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The SARS-CoV-2 virus took us by surprise! We are under constant attack from the tiny, invisible predators in this world. We go about our day-to-day business unaware of the war within us. Microorganisms are attempting to invade our bodies every minute of the day. The sentinel elements of our immune system recognize substances by their genetic code.  If the code is deemed dangerous, these guardians “paint” the foreign bodies so the soldiers of our immune system can find and destroy them. The secret genetic codes of these enemies have been stolen by those they infected in the past. The guardian cells of these pathogenic attacks remember and pass on these genetic descriptions. Billions of our ancestors have sacrificed their lives to develop the powerful, complex immune system that now defends our bodies.  The collective memories of our species protect us. We are defenseless without them.  

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Most of humanity has never experienced anything like SARS-CoV-2. With no description of the new virus, our immune defenses were blind.  This virus laid in wait for us, not just unseen, it was camouflaged, like a leopard hidden in the grass. It was the first time the immune systems of the human race were exposed to this new virus. Our immune systems were oblivious to its existence.

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A virus survives by invading a cell and taking over the cell’s reproductive process. The invading virus then substitutes its genetic code for that of cell. The organelles of the “hijacked” cell then begin producing copies of the virus. This happens billions of times in an infected organism. The possibility of mistakes during the transfer of all that genetic information is extremely high. These changes in the construction of new viral particles either weaken or strengthen the new virus. An improvement might help the new virus disguise itself from the immune systems of potential hosts, or it might improve its ability to reproduce. Such a change would result in more of the improved versions of the virus. Eventually, the improved virus replaces the old version. This process results in new versions of the virus called variants.

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When new genetic variations begin showing up among infected persons, the changes are noted by data collection agencies and they are included in a database called NS3.  When a new variant begins to show progress, it is listed as a VOC (Variant of Concern). Once the variant attains a large enough proportion of infected individuals it is named and warnings are issued.

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The most recent variants have been assigned a genetic number and a name based on Greek letters. Arcturus XBB.1.16, Pi BA.6, Eris EB.5.1., and Pirola BA.3.86. All of these strain are being carefully monitored.

 

Several organizations monitor data from people infected with the virus. The genetic sequence data generated by CDC and state and local public health laboratories are submitted to publicly accessible databases maintained by the National Center for Biotechnology Information (NCBI) and the Global Initiative on Sharing Avian Influenza Data (GISAID). Integration of surveillance across the United States maximizes the sequencing capacity, expertise, and data that is available to inform public health decision making. NS3 Specimens Displayed as Phylogenic Trees

 

SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES)

A national genomics consortium to coordinate SARS-CoV-2 sequencing across the United States.

www.cdc.gov/coronavirus/2019-ncov/covid-data/spheres.html

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The SPHERES consortium is being led by CDC’s Advanced Molecular Detection (AMD) program, which over the past six years has invested in federal, state, and local public health laboratories to expand the use of pathogen genomics and other advanced laboratory technologies to strengthen infectious disease surveillance and outbreak response. SPHERES aims to

• Accelerate the use of real-time pathogen sequence data and molecular epidemiology for the COVID-19 pandemic response.

• Organize and manage public health sequencing and response efforts across the United States.

• Coordinate and support sequencing at state and local public health laboratories across the country.

• Better engage US clinical, academic, and commercial laboratories that are sequencing—or planning to sequence—SARS-CoV-2 data on any scale.

• Improve communication and knowledge-sharing between US laboratories.

• Develop consensus guidance on critical data and metadata standards.

• Reduce barriers to bioinformatic analysis and data sharing.

• Better align sequencing requirements and resource needs with different sources of funding, technology, expertise, and other means of support.