Step 1 · Microbiology

Viral Replication, Genetics & Laboratory Diagnosis

Name: Viral Replication, Genetics & Laboratory Diagnosis
Creator: Veli Bakalov, MD

The rules every virus follows, from receptor to lab test

Microbiology·Virology·5 min read·9 high-yield points·Reviewed by Veli Bakalov, MD @HemeOncBuddy

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Receptors set tropism: HIV gp120–CD4 plus CCR5/CXCR4, EBV gp350–CD21, parvovirus B19–P antigen, influenza hemagglutinin–sialic acid, rabies–nicotinic AChR, rhinovirus–ICAM-1.
DNA viruses replicate in the nucleus except poxviruses (cytoplasm, own DNA-dependent RNA polymerase); RNA viruses replicate in the cytoplasm except influenza and retroviruses.
Positive-sense ssRNA acts as mRNA, so purified genome is infectious; negative-sense virions must package RNA-dependent RNA polymerase.
Retroviruses and HBV both use reverse transcriptase (HBV via a pregenomic RNA intermediate); parvovirus is the only ssDNA virus and reoviruses the dsRNA exception.
Enveloped viruses bud (herpesviruses from the nuclear membrane) and are fragile; naked viruses exit by lysis, survive acid and alcohol, and spread fecal-orally.
Reassortment of segmented genomes (influenza, rotavirus) produces antigenic shift and pandemics; phenotypic mixing changes only the coat, so progeny revert to the genome's own coat.
Latency: HSV/VZV in sensory ganglia, EBV in B cells, CMV in monocytes; HPV E6 degrades p53, E7 inactivates Rb, HTLV-1 Tax transactivates growth genes.
IgM means current or recent infection, IgG alone means past infection or immunity, and a fourfold titer rise between paired sera confirms recent infection.
Type I interferons induce RNase L (via 2′,5′-oligoadenylate synthetase) and protein kinase R (phosphorylates eIF2α) to create an antiviral state in neighboring cells.

Attachment, entry, and uncoating

Tropism. A virus can infect only cells that display the receptor its attachment protein recognizes, so receptor distribution explains much of a virus's disease pattern.

Classic virus–receptor pairs

Virus	Attachment protein	Receptor	Cells targeted
HIV	gp120	CD4 + CCR5 or CXCR4	Helper T cells, macrophages
EBV	gp350	CD21 (CR2)	B cells
Parvovirus B19	Capsid	P antigen (globoside)	Erythroid precursors
Influenza	Hemagglutinin	Sialic acid	Respiratory epithelium
Rabies	Glycoprotein	Nicotinic AChR	Neuromuscular junction, then neurons
Rhinovirus	Capsid	ICAM-1	Nasal epithelium

People homozygous for the CCR5 Δ32 deletion resist CCR5-tropic HIV.

Entry. Enveloped viruses fuse their envelope with the plasma membrane (HIV gp41) or are endocytosed and fuse once the endosome acidifies (influenza hemagglutinin). Naked viruses enter by receptor-mediated endocytosis.

Uncoating and eclipse. Removing the capsid frees the genome for gene expression, genome replication, and assembly. From uncoating until new virions assemble, no infectious virus can be recovered from the cell — the eclipse period.

Genome logic

Site of replication. DNA viruses replicate in the nucleus, where host polymerases live, except poxviruses, which carry their own DNA-dependent RNA polymerase and replicate in cytoplasmic factories (Guarnieri bodies). RNA viruses replicate in the cytoplasm, except influenza (nuclear; snatches 5′ caps from host mRNA) and retroviruses (integrated DNA copy).

Sense of the genome. Positive-sense ssRNA is itself mRNA: ribosomes translate it into a polyprotein, so purified genome alone is infectious and no polymerase needs packaging. Negative-sense RNA must first be transcribed, so its virions carry RNA-dependent RNA polymerase (RdRp) and purified RNA is not infectious. Purified DNA of most dsDNA viruses is also infectious; poxviruses and HBV are the classic exceptions.

Reverse transcription. Retroviruses package reverse transcriptase to copy their ssRNA into dsDNA, which integrase inserts into host DNA. HBV has a partially double-stranded circular DNA genome yet replicates through a pregenomic RNA intermediate using its own reverse transcriptase, which is why lamivudine and tenofovir act on both HIV and HBV.

What the genome predicts

Genome	Where it replicates	Enzyme packaged in virion	Purified genome infectious?
dsDNA (most)	Nucleus	None required	Yes
Poxvirus DNA	Cytoplasm	DNA-dependent RNA polymerase	No
Positive-sense ssRNA	Cytoplasm	None	Yes
Negative-sense ssRNA	Cytoplasm (influenza: nucleus)	RdRp	No
Retrovirus RNA	Nucleus (integrated provirus)	Reverse transcriptase, integrase	No

Strandedness exceptions: parvovirus is the only ssDNA virus; reoviruses such as rotavirus are the dsRNA exception.

Assembly, release, and envelopes

Release. Naked viruses usually leave by lysing the cell. Enveloped viruses bud, wrapping themselves in host membrane studded with viral glycoproteins: the plasma membrane for most, the nuclear membrane for herpesviruses, and the ER/Golgi for flaviviruses and coronaviruses.

Stability predicts transmission. A lipid envelope is destroyed by detergents, drying, acid, and bile, so enveloped viruses need close contact: respiratory droplets, sex, blood, or transplanted tissue. Naked capsids survive stomach acid, bile, drying, and alcohol, so they spread fecal-orally and persist on surfaces.

Alcohol hand rub is weak against naked norovirus; during outbreaks, wash hands with soap and water.

Viral genetics and outcomes

Recombination — genes are exchanged between two related genomes by crossing over at regions of sequence homology.
Reassortment — only in segmented genomes (influenza, rotavirus). When two strains infect one cell, progeny package whole segments from each parent. In influenza A (8 segments) a new hemagglutinin/neuraminidase combination (antigenic shift) can cause a pandemic; point-mutation drift causes seasonal epidemics.
Complementation — one virus in a coinfected cell supplies a functional protein that its mutant partner cannot make, so both replicate; the mutant's progeny still carry the mutation.
Phenotypic mixing — the genome of virus A is packaged in the coat of virus B. The hybrid infects cells as B would, but its progeny wear A's coat because no genes were exchanged.

Outcomes of infection. Lytic infection kills the cell (poliovirus). Persistent infection releases virus for long periods without killing the cell (chronic HBV). Latent infection keeps a silent genome that can reactivate: HSV and VZV in sensory ganglia, EBV in B cells, CMV in monocytes. Transforming infection drives cancer: HPV E6 degrades p53 and E7 inactivates Rb; HTLV-1 Tax transactivates host growth genes (adult T-cell leukemia/lymphoma); EBV (Burkitt and Hodgkin lymphoma, nasopharyngeal carcinoma), HBV (hepatocellular carcinoma), and HHV-8 (Kaposi sarcoma) complete the list.

Laboratory diagnosis and interferons

Nucleic acid and antigen tests. PCR (RT-PCR for RNA viruses) detects viral genomes with high sensitivity; quantitative PCR measures viral load to guide therapy for HIV, HBV, HCV, and CMV. Antigen tests detect viral proteins directly, such as HBsAg, HIV p24, and rapid influenza antigen.

Serology. IgM signals current or recent infection; IgG alone signals past infection, vaccination, or immunity. A ≥4-fold rise in titer between acute and convalescent sera drawn 2–4 weeks apart confirms recent infection.

Culture. Virus grown in cell culture shows cytopathic effect: rounding and lysis; multinucleated syncytia (RSV, measles, HSV/VZV, HIV); inclusion bodies (intranuclear Cowdry A in HSV/VZV, owl's-eye in CMV, cytoplasmic Negri bodies in rabies); or hemadsorption (influenza, parainfluenza). Culture is slow and largely replaced by PCR.

Interferon antiviral state. Infected cells sense viral dsRNA and secrete type I interferons (IFN-α/β). These do not act on the virus itself; they signal neighboring cells to make 2′,5′-oligoadenylate synthetase, which activates RNase L to degrade viral and host mRNA, and protein kinase R, which phosphorylates eIF2α to halt translation. Type I interferons also raise MHC I expression and NK-cell killing.