NYC Public Health testing laboratory manual (good resource for types of viral and bacterial diseases and tests used to identify them)

Global Center for Health Security

Introduction; Definitions:

Viruses come in a variety of different sizes, morphologies and types of genomes. For example, viral genomes can be linear or circular, and single or double stranded. The polarity of genome in that the RNA can be sense (+) stranded or antisense (-) stranded. This will be important later in in respect to replication of the virus.

Viral particles (virions) are not cell because they generally lack metabolic activity, do not have cytoplasm, and cannot replicate outside of a host organism.

Particular kinda of viruses can infect only particular types of cells: either the virus can recognize only one kind of cell type or it cannot replicate efficiently inside a cell type. For example, Rhabdovirus, the virsu that casues rabies, infects and replicates only within neurons.

Viruses have to take over the host cell’s machinery to replicate theri geneomes, express their genes, and use the proteins produced to build new virions. Although viral geneomes include genes making capsid proteins, they often do not code for proteins involved in the expression and replication of their genomes, and never contain genes to make ribosomes.

Host range: the cell or organism types that a particular virus can infect.

–-Tissue Tropism: Within a multicellular host, many viruses also exhibit tissue tropism, targeting only a specific subset of cells. The tissue tropism will determine the nature of the infection and the disease symptoms caused by any particular virus.

Naked viruses: Viruses with no envelope.

Giant viruses: The largest known virus is Pithovirus, which was revived form 30sk year old Siberian ice in 2014. With virions 1.5 um long, it is larger than some bacteria, and even than some eukaryotic cells. Metagenomics, the study of genetic material isolated form the environment and not directly from organisms, has been used to dientify a new group of giant viruses, the Klosneuivirses. This group challenge assumptions about the size of viruses but in that the hypothetical genome contains genes for all 20 aminoacyl-tRNA synthetase enzymes. Evidence suggests that these giant viruses aquired translation related genes form hosts as once smaller viruses.

Proteins which Viruses Make

3 types of proteins are common to all retroviruses (like HIV): (1) GAG proteins for the capsid, (2) Env proteins for the envelope and (3) Pol proteins for reverse transcriptase and integrase.

Growth of virus under benign laboratory conditions lacks the selective pressures of the body and allows weaker strains to survive. This process is used to develop attenuated virus strains for use in vaccines.

Virus Identification and Detection:   

Some ways to identify and detect viruses include the following:

• PCR where nucleic acid is extracted from a specimen (if RNA virus, RNA is converted to cDNA by reverse transcriptase) viral DNA is amplified by virus-specific primer pairs and DNA fragment is analyzed by agarose gel electrophoresis.
• ELISA where viral antigen is bound to plastic surface and antibodies in the patient’s sera specifically bind the viral antigen. This antigen-antibody complex is then reacted with anti-human IgG conjugated with an enzyme (e.g., alkaline phosphatase). This complex is then visualized by adding chemical colorigenic substrates.
• Western Blot is a more confirmatory assay than ELISA for HIV. Viral proteins (e.g., gp120, gp41 and p24 in the case of HIV) are transfered to filter and filter is incubated with patient’s serum. Filter is then incubated with labeled anti-human Ig serum.