As we continue to follow the SARS-CoV-2 developments in our world, it has become abundantly clear how crucial it is to monitor the emergence and spread of various viral variants.
The SARS-CoV-2 virus, which causes COVID-19, stayed relatively stable through last fall. Now all of a sudden, many variants are being identified that appear to change how the virus behaves. How does a virus change, and why are these variants emerging so quickly now?
To put it simply, viruses are designed to reproduce quickly, but not with 100% accuracy all the time. The SARS-CoV-2 virus has an RNA genome that is about 30,000 nucleotides long and encodes eleven genes Viruses that have RNA genomes, including coronaviruses, usually mutate at a particularly high rate, because the proteins that copy RNA are error prone. Indeed, it was a mutation (or mutations) in the “spike” protein of SARS-CoV-2, likely in late 2019, that allowed it to emerge from its animal host(s) and efficiently infect humans. SARS-CoV-2 doesn’t mutate as fast as many other coronaviruses, however, because of its “spell-check” mechanism, an additional protein that corrects major copying mistakes. So during the first wave of infections last spring, many minor variants were tracked but nothing of particular concern emerge.
The JAX COVID-19 Whole Genome Sequencing (WGS) Assay test system is an amplicon-based NGS assay, with 98 amplicons designed to amplify SARS-CoV-2 -virus-specific amplicons utilizing the Illumina COVIDSeq next generation sequencing (NGS) assay.
The intended purpose of theJAX COVID-19 Whole Genome Sequencing (WGS) test system is to provide clinicians and epidemiologists with classification of SARS-CoV-2 lineages from upper respiratory samples identified as Positive SARS-CoV-2 by Real Time Polymerase Chain Reaction (RT-PCR). The assay is not intended to determine patient infection status. Positive results are indicative of the presence of a SARS-CoV-2 RNA; clinical correlation with patient history and other diagnostic information is necessary to determine patient infection status. If there are any specific questions on performance characteristics of this test, please reach out to CGL_COVID_CS@jax.org. For more details about JAX Whole Genome Sequencing, please refer to our Whole Genome Sequencing flyer.
Various sample types are acceptable for SARS-CoV-2 processing. The sample is first processed for the detection of SARS-CoV-2. Sensitivity of the JAX COVID-19 RT-PCR test is 10 GCE/reaction or 250 viral RNA copies/mL of specimen. A sample is entered into the JAX COVID-19 Whole Genome Sequencing (WGS) workflow once it has been confirmed as Positive for SARS-CoV-2 at JAX, and the N gene CT value is ≤ 30. WGS Library prep and sequencing follow this step, leading to lineage/cade analysis before reports are generated and delivered.