COVID-19 Resource Centre

COVID-19 Resource Centre

• Elsevier created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19, hosted on Elsevier Connect.
• The centre grants permission for immediate availability of COVID-19-related research in PubMed Central and other publicly funded repositories, with rights for unrestricted research re-use and analyses.

Viruses Characteristics

• Viruses are small, have DNA or RNA genomes, and are obligate intracellular parasites.
• The virus capsid protects the nucleic acid from the environment, and some viruses surround their capsid with a membrane envelope.
• Most viruses have icosahedral or helical capsid structure, although a few have complex virion architecture.

Classification of Viruses

• The International Committee on Taxonomy of Viruses classifies viruses into order, family, genus, and species taxa.
• There are currently seven orders of viruses.

Genome Size

• The genome size of a virus can vary greatly, typically ranging from 7000–20,000 base pairs (bp) or 7–20 kilobase pairs (kb).
• Smaller virions hold less nucleic acid than larger virions, but large viruses do not necessarily have large genomes.
• Some dsDNA viruses have very large genomes, such as herpesviruses (120–200 kb) and pandoraviruses (up to 2.5 million bases).

Comparison to Eukaryotic Cells

• Eukaryotic cells have much larger genomes, such as the red alga (8 million base pairs), human cells (over 3 billion nucleotides), and the loblolly pine tree (over 22 billion base pairs).

Viral Replication

• Viruses make contact with and bind the surface of a cell to gain entry into the cell.
• The virus disassembles and its genetic material encodes the instructions for proteins that spontaneously assemble into new virions.
• Viruses use the cell’s energy and machinery to create and assemble new virions piece by piece, completely from scratch.

Size Variation

• Viruses can vary significantly in size, with some viruses larger than 100 nm, such as poxviruses (up to 400 nm) and filoviruses (up to 80 nm in diameter, but extending into long threads).

PFGE Limitations and Applications

• PFGE is most informative when there is epidemiologic linkage, such as in an outbreak situation or when comparing isolates from a single individual over time.
• PFGE supports or refutes the epidemiologic evidence in these cases.

Resequencing Microarrays

• Resequencing refers to sequencing a genetic region where a reference genome is available to determine genetic variation.
• Microarrays consist of probes that enable pathogen detection and strain variation.
• Sample DNA is hybridized against the probes on the microarray, and the detected pattern determines the pathogen and variant.
• Microarrays can detect bacteria and viruses using a single array, whereas other techniques like PCR require separate tests for each suspected pathogen.
• The microarray format promises to be a useful screening tool for detecting both known and unknown pathogens.

Microarray Advantages

• Microarrays can detect a class of pathogens, allowing for the development of more specific tests.
• The costs of microarrays are falling, and their validity and reliability are improving.

Transcriptomics

• The transcriptome measures messenger RNA (mRNA), which is the message translated into protein.
• The transcriptome tells what genes are currently being transcribed and translated into proteins, unlike the genome which shows what genes are present.
• There is no exact correlation between mRNA levels and protein production, and high levels of mRNA do not necessarily translate into high levels of protein production.
• Studying the transcriptome is technically less challenging than studying the proteome for many applications.

Applications of Transcriptomics

• Transcriptomics enables the measurement of host gene response to infection and identification of host genes or proteins essential for pathogen invasion, growth, or survival.
• Studying the transcriptome of the microorganism enables identification of genes associated with transmission, pathogenesis, and survival in different environments.