Viral Genomics and Diversity: Study Notes for Microbiology Students

Chapter 11: Viral Genomics and Diversity

11.1 Size and Structure of Viral Genomes

This section explores the diversity in viral genome size and structure, highlighting key differences between DNA and RNA viruses and their evolutionary implications.

• Viral Genome Size:

  • Viral genomes vary approximately 1,000-fold from the smallest to the largest.

  • They are usually smaller than cellular genomes.

  • Smallest circovirus: 1.75-kilobase single-stranded DNA.

  • Largest Pandoravirus: 2.5-megabase pairs, infects marine amoebae and is larger than some bacterial genomes.

• RNA Genomes:

  • Generally smaller than DNA viruses.

  • Viroids (naked infectious RNAs) have the smallest genomes of all.

Figure 11.1 Comparative Genomics

Comparative chart showing genome sizes of various viruses and cellular organisms.

11.1 Viral Infection and Genome Expression

Upon infection, viruses must express their genes and replicate their genomes before assembling new virions.

• Transcription of viral genes is required for replication.

• New genome copies are synthesized, followed by viral assembly.

• For some RNA viruses, the genome itself serves as mRNA.

• Most viruses require transcription to produce viral mRNA.

11.1 The Baltimore Classification Scheme

The Baltimore scheme classifies viruses based on their genome type and the relationship to mRNA synthesis. There are seven classes:

• Class I: Double-stranded DNA (dsDNA)

• Class II: Single-stranded DNA (ssDNA), usually positive-strand; requires a double-stranded DNA intermediate for replication.

• Class III: Double-stranded RNA (dsRNA)

• Class IV: Single-stranded (+) RNA; genome serves directly as mRNA.

• Class V: Single-stranded (−) RNA; RNA replicase synthesizes (+) strand for mRNA and as template for more (−) strand genomes.

• Class VI: ss(+)RNA viruses (retroviruses); replicate through a DNA intermediate using reverse transcriptase. Example: Human immunodeficiency virus (HIV)

• Class VII: dsDNA viruses that replicate through an RNA intermediate using reverse transcriptase. Example: Hepatitis B virus

Figure 11.2 The Baltimore Classification of Viral Genomes

Diagram showing the seven Baltimore classes and their replication strategies.

11.1 Hosts for Viruses of Each Baltimore Class

Different Baltimore classes infect specific domains of life.

• Two classes in Archaea, four in Bacteria, all seven in animals.

• Class I (dsDNA): Primary prokaryotic viruses.

• Class IV (ss+RNA): Primary eukaryotic viruses.

• Fungi are only infected by classes III and IV.

• Most class I and class V viruses have animal hosts; most class II viruses have plant hosts.

• Class VI (Retroviruses): Infect only animals.

• Class VII (dsDNA): More common in plants than animals.

Figure 11.3 Viral Hosts and Viral Diversity

Graphical representation of host range and diversity among viral classes.

11.2 Viral Taxonomy and Phylogeny

Viral Taxonomy

Viruses are classified using a polyphasic approach, considering phenotypic, genotypic, and phylogenetic analyses.

• The International Committee on Taxonomy of Viruses (ICTV) oversees classification and naming.

• As of August 2022, ICTV recognized 6 realms, 10 kingdoms, 17 phyla, 2 subphyla, 39 classes, 65 orders, 8 suborders, 233 families, 168 subfamilies, 2,606 genera, 84 subgenera, and 10,434 species.

• Distribution among three domains of life: 90% of bacteriophages are in the Caudovirales order; many orders remain unclassified.

Figure 11.4 Taxonomic Classification of Viruses Infecting the Three Domains of Life

Domain	Major Viral Orders	Percent
Bacteria	Caudovirales	90%
Archaea	Ligamenvirales, others	63%
Eukarya	Herpesvirales, Picornavirales, others	77%

Viral Phylogeny

Mapping viral evolutionary relationships is challenging due to the lack of ribosomal RNA and high mutation rates.

• A universal phylogenetic tree is constructed from conserved protein sequences and structural features.

• Some groups, such as nucleocytoplasmic large DNA viruses (NCLDV) like Mimivirus, have phylogenetic trees based on shared genes.

• Most viral genes have no known homologs, making much of viral genomics a frontier for new biology.

Figure 11.5 Phylogeny of Nucleocytoplasmic Large DNA Viruses (NCLDV)

Virus Group	Examples
Chordate pox virus	Chordate pox virus
Insect pox virus	Insect pox virus
Fish iridoviruses	Fish iridoviruses
Amphibian iridoviruses	Amphibian iridoviruses
Mimiviruses	Mimivirus
Phycodnaviruses	Phycodnavirus

11.3 Single-Stranded DNA Bacteriophages: φX174 and M13

Single-stranded DNA bacteriophages are important models for understanding viral replication and genetic engineering.

• Bacteriophage φX174:

  • Circular single-stranded DNA genome inside an icosahedral virion.

  • Very small genome with overlapping genes (multiple reading frames).

  • A* protein shuts down host DNA synthesis.

  • Replication via rolling circle replication (see Figure 11.7).

  • Lysis occurs through inhibition of peptidoglycan synthesis by E protein.

• Bacteriophage M13:

  • Filamentous phage with helical symmetry, attaches to host pilus.

  • Released without lysis (extrusion); cells continue to grow, no plaques observed.

  • Coat proteins cover DNA as it exits cell envelope.

  • Causes chronic infection, used as a cloning and DNA-sequencing vector.

Figure 11.6 Bacteriophage φX174, a Single-Stranded DNA Phage

Figure 11.7 Rolling Circle Replication in Phage φX174

Figure 11.8 Release of Phage M13

11.4 Double-Stranded DNA Bacteriophages: T4, T7, and Lambda

Double-stranded DNA bacteriophages are among the best-studied viruses, providing insights into viral replication, gene regulation, and host interactions.

• Bacteriophage T4:

  • Large, tailed dsDNA virus of E. coli; always kills host (virulent).

  • Genome contains modified 5-hydroxymethylcytosine instead of cytosine, protecting against host restriction enzymes.

  • Encodes its own DNA polymerase, primases, helicases, and an 8-protein DNA replisome complex.

  • Does not encode its own RNA polymerase; modifies host RNA polymerase specificity.

  • Features circular permutation and terminal redundancy in genome structure.

  • Replicated as a unit, forms concatemers, and uses headful packaging for DNA.

• Bacteriophage T7:

  • Infects E. coli and related bacteria; icosahedral head, short tail.

  • Early proteins inhibit host restriction system and include T7 RNA polymerase.

  • DNA replication uses T7 DNA polymerase, bidirectional from origin, with terminal repeats and concatemers.

  • Sequence of each virion is identical due to phage-encoded endonuclease activity.

• Bacteriophage Lambda:

  • Linear dsDNA virus with head and tail; temperate (lytic or lysogenic pathways).

  • Lytic: kills host; lysogenic: stable relationship, DNA integrates into E. coli chromosome at the att site using lambda integrase.

  • Upon penetration, DNA ends base pair, forming the cos site and cyclizing the genome.

  • Rolling circle replication produces long concatemers, which are cut into genome-sized lengths at cos sites and packaged into phage heads.

  • Transduction (packaging of host genes) can occur.

  • Regulation depends on two repressor proteins: cI protein (represses lytic events) and Cro repressor (activates lytic events).

Figure 11.9 Circular Permutation and the Unique DNA of Bacteriophage T4

Figure 11.10 Replication of the Bacteriophage T7 Genome

Figure 11.11 Bacteriophage Lambda: Virions, Integration of Viral DNA and Rolling Circle Replication

Phage	Genome Type	Replication Strategy	Host Interaction
T4	dsDNA	Concatemer, headful packaging	Virulent, kills host
T7	dsDNA	Bidirectional, concatemers	Virulent, inhibits host restriction
Lambda	dsDNA	Rolling circle, concatemers	Temperate, lysogenic or lytic

Additional info:

• Rolling circle replication is a mechanism where a circular DNA molecule is replicated to produce multiple linear copies, often seen in phages and plasmids.

• Concatemers are long DNA molecules composed of repeated genome units, which are later cut into individual genomes for packaging.

• Transduction is a process by which bacteriophages transfer genetic material between bacteria, contributing to horizontal gene transfer.