Proposals on virus taxonomy using the examples from the families of Phenuiviridae, Nairoviridae, and Peribunyavidae

In recent years, the taxonomy of the families of Phenuiviridae, Nairoviridae, and Peribunyavidae in Bunyavirales was updated frequently, because many novel viruses in these families have been identified and the species demarcation criteria of these families have been changed. As per these criteria and sequence analysis, we found that the taxonomy of 19 species in these families should be revised. We presented six proposals for optimizing virus species taxonomy using the examples from these families. First, the species demarcation criteria for the same family (e.g., Peribunyavidae) should be unified. Second, the methods and parameters for the taxonomic calculation in the same order (e.g., Bunyavirales) should be unified. Third, virus species taxonomy should be based on phylogenetic relationships, rather than a cutoff value of sequence identities that is a self-contradictory demarcation criterion, although sequence identities aid virus taxonomy greatly. Fourth, virus species taxonomy should be based on the phylogenetic relationship of a key viral gene (e.g., the RdRp gene of Bunyavirales), which is important for the taxonomy of virus recombinants or reassortants. Fifth, a virus can be demarcated without a species before its biomedical significance has been revealed. Sixth, names of all viruses and virus species should be constituted exclusively with Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 8 February 2022 doi:10.20944/preprints202202.0117.v1 © 2022 by the author(s). Distributed under a Creative Commons CC BY license. 2 common characters (English letters and Arab numbers), to minimize difficulty in spelling and communication. These proposals are rational, flexible, and can accommodate all known viruses. They can also bridge the taxonomy history and the future demands due to their flexibility.


Introduction
The family Bunyaviridae was upgraded by the International Committee on Taxonomy  Currently, Bunyavirales accommodates 12 families: Arenaviridae, Cruliviridae, Fimoviridae,Hantaviridae,Leishbuviridae,Mypoviridae,Nairoviridae,Peribunyaviridae,Phasmaviridae,Phenuiviridae,Tospoviridae,and Wepedeviridae. 5 In recent years, the taxonomy of the genera and species in the families of Phenuiviridae, Nairoviridae, and Peribunyavidae in Bunyavirales was updated frequently, because many novel viruses in these families have been identified and the species demarcation criteria of these families have been changed. [6][7][8][9][10][11] As per these criteria and sequence analysis, we found that the taxonomy of 19 species in these families should be revised.
We found some problems about the species taxonomy of viruses through this work. We presented the relevant proposals for optimizing virus species taxonomy using the examples from the above three families.

Abbreviations
To simplify relevant expressions, the Razdan virus strain LEIV-Arm2741 corresponding to the GenBank accession number NC022630 in the species Razdan bandavirus was abbreviated as Razdan virus (NC022630), Razdan virus (NC022630, Razdan bandavirus), or Razdan bandavirus (NC022630), as appropriate. Other viruses in this report were abbreviated in the same way. "As per Table

Taxonomy information
The current taxonomy information of the viruses in Nairoviridae listed in Section 3.13.2 was from an ICTV report; 6 the current taxonomy information of the viruses in Peribunyaviridae listed in Section 3.33.17 was from another ICTV report; 7 and the current taxonomy information of the viruses in Phenuiviridae listed in Section 3.183.19 was from the menu of "Taxonomy" in the ICTV website. 8 The species demarcation criteria of some genera and families currently employed by ICTV were from the ICTV reports or proposals, and they were summarized in Table 1.

Sequence alignment and sequence identity calculation
Sequences were downloaded from GenBank and aligned with the software tools Clustal W using the default settings, as the same as the ICTV report for the family Peribunyaviridae. 7 Sequence identities were calculated using the software tool Mega (version X) and the aligned sequences. 9

Phylogenetic relationship calculation
Phylogenetic relationships were calculated using the software tool Mega (version X) using the neighbor-joining method and the Jones-Taylor-Thornton model, as the same as the ICTV report for the family Peribunyaviridae. 7 Bootstrap values were calculated with 1000 replicates.
If strictly according to the species demarcation criterion, Gamboa orthobunyavirus (KX900438) and Gamboa orthobunyavirus (KM272183) should be classified into two species. The identities in the amino acid sequences of the RdRp protein between these viruses were 93.195.5% (Table 3), lower than the species demarcation criterion (96%) of Peribunyaviridae (Table1).

Tete orthobunyavirus and Matruh orthobunyavirus in Peribunyaviridae.
Bahig virus (KP792654, Tete orthobunyavirus) and Matruh virus (KP792693, Matruh orthobunyavirus) should be classified into the same species, as per Table 3 and Figure 2. The identities in the amino acid sequences of the RdRp protein between these viruses were 99.1% (Table 3), higher than the species demarcation criterion (96%) of Perbunyaviridae (Table1).

Aino orthobunyavirus and Shuni orthobunyavirus in Peribunyaviridae
Aino virus (HE795087, Aino orthobunyavirus) should be classified into Shuni orthobunyavirus with Kaikalur virus (MH484297, Shuni orthonairovirus), as per Table 3 and  These strains should be classified into four species, as per Table 3 and Figure 2. These four species were tentatively marked as Bakau orthobunyavirus AD in Table 3 Table 3 and Figure 2.
The identities in the amino acid sequences of the RdRp protein between these viruses were 99.299.8% (Table 3), higher than the species demarcation criterion (96%) of Perbunyaviridae (Table1).

Bushbush orthobunyavirus in Peribunyaviridae.
Bushbush orthobunyavirus contains multiple strains, including Bushbush virus (MK896599), Benfica virus (MK896617) and Juan Dí az virus (MK896554). These strains should be classified into three species, as per Table 3 and Figure 2. These three species were tentatively marked as Bushbush orthobunyavirus AC in

Acará virus (MK896653, Acara orthobunyavirus) and Benevides virus (MK896620,
Benevides orthobunyavirus) should be classified into the same species, as per Table 3 and Figure 2. The identities in the amino acid sequences of the RdRp protein between these viruses were 99.5% (Table 3), higher than the species demarcation criterion (96%) of Perbunyaviridae (Table1).

Marituba orthobunyavirus in Peribunyaviridae.
Marituba orthobunyavirus contains multiple strains, including Murutucú virus  Table 3 and Figure 2. These four species were tentatively marked as Marituba orthobunyavirus AD in

Bimiti orthobunyavirus and Guama orthobunyaviru in Peribunyaviridae.
The two species corresponding to bimiti virus (KP792657, Bimiti orthobunyavirus) and Guamá virus (KP792666, Guama orthobunyaviru) should be classified into the same species, as per Table 3 and Figure 2. The identities in the amino acid sequences of the RdRp protein between these viruses were 98.0% (Table 3), which is higher than the species demarcation criterion (96%) of Perbunyaviridae (Table1).

Catu orthobunyavirus and Moju orthobunyavirus in Peribunyaviridae.
The two species corresponding to Catu virus (KP792660, Catu orthobunyavirus) and Moju virus (KP792675, Moju orthobunyavirus) should be classified into the same species, as per Table 3 and Figure 2. The identities in the amino acid sequences of RdRp protein between four species were 96.2% (Table 3), which are much higher than the species demarcation criterion (96%) of Perbunyaviridae (Table 1).

Frijoles phlebovirus (MK330765) and
Frijoles phlebovirus (KX611391) should be classified into two species, as per their identity in the viral RdRp gene amino acid sequence (77.0%) which was higher than the species demarcation criterion (95%) of Phlebovirus (Table 1). Moreover, the phylogenetic relationships of this family also demonstrated that

Discussion
The taxonomic errors shown in Sections 3.13.19 also existed in the taxonomy report of Negarnaviricota. 5 Besides these errors, there were some writing errors in the ICTV report on incorrectly to Dera Ghazi Khan orthonairovirus. 6 Additionally, Toscana phlebovirus (NC006319) and Leticia phlebovirus (HM566167) were incorrectly assigned to the species of Naples phlebovirus in the GenBank (Figure 3), possibly by the relevant sequence submitters.
All the above suggestions on species taxonomy revision were based on sequence alignment using Clustal X and phylogenetic relationships calculated using the neighbor-joining method and the Jones-Taylor-Thornton model. We found that these suggestions keep valid if the relevant sequences were aligned with the software tools Clustal W, Muscle, or MAFFT, or the relevant phylogenetic relationships were calculated with the maximum likelihood or the minimum evolution method, or the amino acid substitution were set in the Poisson or Dayhoff model.