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
Videos: Giant Viruses. (include ribosomes for translating RNA)
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. DNA viruses can have single-stranded (ss) or double-stranded (ds) DNA; the dsDNA can be arranged linearly or in ds circels. RNA viruses can be double-stranded but are more often single-stranded. RNA genomes may also be segmented, meaning that hte individual genes exist on separate pieces of RNA.
The polarity of genome in that the RNA can be sense (+) stranded or antisense (-) stranded. Single-stranded RNA genomes that are ready for immediate tranxlation into proteins are called positive sense RNA (e.g., SARS-CoV-2). Other viral RNA genomes have to be converted into the proper from to be translated into proteins and these are called negative-sense RNA.
Viruses are composed of a genetic material core, either single- (ss) or double-stranded (ds) DNA or RNA, and an outer shell. The genome of ssRNA viruses may be either positive-sense, the (+) strand, or negative-sense, the (-) strand. Upon infection, the genome of positive-strand RNA viruses, for example hepatitis C virus (HCV), SARS virus, and an alphavirus-like superfamily of viruses, is immediately ready to be translated into viral proteins. On the other hand, negative-strand RNA viruses, for example influenza or Ebola viruses, and dsRNA viruses, for example reoviruses, genomes are unreadable by ribosomes; thus requiring transcription by viral RNA (vRNA)-dependent RNA polymerase (RdRp) into positive-sense RNA strands prior to initiating viral gene expression
In addition to the protein capsid, the protein an lipid envelopes, and the nucleic acid core, viruses can contain enzymes such as polymerases that synthesize DNA and RNA and replicases that copy RNA, for specific operations within their host cell. HIV comes prepared with its essential machinery, including Reverse Transcriptase, already packaged within the viral particle. It doesn’t need to be translated after the virus enters the cell to begin the process of converting its RNA to DNA. However, viral particles (virions) are not cells because they generally lack metabolic activity, do not have cytoplasm, and cannot replicate outside of a host organism.
Viruses with an RNA genome utilize an enzyme called RNA-dependent RNA polymerase (RdRp), also known as RNA replicase, to copy their RNA. This enzyme synthesizes new RNA strands using an existing RNA molecule as a template.
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 causes rabies, infects and replicates only within neurons.
Viruses have to take over the host cell’s machinery to replicate their 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.
Capsid: All viruses have a protein capside, or shell, that surrounds the nucleic acdi in the central core. Together the capsid and nucleic acid are referred to as the nucleocapsid. Virues that consist of only a nucelocapsid are considered naked viruses.
Envelope: Many animals virues also possess and additional coveirng on the outside of the capsid called an envelope, which is usually a modifed piece of the host’s cell mbrane. Most viruses that infect humans have envelopes.
When enveloped viruses are released form the host cell, they take with them a bit of the cell’s membrane.
Spikes: both naked and enveloped viruses display proteins on their outer surfaces that project from either the nucleocapside or the envelope hwich allow viruses to dock with their host cells and are called spikes.
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.