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28 February 2023

Pending Reorganization of Hantaviridae to Include Only Completely Sequenced Viruses: A Call to Action

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1
Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
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Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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Colorado State University, Fort Collins, CO 80523, USA
4
Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, 84505 Bratislava, Slovakia
Viruses2023, 15(3), 660;https://doi.org/10.3390/v15030660
This article belongs to the Special Issue Hantavirus Ecology, Epidemiology, and Disease, in Memory of Dr. Ho Wang Lee
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Abstract

The official classification of newly discovered or long-known unassigned viruses by the International Committee on Taxonomy of Viruses (ICTV) requires the deposition of coding-complete or -near-complete virus genome sequences in GenBank to fulfill a requirement of the taxonomic proposal (TaxoProp) process. However, this requirement is fairly new; thus, genomic sequence information is fragmented or absent for many already-classified viruses. As a result, taxon-wide modern phylogenetic analyses are often challenging, if not impossible. This problem is particularly eminent among viruses with segmented genomes, such as bunyavirals, which were frequently classified solely based on single-segment sequence information. To solve this issue for one bunyaviral family, Hantaviridae, we call on the community to provide additional sequence information for incompletely sequenced classified viruses by mid-June 2023. Such sequence information may be sufficient to prevent their possible declassification during the ongoing efforts to establish a coherent, consistent, and evolution-based hantavirid taxonomy.

1. Introduction

In 2017, the International Committee on Taxonomy of Viruses (ICTV) reacted to the rapid increase in virus discovery via metagenomics and metatranscriptomics by permitting an official virus classification based only on genomic sequence information, as long as that information is coding-complete (i.e., covers all open reading frames) or -near-complete (i.e., lacks only very few terminal or internal nucleotides that are difficult to resolve) [1]. This decision was based on the realization that a true depiction of the virosphere [2] would be impossible if individually characterizing viruses in the laboratory continued to be required; in addition, genomic sequence information enables large-scale phylogenetic analyses and thereby the establishment of evolutionary relationships among viruses in the absence of replicating representatives [1]. However, this decision was prospective, i.e., it applied to the assembly and evaluation of novel taxonomic proposals (TaxoProps) for the classification of newly discovered or previously unclassified viruses into taxa. (For an overview of the taxonomic classification process, the difference between species and virus, and classification methodologies, see Simmonds et al., 2023 [3]) Viruses classified by the ICTV prior to the 2017 decision remained classified even with, in some cases, the complete absence of genomic sequence information. Consequently, many virus taxa are currently mosaics of classified viruses that were placed into the official taxonomy through disparate methodologies using divergent classification criteria. This situation is untenable because the very goal of the ICTV is to “categorize the multitude of known viruses into a single classification scheme that reflects their evolutionary relationships, i.e., their individual phylogenies” [3,4].
The establishment of phylogenies requires genomic sequence information. More importantly, high quality of a virus genome sequence (e.g., sequence read depth and population analysis), redundancy (availability of equally high-quality genome sequences from different isolates of the same virus), completeness of the virus genome, and, in case of viruses with segmented genomes, each individual genome sequence derived from a single isolate enable improved and possibly complementary phylogenetic analyses using different parts of the genomes and their expression products—thus increasing confidence in the resulting taxonomic structures.
The ICTV first and foremost looks to its Study Groups to continuously improve the taxonomy of, typically, family-rank taxa with the long-term vision of achieving the ICTV goal of an accurate depiction of evolutionary virus relationships. Thus, it is largely up to these Study Groups to decide on virus classification criteria (e.g., minimal information necessary for classification) and taxon demarcation criteria (e.g., methodologies and metrics to be used for species and genus demarcation within a family). Here we express the intent of the ICTV Hantaviridae Study Group to resolve the classification problems plaguing the family Hantaviridae, with a first step envisioned to be an overhaul of the family based on analyses only, including viruses associated with coding-complete/-near-complete genome sequence availability in GenBank. We call on the hantavirid community to determine and/or provide missing sequence information for currently classified hantavirids to prevent their potential declassification and to provide such sequence information for currently unclassified viruses so that they can be assigned to species. With the annual ICTV deadline for the submission of TaxoProps this year being likely at the beginning of July, this information is needed by mid-June 2023 and then annually thereafter.

2. Current (2022–2023) Taxonomy of the Bunyaviral Family Hantaviridae

The official hantavirid taxonomy began relatively soon after the description of Hantaan virus (HTNV) in South Korean striped field mice (Apodemus agrarius (Pallas, 1771)) in 1976 [5,6,7] and the subsequent isolation of HTNV in cell culture in 1981 [8]. In 1983, first calls were issued to create an official genus for HTNV and its relatives [9,10,11,12]. In 1987, the genus Hantavirus was officially accepted by the ICTV as part of the family Bunyaviridae [13,14]. The subsequent discovery of hundreds of novel viruses assignable to this family resulted in the promotion of the family to the order Bunyavirales in 2017 [15]. Along with this promotion, the genus Hantavirus was promoted to the monogeneric family Hantaviridae, and all other already-classified viruses were assigned to the genus Orthohantavirus [15]. In 2019, the ICTV Hantaviridae Study Group designated DivErsity pArtitioning by hieRarchical Clustering (DEmARC) as the method of choice for the classification of novel hantavirids [16]. Analyses led to the establishment of the hantavirid genera Loanvirus, Mobatvirus, and Thottimvirus for divergent viruses discovered in bats and eulipotyphlans [17] and the genera Actinovirus, Agnathovirus, and Reptillovirus for divergent viruses discovered in fish and reptiles [18]. The family was then subdivided into four subfamilies: Acanthavirinae (Actinovirus), Agantavirinae (Agnathovirus), Mammantavirinae (Loanvirus, Mobatvirus, Orthohantavirus, and Thottimvirus), and Repantavirinae (Reptillovirus) [18] (for a more detailed history of the taxonomy of family Hantaviridae, see Kuhn and Schmaljohn, 2023 [19]). The current (2022–2023) taxonomy of Hantaviridae [20] is outlined in Table 1.

3. Future (2024–) Taxonomy of the Bunyaviral Family Hantaviridae

The 2019 taxonomic reorganization of the family Hantaviridae via DEmARC was limited to hantavirids for which coding-complete genome sequence information for the small (S) and medium (M) segments was available; concatenated S + M sequences were used for multiple-sequence alignment to infer phylogeny, and pairwise evolutionary distance (PED) values were calculated using a maximum-likelihood approach with a Whelan and Goldman (WAG) substitution model. A PED cut-off value of 0.1 was used for species demarcation within Hantaviridae [16]. The analysis was limited to the sequences of the S and M segments to maintain the previous hantavirid classification, which was largely based on phenotypic characters and limited protein sequence similarities of individual viruses [21], as much as possible and, in particular, to prevent the declassification of “important” orthohantaviruses (i.e., human pathogens) for which there was no or only fragmented sequence information for the large (L) segment [16].
However, the absence of L-segment sequence information in hantavirid taxonomic analyses is problematic for several reasons. First, the entire taxonomy of the realm Riboviria, which includes negarnaviricot Hantaviridae, is based on a single “hallmark gene”. This hallmark gene is the open reading frame (ORF) encoding an RNA-directed RNA polymerase (RdRp) [22,23], which in the case of hantavirids is a part of the L protein, encoded by the L segment. Thus, the absence of RdRp sequence information prevents the classification of a virus into this realm and, ipso facto, also into any lower-ranked ribovirian taxon. Second, as the name implies, L is by far the longest protein encoded by hantavirids; generally speaking, the main S-segment ORF is 1–3 kb long; the M-segment ORF is 3.2–4.9 kb long; and the L-segment ORF is 6.8–12 kb long (judged by GenBank entries). Thus, an analysis of, for example, concatenated S + M sequences ignores a substantial percentage of a hantavirid’s genome sequence. Third, sequence variability is unevenly distributed among hantavirid segments; the M-segment sequence is the least conserved, whereas the L-segment sequence is the most conserved. Both extremes can be used to achieve disparate goals, such as species and sub-species classifications, which require sequence divergence, and family and subfamily cohesiveness, which requires relatively conserved sequences. Finally, increasing structural information suggests that the Gn/Gc polyprotein encoded by hantavirid and other bunyaviral M segments (at least those of certain nairovirids, phenuivirids, peribunyavirids, and tospovirids) share a common ancestor with the membrane fusion machinery of distantly related positive-strand RNA viruses: alphaviruses (Martellivirales: Togaviridae), rubella virus (Hepelivirales: Matonaviridae), and flaviviruses sensu stricto (Amarillovirales: Flaviviridae) [24]; hence, the M segments are likely independent acquisitions in bunyaviral genome evolution. In addition, an increasing number of negarnaviricots that are being discovered in fungi and invertebrates do not appear to have M segments. Thus, although all currently classified hantavirids have M segments, the reliance on M segments within concatenated S + M data may become insufficient for family-wide analyses and may be inadequate for order-wide analyses.
The ICTV Hantaviridae Study Group decided to reassess the entire family for the 2023–2024 taxonomic cycle and plans to submit a TaxoProp proposing a new family taxonomy by the 2023 submission deadline (beginning of July). While the approaches/methodologies for reanalysis remain under discussion, a decision was made to only assess viruses for which there is S + M + L coding-complete or near-complete sequence information and deem all other viruses unclassifiable a priori. This stringent criterion would, at a minimum, result in the abolishment of six orthohantavirus species (Table 1, red), the declassification (removal from established species) of an additional 11 orthohantaviruses (Table 1, orange), and the possible renaming of two species (Table 1, purple) if word stem links between species and member viruses are desired to be maintained.
Table 1. Scheme of the 2022 [20] and projected 2023 [25] % taxonomy of the bunyaviral family Hantaviridae.
Table 1. Scheme of the 2022 [20] and projected 2023 [25] % taxonomy of the bunyaviral family Hantaviridae.
GenusSpecies Name (2022)Projected Species Name (2023)Virus Name (Abbreviation)Coding-Complete/-Near-Complete Genome Sequence Available in GenBank? ^
Subfamily Acanthavirinae
ActinovirusBatfish actinovirusActinovirus halieutaeaeWēnlǐng minipizza batfish virus (WEMBV)Yes
Goosefish actinovirusActinovirus lophiiWēnlǐng yellow goosefish virus (WEYGV)Yes
Perch actinovirusActinovirus bernenseBern perch virus (BRPV)Yes
Spikefish actinovirusActinovirus triacanthodisWēnlǐng red spikefish virus (WERSV)Yes
Subfamily Agantavirinae
AgnathovirusHagfish agnathovirusAgnathovirus eptatretiWēnlǐng hagfish virus (WEHV)Yes
Subfamily Mammantavirinae
LoanvirusBrno loanvirusLoanvirus brunaenseBrno virus (BRNV)Yes
Longquan loanvirusLoanvirus longquanenseLóngquán virus (LQUV)Yes
MobatvirusLaibin mobatvirusMobatvirus laibinenseLáibīn virus (LAIV)Yes
Lena mobatvirusMobatvirus lenaenseLena virus (LENV)Yes
Nova mobatvirusMobatvirus novaenseNova virus (NVAV)Yes
Quezon mobatvirusMobatvirus quezonenseQuezon virus (QZNV)Yes
Xuan Son mobatvirusMobatvirus xuansonenseXuân Sơn virus (XSV)Yes
OrthohantavirusAndes orthohantavirusOrthohantavirus andesenseAndes virus (ANDV)Yes
Castelo dos Sonhos virus (CASV)No
Lechiguanas virus (LECV = LECHV)No
Orán virus (ORNV)No
Asama orthohantavirusOrthohantavirus asamaenseAsama virus (ASAV)Yes
Asikkala orthohantavirusOrthohantavirus asikkalaenseAsikkala virus (ASIV)Yes
Bayou orthohantavirusOrthohantavirus bayouibayou virus (BAYV)Yes
Catacamas virus (CATV)Yes
Black Creek Canal orthohantavirusOrthohantavirus nigrorivenseBlack Creek Canal virus (BCCV)Yes
Bowe orthohantavirusOrthohantavirus boweenseBowé virus (BOWV)Yes
Bruges orthohantavirusOrthohantavirus brugesenseBruges virus (BRGV)Yes
Cano Delgadito orthohantavirusOrthohantavirus delgaditoenseCaño Delgadito virus (CADV)Yes
Cao Bang orthohantavirusOrthohantavirus caobangenseCao Bằng virus (CBNV)Yes
Liánghé virus (LHEV)No
Choclo orthohantavirusOrthohantavirus chocloenseChoclo virus (CHOV)Yes
Dabieshan orthohantavirusOrthohantavirus dabieshanenseDàbiéshān virus (DBSV)No
Dobrava-Belgrade orthohantavirusOrthohantavirus dobravaenseDobrava virus (DOBV)Yes
Kurkino virus (KURV)Yes
Saaremaa virus (SAAV)No
Sochi virus (SOCV)Yes
El Moro Canyon orthohantavirusOrthohantavirus moroenseCarrizal virus (CARV)Yes
El Moro Canyon virus (ELMCV)No
Huitzilac virus (HUIV)Yes
Fugong orthohantavirusOrthohantavirus fugongenseFúgòng virus (FUGV)Yes
Fusong orthohantavirusOrthohantavirus fusongenseFǔsōng virus (FUSV)No
Hantaan orthohantavirusOrthohantavirus hantanenseAmur virus (AMRV)Yes
Hantaan virus (HTNV)Yes
Soochong virus (SOOV)Yes
Jeju orthohantavirusOrthohantavirus jejuenseJeju virus (JJUV)Yes
Kenkeme orthohantavirusOrthohantavirus kenkemeenseKenkeme virus (KKMV)Yes
Khabarovsk orthohantavirusOrthohantavirus khabarovskenseKhabarovsk virus (KHAV)Yes
Topografov virus (TOPV)Yes
Laguna Negra orthohantavirusOrthohantavirus negraenseLaguna Negra virus (LANV)No
Maripa virus (MARV)Yes
Rio Mamoré virus (RIOMV)Yes
Luxi orthohantavirusOrthohantavirus luxienseLúxī virus (LUXV)Yes
Maporal orthohantavirusOrthohantavirus maporalenseMaporal virus (MAPV)Yes
Montano orthohantavirusOrthohantavirus montanoenseMontaño virus (MTNV)Yes
Necocli orthohantavirusOrthohantavirus necoclienseNecoclí virus (NECV)No
Oxbow orthohantavirusOrthohantavirus oxbowenseOxbow virus (OXBV)No
Prospect Hill orthohantavirusOrthohantavirus prospectenseProspect Hill virus (PHV)Yes
Puumala orthohantavirusOrthohantavirus puumalaenseHokkaido virus (HOKV)Yes
Muju virus (MUJV)Yes
Puumala virus (PUUV)Yes
Robina orthohantavirusOrthohantavirus robinaenseRobina virus (ROBV) *Yes
Rockport orthohantavirusOrthohantavirus rockportenseRockport virus (RKPV)Yes
Sangassou orthohantavirusOrthohantavirus sangassouenseSangassou virus (SANGV)Yes
Seewis orthohantavirusOrthohantavirus seewisenseSeewis virus (SWSV)No
Seoul orthohantavirusOrthohantavirus seoulensegōu virus (GOUV)No
Seoul virus (SEOV)Yes
Sin Nombre orthohantavirusOrthohantavirus sinnombreenseNew York virus (NYV)No
Sin Nombre virus (SNV)Yes
Tatenale orthohantavirusOrthohantavirus tatenalenseTatenale virus (TATV)Yes
Thailand orthohantavirusOrthohantavirus thailandenseAnjozorobe virus (ANJZV)Yes
Serang virus (SERV)No
Thailand virus (THAIV)Yes
Tigray orthohantavirusOrthohantavirus tigrayenseTigray virus (TIGV)Yes
Tula orthohantavirusOrthohantavirus tulaenseAdler virus (ADLV)No
Tula virus (TULV)Yes
Yakeshi orthohantavirusOrthohantavirus yakeshienseYákèshí virus (YKSV)No
ThottimvirusImjin thottimvirusThottimvirus imjinenseImjin virus (MJNV)Yes
Thottapalayam thottimvirusThottimvirus thottapalayamenseThottapalayam virus (TPMV)Yes
Subfamily Repantavirinae
ReptillovirusGecko reptillovirusReptillovirus hemidactyliHǎinán oriental leaf-toed gecko virus (HOLGV)Yes
Per the ICTV, viruses are real objects that are assigned to concepts/categories called taxa. Species, genera, subfamilies, families, and orders are taxa. Taxon names are always italicized and always begin with a capital letter. Virus names are not italicized and are not capitalized, except if the name or a name component is a proper noun [3,26]. This table lists the virus names with their correct (lack of) capitalization; % if ratified in the March 2023 ICTV-wide vote; ^ as judged by preliminary analyses of GenBank-deposited sequences but requiring careful reanalysis; * Robina virus might be a mobatvirus, possibly requiring reclassification [27].
On the other hand, the forthcoming analysis may include previously unclassified potential hantavirids for which sufficient S + M + L sequences have been deposited. A cursory survey revealed that at least two potential loanviruses, one potential mobatvirus, 16 potential orthohantaviruses, and one potential thottimvirus could be classified or be identified as isolates of already-classified viruses (Table 2, green).
Table 2. Unclassified potential hantavirids.

4. Discussion

Hantavirid taxonomy is clearly in disarray, as exemplified by the numerous viruses with different names in the literature that may only represent isolates of other named viruses rather than being distinct viruses (species with several members in Table 1; numerous viruses listed in Table 2). Table 1 and Table 2 clarify that the diversity of hantavirids is only incompletely represented by the current taxonomy and family-wide analyses of hantavirids, and, therefore, the most appropriate sub-family taxon distribution is largely impossible because of the lack of evolutionary meaningful taxonomic markers (e.g., segment sequences, hallmark genes, and gene motifs). Even a relatively limited hantavirid classification inclusion criterion, such as the requirement of coding-complete/-near-complete sequences, will have a noticeable impact on the current taxonomy through the declassification of at least 17 orthohantaviruses (Table 1) and the classification of up to 20 hantavirids (Table 2). Taxonomic changes would likely be even more drastic if classification inclusion criteria were set more stringently; for instance, the ICTV Hantaviridae Study Group might additionally require that the S, M, and L genome segment sequences of a particular virus must be derived from the same isolate (rather than being a mosaic from isolates collected in different places at different times) and/or that specific sequencing standards [93,94] would have to be fulfilled to increase “trust” that the sequence is correct.
We call on the hantavirid and wider bunyaviral community to provide additional and/or improved sequence information for any incompletely sequenced putative hantavirid prior to mid-June 2023 to support the ICTV Hantaviridae Study Group’s current effort to establish an updated, coherent, consistent, and evolution-based hantavirid taxonomy. These sequences ought to be deposited into GenBank, ideally along with notifying the Study Group that additional information has become available for inclusion in analyses.
During the upcoming months, the ICTV Hantaviridae Study Group will make initial decisions on:
  • the minimal requirement(s) for hantavirid classification (e.g., definitions of “near-complete genome sequence” and minimal sequence quality);
  • the method(s) for hantavirid classification (e.g., DEmARC and/or pairwise sequence comparison [PASC]);
  • the minimum input information (e.g., concatenated S + M or S + L or M + L or S + M + L genomic segment sequences; individual phylogenies and pairwise sequence comparisons for each genome segment);
  • the possible resolution of “species complexes” (i.e., species that currently harbor more than one member virus [e.g., Andes orthohantavirus/Orthohantavirus andesense]);
  • which particular sequences should be regarded as type/reference sequences for each species and be ultimately represented in The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database.
All of these decisions will crucially depend on the availability of expanded high-quality hantavirid genomic sequence information. In the absence of this information, a decision may be forced to drastically reboot and simplify hantavirid taxonomy by removing the “virus status” from many unclassified hantavirids to discourage the use of their currently assigned names—effectively putting many hantavirids “on hold” until sufficient sequence information becomes available to assess their taxonomic statuses.

Author Contributions

Conceptualization, J.H.K.; writing—original draft preparation, J.H.K.; writing—review and editing, all authors. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported in part through Laulima Government Solutions, LLC, prime contract with the National Institutes of Health (NIH) National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under Contract No. HHSN272201800013C.

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Not applicable.

Acknowledgments

The authors thank Anya Crane (Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA) for critically editing the manuscript.

Conflicts of Interest

The authors declare no conflict of interest.

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