Viral Genomics, Diversity, and Ecology: Study Notes for Microbiology

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Viral Genomics, Diversity, and Ecology

Introduction

This study guide covers the fundamental aspects of viral genomics, diversity, and ecology, focusing on medically important viruses such as Zika virus and coronaviruses, as well as the structure, evolution, and classification of viral genomes. The material is suitable for college-level microbiology students.

Zika Virus

Overview

Zika virus is a member of the Flaviviridae family, transmitted primarily by Aedes mosquitoes.
First identified in Uganda in 1947 in monkeys.
Recent outbreaks linked to birth defects and autoimmune neurological syndromes.
Reported cases of congenital microcephaly and Guillain-Barré syndrome.

Signs and Symptoms

Incubation period: 3–14 days.
Most infected individuals are asymptomatic.
Symptoms (when present): mild fever, rash, conjunctivitis, muscle and joint pain, malaise, headache; duration 2–7 days.

Complications

During pregnancy, Zika virus can cause microcephaly and other congenital abnormalities.
Microcephaly: condition where head circumference is smaller than normal, often due to genetic, viral, or toxic factors affecting fetal brain development.
Other complications: fetal loss, stillbirth, preterm birth, and neurological syndromes (e.g., Guillain-Barré syndrome).

Structure and Genome

Enveloped virus with a (+) RNA genome (~11,000 bases).
Icosahedral shell: 180 copies each of envelope (E) glycoprotein (~500 amino acids) and membrane (M) protein (~75 amino acids) or precursor membrane (prM) protein (~165 amino acids).
Genome encodes seven nonstructural proteins for replication, assembly, and host immune evasion.

Life Cycle

Three major states: immature (noninfectious), mature (infectious), and fusogenic (host membrane-binding).

Coronaviruses (CoVs) Overview

General Features

Belong to Coronaviridae subfamily.
Single-stranded RNA genome (30–32 kb).
Four genera: alpha, beta, gamma, delta.
Seven coronaviruses known to infect humans.
Notable human pathogens: SARS-CoV (2003), MERS-CoV (2012), SARS-CoV-2 (2019) – all betacoronaviruses.

SARS-CoV-2 Outbreak and Current Situation

COVID-19 pandemic began in Wuhan, China, December 2019.
Rapid global spread, millions of cases and deaths worldwide.

Structural Proteins

Matrix (M) protein: RNA packaging, virion shape.
Envelope (E) protein: Assembly and release.
Nucleocapsid (N) protein: Binds viral RNA, involved in replication and host response.
Spike (S) protein: Mediates entry into host cells via ACE2 receptor; trimeric, 1273 amino acids, two subunits (S1, S2).

Spike Glycoprotein Structure

Trimeric transmembrane protein (~150 kDa).
Responsible for receptor recognition, cell attachment, and fusion.
Recognizes human ACE2 receptor; S1 contains receptor-binding domain (RBD), S2 mediates fusion.

Detection and Diagnosis

ELONA (Enzyme-linked oligonucleotide assay): Detects viral proteins using aptamers or antibodies.
Steps: coating, blocking, immobilization, detection, absorbance measurement.
Other methods: qRT-PCR (gold standard), immunoassays, imaging, point-of-care tests.

Diagnostic Method	Principle
qRT-PCR	Detects viral RNA
Immunoassays	Detects antibodies
ELONA	Detects viral proteins

Viral Genomes and Evolution

Size and Structure of Viral Genomes

Genome sizes vary ~1000-fold from smallest to largest.
Smallest: Circovirus (1.75 kb, ssDNA, non-enveloped, icosahedral/round).
Largest: Pandoravirus (2.5 Mb, dsDNA, infects marine amoebae, larger than some bacteria).
RNA genomes are typically smaller than DNA viruses (e.g., poliovirus, influenza, coronavirus).

Baltimore Classification and Hosts

Class I (dsDNA): primary prokaryotic viruses.
Class IV (ss(+)RNA): primary eukaryotic viruses.
Fungi: infected by classes II and IV.
Class VI (Retroviruses): infect only animals.
Class VII: more common in plants than animals.

Baltimore Class	Genome Type	Primary Host
I	dsDNA	Prokaryotes
IV	ss(+)RNA	Eukaryotes
VI	ss(+)RNA-RT	Animals
VII	dsDNA-RT	Plants

Viral Protein Synthesis

Early proteins: synthesized soon after infection, usually enzymes, made in small amounts (e.g., nucleic acid polymerases).
Late proteins: synthesized later, structural and assembly proteins, made in large amounts.
Virion assembly and exit by lysis or budding.

Viral Evolution

Viruses may have arisen after cells, as remnants or as part of the "RNA world" (role in RNA to DNA transition).
May have been first forms of life (precellular).
Mechanism for rapid gene movement.
Proteomics suggests ancient origin from segmented RNA genomes before LUCA.
RNA viruses are older than DNA viruses; dsRNA is the oldest.

RNA to DNA Transition

DNA viruses may have arisen for protection from ribonucleases.
Reverse transcriptase was key in transition.
DNA is more stable than RNA.

Viral Phylogeny

Universal phylogenetic tree constructed from protein sequences and structural features.
RNA viruses precede DNA viruses, leading to three domains of cellular life.
Some viral groups (e.g., NCLDV: Mimivirus and relatives) have trees based on shared genes/proteins.
Most viral genes are novel, with no existing homologs.

DNA Viruses

Single-Stranded DNA Bacteriophages: φX174 and M13

Infect a wide variety of organisms, mostly prokaryotes.
φX174: circular ssDNA genome, icosahedral virion, infects Escherichia coli.
First DNA-based genome sequenced (Fred Sanger, 1977).
Very small genome with overlapping genes (different reading frames).
A* protein shuts down host DNA synthesis.
Replication via rolling circle mechanism.
Lysis by inhibition of peptidoglycan synthesis.

Bacteriophage M13

Model filamentous bacteriophage.
Attaches to host pilus, released without lysis.
Coat proteins cover DNA as it exits cell envelope.
Causes chronic infection, no intracellular accumulation.
Used as cloning and DNA-sequencing vector in genetic engineering.

Phage	Genome Type	Replication	Release
φX174	ssDNA, circular	Rolling circle	Lysis
M13	ssDNA, filamentous	Rolling circle	Non-lytic

Additional info: These notes expand on the original slides by providing definitions, context, and comparative tables for viral classification and diagnostic methods, ensuring a comprehensive and self-contained study guide for exam preparation.