MODULE 4

MCB 102

LECTURE

MODULE 4: VIRUS TAXONOMY

• official body mandated by INTERNATIONAL UNION OF MICROBIOLOGY SOCIETIES
• develop and maintain A TAXONOMY OF VIRUSES and the NAMING OF THEIR TAXA
• rules and codes are updated many times in response to:

1. NEW DISCOVERIES
2. CHANGES IN THE UNDERSTANDING OF EVOLUTIONARY RELATIONSHIPS AMONG VIRUSES
3. ADVENT OF NEW TECHNOLOGIES

• tasked with DEVELOPING, REFINING, AND MAINTAINING A UNIVERSAL VIRUS TAXONOMY
• established the INTERNATIONAL CODE OF VIRUS CLASSIFICATION AND NOMENCLATURE
• maintains a COMPLETE CATALOG OF KNOWN VIRUSES at ICTVdb

• a BIOLOGICAL CLASSFICIATION based on EVOLUTIONARY RELATIONSHIPS
• viruses are assigned to:

1. SERIES OF HIERARCHAL TAXA (CLASSIFICATION) WITH;
2. REGULATED NAMING OF COMPONENT TAXA (NOMENCLATURE)

• process of ASSIGNING VIRUSES INTO GROUPS (called TAXA)
• can be performed on DIFFERENT SETS OF FEATURES leading to DIFFERENT CLASSIFICATION SCHEMES
• EVOLUTIONARY BASED AND HIERARCHAL (ICTV)

• NAMING of viruses or taxa
• TAXON NOMECLATURE: REGULATED BY ICTV with TYPOGRAPHICAL RESTRICTIONS on italicization and capitalization
• SPECIES NOMENCLATURE: NOT REGULATED BY ICTV; FOLLOWS A BINOMIAL FORMAT (genus + species)

IMPORTANT!!

taxon names ABOVE THE RANK OF SPECIES possess SUFFIXES to indicate taxonomic rank

• a RELATIVE POSITION IN HIERARCHY
• 15 RANKS (ICTV)

highest: REALM

lowest: SPECIES

• taxonomic category for A GROUP OF VIRUSES that are EVOLUTIONARILY RELATED AND SHARE SIMILAR PROPERTIES
• DEMARCATION CRITERIA (hierarchal classification)

define higher taxa that are shared with all lower-taxa level within

• based on OBSERVATIONAL PROPERTIES of virus isolates

1. MORPHOLOGY OF VIRION PARTICLES
2. TYPE OF NUCLEIC ACID in their genomes
3. PHYSICAL ATTRIBUTES

susceptibility to inactivation by high temperature

organic solvents

low ph

POLICY: ALLOW VIRUSES KNOWN FROM THEIR GENOMIC SEQUENCES ALONE TO BE INCORPORATED INTO VIRUS TAXONOMY

• enables TAXONOMIC ASSIGNMENTS without requiring prior knowledge of A VIRUS’ PHENOTYPIC PROPERTIES

UNIFIED EVOLUTIONARY TAXONOMY

• incorporates viruses classified by both TRADITIONAL AND METAGENOMICS-BASED ANALYSES
• requires considerable knowledge on:

1. HOW VIRUS PROPERTIES ARE GENOMICALLY ENCODED
2. EVOLUTIONARY HISTORIES
3. INFLUENCE OF PAST RECOMBINATION OR REASSORTMENT OF GENOMIC REGIONS ON PHYLOGENETIC CONGRUENCE

TO DEVELOP CRITERIA FOR ASSIGNING VIRUSES TO TAXA

CONSENSUS is required on WHICH GENES ARE MOST INFORMATIVE in recovering relationships that best represent EVOLUTIONARY HISTORIES

APRIL 2022: 45 EXPERTS MET IN OXFORD, UNITED KINGDOM TO:

develop a COMMUNITY-WIDE CONSENSUS ON METHODOLOGIES used for VIRUS CLASSIFICATION and to establish an INTEGRATED AND INTERNALLY CONSISTENT TAXONOMIC FRAMEWORK

1. VIRUS TAXONOMY SHOULD REFLECT EVOLUTIONARY HISTORY OF VIRUSES
2. VIRUS PROPERTIES MAY GUIDE ASSIGNMENT OF RANKS TO MAXIMIZE THEIR UTILITY
3. TAXONOMY IS BUT ONE OF MANY POSSIBLE MEANS TO CLASSIFY VIRUSES
4. TAXONOMIC ASSIGNMENT OF VIRUSES INFERRED FROM METAGENOMIC SEQUENCES REQUIRE STRICT SEQUENCE QUALITY CONTROL

“VIRUS TAXONOMY SHOULD REFLECT EVOLUTIONARY HISTORY OF VIRUSES”

• viruses are assigned to DIFFERENT VIRUS REALMS WITH INFERRED SEPARATE EVOLUTIONARY ORIGIN
• members of each realm possess ORTHOLOGOUS GENES (HALLMARK GENES) that corresponds to REPLICATION OR VIRION FORMATION MODULES within their genomes
• EVOLUTIONARY RELATIONSHIPS define MONOPHYLETIC TAXONOMIC ASSIGNMENTS within virus groups

REALM

SUBREALM

KINGDOM

SUBKINGDOM

PHYLUM

SUBPHYLUM

CLASS

SUBCLASS

ORDER

SUBORDER

FAMILY

SUBFAMILY

GENUS

SUBGENUS

SPECIES

“VIRUS PROPERTIES MAY GUIDE ASSIGNMENT OF RANKS TO MAXIMIZE THEIR UTILITY”

• PLACEMENT OF VIRUSES SHOULD FOLLOW PATTERNS OF EVOLUTIONARY, GENOMIC, AND PHENOTYPIC PROPERTIES

• used from 1991 TO 2017
• VIRUS SPECIES DIFFERENTIATED USING:

1. RELATEDNESS OF GENOME SEQUENCE
2. NATURAL HOST RANGE
3. CELL AND TISSUE TROPISM
4. PATHOGENICITY AND CYTOPATHOLOGY
5. MODE OF TRANSMISSION
6. PHYSICOCHEMICAL PROPERTIES OF VIRIONS
7. ANTIGENIC PROPERTIES OF VIRAL PROTEINS

5-RANK HIERARCHY

ORDER

FAMILY

SUBFAMILY

GENUS

SPECIES

• 8 PRINCIPAL (PRIMARY) RANKS AND 7 DERIVATIVE (SECONDARY) RANKS
• accommodate ENTIRE SPECTRUM OF GENETIC DIVERGENCE in virosphere
• emphasizes COMPARATIVE SEQUENCE ANALYSES of conserved genes and proteins

“TAXONOMY IS BUT ONE OF MANY POSSIBLE MEANS TO CLASSIFY VIRUSES”

• ICTV TAXONOMY: provides an OVERARCHING FRAMEWORK for classifying viruses based on EVOLUTIONARY RELATIONSHIPS

• groups families based on GENETIC CONTENTS AND REPLICATION STRATEGIES
• by DAVID BALTIMORE
• 7 CLASSES/GROUPS

BASIS:

1. VIRUS TROPISMS
2. MODES OF TRANSMISSION

• Acquired by INGESTION (fecal-oral transmission) and replicate primarily in the digestive tract

• Acquired by INHALATION (respiratory transmission) or by FOMITES (inanimate objects carrying contagion) and replicate primarily in the respiratory tract

• “arthropod-borne viruses”
• Replicate in their hematophagous arthropod vectors
• Transmitted by bite to vertebrate hosts
• Virus replication: VIREMIA

• “rodent-borne viruses”

• Acquired by close contact, injection, fomites, and unknown means
• Infect only SPECIFIC CELLS in particular TARGET ORGANS

“TAXONIMIC ASSIGNMENT OF VIRUSES INFERRED FROM METAGENOMIC SEQUENCES REQUIRE STRICT SEQUENCE QUALITY CONTROL”

• Sequence based assignment of new taxon in the absence of other virus characterization requires it to be both ACCURATE AND COMPLETE

VIRUS NAMES:

• NOT REQUIRED to be LATINIZED
• NOT RESTRICTED to BINOMIAL NOMENCLATURE

1. SPECIES NAME

• Written in ITALICS with First word beginning with a capital letter
• Should not be abbreviated
• The genus Iflavirus includes the species Deformed wing virus.
• The species Sandfly fever Naples phlebovirus has many diverse member viruses.

1. VIRUS NAME

• Should NEVER be italicized and should be written in lowercase
• first letters of words in a virus name, including the first word, should only begin with a capital when these words are proper nouns or start a sentence
• can be abbreviated
• Isolates of dengue virus 2 were obtained
• Salmonella phage SE1 was isolated

1. HIGHER TAXON NAME

• Written as SINGLE WORD with TAXON SPECIFIC SUFFFIX, written in ITALICS and begins with a Capital letter
• Often preceded with taxon level identifier
• a new species in the genus Fabavirus
• The order Picornavirales includes viruses infecting hosts of a range of species.

1. COLLECTIVE NAME FOR VIRUS GROUP

• NEITHER CAPITALIZED NOR ITALICIZED
• The first letter of a collective name may be capitalized if it begins a sentence.
• ourmiaviruses, ourmiavirus
• Guernseyviruses are distributed worldwide.
• The guernseyviruses are distributed worldwide.