-finger domain-containing proteins imply potential roles in modulating host or viral transcriptional regulation (Sheppard and Werner 2017).

Derivation of names

Baiafusivirus: from the Italian baia meaning bay, referring to the sampling site of isolates in the genus, and the Latin fusi meaning spindles referring to the possible morphology

Marefusivirus: from the Italian mare meaning sea, referring to the sampling site of isolates in the genus, and the Latin fusi meaning spindles referring to the possible morphology

Nipumfusiviridae: from the presumed host Nitrosopumilaceae and the Latin fusi meaning spindles referring to the possible morphology

Terrafusivirus: from the Italian terra meaning soil, referring to the sampling site of isolates in the genus, and the Latin fusi meaning spindles referring to the possible morphology

Yangshanfusivirus: from Yangshan Harbor in China, referring to the sampling site of isolates in the genus, and the Latin fusi meaning spindles referring to the possible morphology

Demarcation criteria for taxa within the family

Novel members must satisfy the following genomic criteria to be classified within the family but distinct from established genera: (i) Demonstration of a mean amino acid identity of 30–50% with established representatives of Nipumfusiviridae; and (ii) Retention of at least the major capsid protein (MCP) and the conserved ATPase as essential genetic markers.

Relationships within the family

The family Nipumfusiviridae currently contains four established genera (Baiafusivirus, Marefusivirus, Terrafusivirus, and Yangshanfusivirus) with ten classified species (Baiafusivirus chesapeakense and Baiafusivirus delawarense; Marefusivirus columbiaense, Marefusivirus helgoense, Marefusivirus jervisense, Marefusivirus montereyense, and Marefusivirus pacificense; Terrafusivirus michiganense and Terrafusivirus tennesseense; Yangshanfusivirus mimetica) (Figure 3 Nipumfusiviridae).

Figure 3 Nipumfusiviridae. Proteomic tree (Nishimura et al., 2017) of members in the family Nipumfusiviridae. The colored circles preceding the virus names denote their respective genus.

Relationships with other taxa

Nipumfusivirids show no close phylogenetic relationship to other classified viruses, including other spindle-shaped viruses infecting ammonia-oxidating archaea (family Thaspiviridae) (Kim et al., 2019, Kim et al., 2021). Nipumfusiviridae is unassigned to any established viral order or class, representing a distinct family-level taxon.