We think that the N11 and N10 proteins should be characterized as “+/-” functions rather than “-like” for the following reasons:

“+” AND “-” NOTATION IS CONSISTENT WITH EXISTING MUTATION LANGUAGE

With respect to mutations in enzymes, we state “wild type enzyme” (or “+”) when there are no mutations and we state “mutant enzyme” (or “-”) when there are one or more mutations impacting function, but we do not refer to an enzyme that no longer functions because of one or more mutation(s) as “enzyme-like.”

THE USE OF “+” AND “-” MAKES THE BIOLOGICAL ORIGINS CLEAR

By way of example, any nomenclature needs to be absolutely clear that the N11 and N10 viral proteins have a viral derivation. As we have previously discussed with Adolfo Garcia-Sastre, our detailed structural analysis of the N11 protein (http://dx.doi.org/10.1371...) produced the conclusion that THE N11 PROTEIN IS A FUNCTIONALLY ALTERED VIRAL NEURAMINIDASE that no longer supports viral entry of cells by processing sialic acid but contains domains that may allow the virus to enter cells using receptors that are highly unusual for the viral class:

THE FUNCTIONALLY ALTERED N11 PROTEIN ACTIVE SITE HAS NO CHANGE IN EITHER ITS POSITION OR BULK STRUCTURAL CHARACTERISTICS NOR IS THERE ANY CHANGE IN THE SECONDARY STRUCTURE OF THE N11 PROTEIN THAT POSITIONS RESIDUES TO THE AREA OF THE CONSENSUS ACTIVE SITE. The functionally altered N11 protein has changes in critical residues that eliminate the ability to process sialic acid, process MUNANA, bind inhibitors (e.g., oseltamivir, peramivir, and zanamivir), and that eliminate detection of the virus by PCR probes (to the usually conserved 151-152 loop). Simply, these changes are equivalent to multiple, nested: mutations, insertions, and deletions.

NEW CELL ENTRY DOMAINS APPEAR ON THE N11 PROTEIN, including a nearly perfect multi-strand copy of the ALPHA-BUNGAROTOXIN domain that binds the nicotinic acetylcholine receptor. Alpha-bungarotoxin is a component of snake venom that shares the same residues that are found in the functionally altered N11 protein with SEI, botulinum toxin, tetanus toxin, and anthrax lethal factor.

The changes seen in the N11 protein are not simple mutations but reflect multiple changes that alter the functionality of the N11 protein while maintaining the position of the consensus active site and the protein's bulk structural characteristics. However, similar to multiple mutations, they represent multiple modifications of an existing consensus structure.

“+” AND “-” NOMENCLATURE USED WITH EXTENSIBLE DESCRIPTORS CAN CONVEY COMPLEX, PRECISE INFORMATION

In order to reflect changes in cell entry (CE), enzymatic activity (EA), and drug-binding (DB) of the N11 neuraminidase, the N11 protein could be referenced in the form of one or more occurrences of

[MODIFICATION](DESCRIPTION)

For example, to specify the changes in cell entry (CE) of a neuraminidase N11 that is unable to bind to the receptor (r1) but had the ability to bind to nicotinic acetylcholine receptors (nAChR):

[CE:-r1,+nAChR](N11)

For example, to specify the enzymatic activity (EA) of a neuraminidase N11 that is unable to process Neu5Ac, Neu5Gc, and KDN:

[EA:-Neu5Ac,-Neu5Gc,-KDN](N11)

For example, to specify the drug-binding (DB) of a neuraminidase N11 that is not responsive to oseltamivir, peramivir, or zanamivir:

[DB:-oseltamivir,-peramivir,-zanamivir](N11)

The above could be combined as:

[CE:-r1,+nAChR; EA:-Neu5Ac,-Neu5Gc,-KDN; DB:-oseltamivir,-peramivir,-zanamivir](N11)

The H17N10 virus appears to be functionally altered such that it cannot reassort with other common, naturally occurring influenza viruses. (http://dx.doi.org/10.1038...). The clustering of viruses into reassortment classes would allow reassortment specificity to be precisely designated. In order to reflect changes in reassortment specificity (RS) for a H17N10 virus that is unable to reassort with viral classes (vc1), (vc2), and (vc3), the entire virus could be referenced as:

[RS:-vc1,-vc2,-vc3](H17N10)

There is no apparent competitive advantage to the H17N10 virus to lose the ability to reassort with other common influenza viruses, so there may exist other, as yet unidentified, functionally altered influenza viruses with which the H17N10 virus can reassort. Any reassortment of functionally altered influenza viruses to produce new, combined characteristics needs to be tracked in order to determine if it represents a serious global health concern. The scientific community should not only be investigating the mechanisms by which viruses in a class become functionally altered but also should be labeling information about the functionally altered viruses so that their characteristics can be easily interpreted, tracked, and verified.

EXTENSIBLE DESCRIPTORS AID IN OVERSIGHT AND REGULATION

Using “+” / “-” notation with extensible descriptors will also make it clear that a derivative molecule or organism falls under any regulation that governs the modification, dissemination, and use of infectious organisms or their components.

SUMMARY

To summarize, using “+” / “-” notation with extensible descriptors , rather that a “-like” designator, for functionally altered biota molecules (e.g., protein, DNA, RNA, …) derived from infectious biota MAKES IT CLEAR IN LANGUAGE THAT IS CONSISTENT WITH LANGUAGE ALREADY WIDELY USED, for each molecule/biota, that it is:

- FUNCTIONALLY ALTERED ALONG WITH THE PRECISE NATURE OF THE ALTERATION
- NOT A NEW CLASS OF MOLECULE/BIOTA
- NOT OUTSIDE OF ANY APPLICABLE REGULATIONS GOVERNING THE MOLECULE'S/BIOTA'S CREATION,
- MODIFICATION, DISSEMINATION, OR USE

The syntax of the above simple example biota nomenclature is given below.

Arthur Weininger and Susan Weininger
Weininger Works
plos@weiningerworks.com

1 Weininger A, Weininger S. (2015) Using Common Spatial Distributions of Atoms to Relate Functionally Divergent Influenza Virus N10 and N11 Protein Structures to Functionally Characterized Neuraminidase Structures, Toxin Cell Entry Domains, and Non-influenza Virus Cell Entry Domains. PLoS One 10(2):e0117499. doi: http://dx.doi.org/10.1371...

2 Juozapaitis M, Aguilar Moreira E, Mena I Giese S, Riegger D, Pohlmann A, Hoper D, Zimmer G, Beer M, Garcia-Sastre A, Schwemmle M. (2014) An infectious bat-derived chimera influenza virus harbouring the entry machinery of an influenza A virus. Nat. Commun. 2014 Jul 23; 5; 4448.
doi: http://dx.doi.org/10.1038...

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The syntax of the above simple example biota nomenclature in WSN (Wirth Syntax Notation):

NOMENCLATURE = COMPONENT { COMPONENT }.
COMPONENT = DESCRIPTION
| “[” MODIFIER_COMPONENT_LIST “]” “(“ DESCRIPTION “)”.
DESCRIPTION = character { character }.
MODIFIER_COMPONENT_LIST = MODIFIER_COMPONENT { “;” MODIFIER_COMPONENT }.
MODIFIER_COMPONENT = MODIFIER “:” MODIFIER_ATTRIBUTE_LIST
| MODIFIER.
MODIFIER = character { character }.
MODIFIER_ATTRIBUTE_LIST = MODIFIER_ATTRIBUTE { “,” MODIFIER_ATTRIBUTE }.
| “+” MODIFIER_ATTRIBUTE
| “-” MODIFIER_ATTRIBUTE.
MODIFIER_ATTRIBUTE = character { character }.
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Not in the syntax definition:

- One might allow DESCRIPTION fields to have multiple components in order to describe sets,
e.g., [CE](H17N10,H18N11]) would mean the set including H17N10 and H18N11 has changes in cell entry.

- One might allow nesting of MODIFIER_COMPONENTs for better organization of detail.
The above syntax is simpler, but will require more MODIFIER and MODIFIER_ATTRIBUTE entries
in lieu of nested handling.

- So that a data file might be completely self-defined, one might add a method for defining MODIFIERs and
MODIFIER_ATTRIBUTES, e.g., “MODDEF(RS,Reassortment Specificity)” would define “RS” to mean
“Reassortment Specificity” and “ATTDEF(vc1,viral class 1)” would define “vc1” to mean “viral class 1”.
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