(U) Genome sequencing: The process of determining the DNA or RNA sequence of an organism’s genome, or its “genetic code.” An organism’s genetic code is the order in which the four nucleotide bases—adenine, cytosine, guanine, and thymine—are arranged to direct the sequence of the 20 different amino acids in the proteins that determine inherited traits.
(U) Intermediate species/host: An organism that can be infected with a pathogen from a reservoir species and passes the pathogen to another host species; infection is not sustained in this population.
(U) Laboratory-adapted viruses have undergone natural, random mutations through human-enabled processes in a laboratory—such as repeated passage through animals or cells—that put pressure on the virus to more rapidly evolve. Specific changes to the viral genome are not necessarily anticipated in these processes, though the virus can be expected to gain certain characteristics, such as the ability to infect a new species. This is a common technique used in public health research of viruses. We consider directed evolution to be under laboratory adaptation.
(U) Laboratory-associated incidents include incidents that happen in biological research facilities or during research-related sampling activities.
(U) Naturally occurring viruses have not been altered in a laboratory. Viruses commonly undergo random mutations as part of the evolutionary process and can continue to change over time; mutations may enable a virus to adapt to its environment, such as evading host immune responses and promoting viral replication.
(U) Outbreak: A sudden increase in occurrences of a disease in a particular time and place. Outbreaks include epidemics, which is a term that is reserved for infectious diseases that occur in a confined geographical area. Pandemics are near-global disease outbreaks.
(U) Pangolin: An African and Asian mammal that has a body covered in overlapping scales. Pangolins are a natural reservoir of coronaviruses and researchers are investigating their potential role as an intermediate host for the COVID-19 virus.
(U) Pathogen: A bacterium, virus, or other microorganism that can cause disease.
(U) Progenitor Virus: A virus that is closely related enough—more than 99 percent—to SARS-CoV-2 to have been its direct ancestor or plausible immediate origin of the outbreak. The closest known relative to SARS-CoV-2 is only about 96 percent similar; to put this into context, humans and chimps are about 99 percent similar, demonstrating the significant differences even at this similarity.
(U) Reverse genetics: A process for determining the natural function of genes by introducing mutations and studying the effect of those mutations.
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