January 20, 2021
Yesterday’s variant L425R has a new name. It’s now referred to as CAL.20C. The term L425R designates one of five mutations that comprise the CAL.20C strain that is rapidly increasing in California. Genomic researchers at Cedars Sinai in Los Angeles reports that the California variant which they only saw once in October now constitutes over a third of the infections in Los Angeles. This is the same strain which Dr. Charles Chiu’s lab at University of California, San Francisco, sequenced and found in many counties across the state. By searching publicly shared databases the researchers could see that it has been found in a few other states as well.
Which leads to the question: How is all this genomic sequencing information tied together? How do researchers know they have found a new variant or one from South Africa or Brazil? How do they know that particular cases of COVID-19 originated at a certain event, for that matter? It all starts with a laboratory identifying the amino acids on the genome of each viral sample and comparing them to each other with specialized software. The labs at Cedars Sinai and UCSF found the variant with the L425R strain and reported it to the California Department of Public Health which partners with labs throughout the state in a network called COVIDNet. Together the laboratories reporting within this network have sequenced several thousand specimens in the state of California.
A similar exchange of information is now accelerating nationwide and throughout the world, which is how, for example, the CDC can report that the B.1.1.7 or UK coronavirus variant has been found in over 50 countries and in 122 cases in 20 states. (1). At the CDC, tracking and coordinating the genomic sequencing of pathogens comes under the Office of Advanced Molecular Detection (AMD) which has been integrating and developing laboratory, bioinformatics and epidemiology technologies since 2014. (2) Genomic sequencing serves to identify and track new and existing strains of the virus as well as to characterize it. For example, it helps us to determine quickly whether a strain spreads faster, is more lethal, infects a different age group, or is resistant to antibodies or vaccines.
The AMD has been building technological infrastructure for tracking COVID variants in the United States through two new initiatives: SPHERES and NS3.
- SPHERES was initiated in May, 2020, to coordinate COVID virus sequencing throughout the United States. The full name of this genomics consortium is the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES). The purpose is to collect information produced by genomic sequencing from laboratories throughout the country so that public health as a whole can benefit from shared, coordinated, and consistent data. (3)
- Input: The sequenced genomic data originates with laboratories managed by public health departments, academic institutions, non-profit public health and research labs, federal agencies and labs, and international collaboration with Genome Canada and COG-UK. In California, for example, Dr. Chiu’s lab at UCSF and the lab at Cedars Sinai in Los Angeles and the California Department of Public Health are part of this information pipeline, along with other institutions in the state.
- Output: Data is shared with the National Center for Biotechnology Information (NCBI) and the Global Initiative on Sharing All Influenza Data (GSAID). (4)
- The National SARS Strain Surveillance (NS3) Program was initiated in November, 2020. to increase tracking the virus throughout the country. Not every state has as many genomic sequencing institutions as California does. While SPHERES brings information from around the country under the CDC umbrella, the NS3 program will bring in at least 10 samples biweekly from every state directly to the CDC for sequencing and characterization. This program will enable detection of new strains in the United States and show how strains spread nationwide.
It’s interesting to note that GSAID was founded in 2008 and the AMD in 2014, both before COVID-19 was on anybody’s radar. As its name indicates, GSAID (Global Initiative on Sharing All Influenza Data) was founded to share influenza data at the time of the very deadly H5N1 bird flu. In spite of the two international coronavirus outbreaks SARS (2003) and MERS (2012), a worldwide flu pandemic appeared more likely. And the next time it might be the flu. But having a structure for international sharing of genomic sequencing in place has been invaluable in tracking the course of the novel coronavirus now and will serve us in the future. As David Quammen says on page 503 of his book Spillover (2012), “The Next Big One could very well be flu.” Both coronavirus and influenza virus can spread to humans from animals and both can be contagious and deadly.
Our own CAL.20C variant made headlines yesterday in a CNN article entitled: “These coronavirus variants are keeping scientists awake at night.” The four variants singled out for this honor are from the UK, South Africa, Brazil, and California. The B.1.1.7 or UK variant is believed to spread faster and has been reported in 20 states. According to the CDC it may become the dominant strain in the U.S. by March. The South Africa and Brazil variants haven’t been reported in the U.S. as yet, and of course the new L425R variant, now called CAL.20C, is right here in California. Not only here, however. A search of publicly shared databases shows that it has been found in a few other states as well.
Flu or coronavirus, we are developing powerful tools.
Today’s Notable Headlines
“New California Variant May Be Driving Virus Surge There, Study Suggests,” New York Times, Jan. 19, 2021. https://www.nytimes.com/2021/01/19/health/coronavirus-variant-california.html
“Local COVID-19 Strain Found in Over One-Third of Los Angeles Patients,” Cedars Sinai, Jan. 18, 2021. https://www.cedars-sinai.org/newsroom/local-covid-19-strain-found-in-over-one-third-of-los-angeles-patients/
“New California Coronavirus Joins Worrisome Strains from UK, South Africa, Brazil,” VOA, Jan. 20, 2021. https://www.voanews.com/covid-19-pandemic/new-california-coronavirus-joins-worrisome-strains-uk-south-africa-brazil
“These coronavirus variants are keeping scientists awake at night,” CNN, Jan. 19, 2021. https://www.cnn.com/2021/01/19/health/coronavirus-variants-what-we-know/index.html
(1) “Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021,” CDC MMWR, Jan. 15, 2021. Updated. https://www.cdc.gov/mmwr/volumes/70/wr/mm7003e2.htm?s_cid=mm7003e2_w
(2) Advanced Molecular Detection (AMD), CDC Advanced Molecular Detection (AMD) and Response to Infectious Disease Outbreaks (cdc.gov)
(3) “SPHERES: A National Open Genomics Consortium for the COVID-19 Response,” CDC, Updated July 27, 2020. SPHERES | CDC .
(4) GSAID: https://www.gisaid.org/
Why am I doing this?
The coronavirus pandemic will be indelibly written on our memories just as the Great Depression or the Battle of Britain left their mark on past generations. I intend to journal the pandemic experience from three perspectives: as a retired medical technologist, as a historian (Ph.D., 2014), and an ordinary person living through an estraordinary world crisis.
You are on History’s Edge.