The COVID Archipelago: Volcanoes and variants

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By Daniel R. Lucey MD, MPH, FIDSA

An 1888 lithograph of the 1883 eruption of Krakatoa

Most archipelagos are created by volcanoes erupting from the ocean floor. Imagining such volcanoes as hotspots of SARS-CoV-2/COVID infections, the virus variants can be imagined as an archipelago of islands above the surface. Each new island has the potential to become its own volcano and spread new variant viruses globally like a COVID Krakatoa.

To see all such islands, both variants of interest and variants of concern, requires the vision provided by surveillance tools: (1) genetic sequencing linked with (2) genomic epidemiology and (3) bioinformatics.

On Friday, the White House announced $1.7 billion “to fight COVID-19 variants.”

Of this $1.7 billion, $1 billion will go to increasing genomic sequencing to 29,000 samples per week from the current 8,000 per week. Importantly, at the White House briefing this morning it was stated that this sequencing capability will be used for future viruses in addition to SARS-CoV-2.

Six “Centers of Excellence in Genomic Epidemiology” will be created with $400 million. The final $300 million will create a “National Bioinformatics Infrastructure” to integrate the sequencing and epidemiologic data “to connect the dots between how pathogens spread and mutate to help solve outbreaks”.

This U.S. initiative “to fight COVID-19 variants” could not have come too soon. While viruses never sleep, humans always do. SARS-CoV-2 has been mutating since late 2019. Variants of interest, and Variants of concern have been identified in the United States and worldwide.

More variants of concern, e.g., those capable of increased transmission and/or virulence and/or immune evasion exist today than have been recognized due to far too little capability in most nations of the world for the required genetic sequencing,  genomic epidemiology, and bioinformatics.

Dr. Daniel Lucey

Daniel Lucey, M.D. MPH, FIDSA, FACP, is a Clinical Professor of Medicine at Dartmouth Geisel School of Medicine, Infectious Disease adjunct Professor at Georgetown Medical Center, senior scholar at Georgetown Law, Anthropology Research Associate at the Smithsonian Museum of Natural History and a member of the Infectious Diseases Society of America Global Health Committee. He served as a volunteer to outbreaks overseas including hands-on Ebola patient care in Sierra Leone and Liberia (Doctors without Borders) 2014, MERS 2013, SARS 2003, as well as HIV, H5N1, Zika, yellow Fever, and pneumonic plague 2017 (with WHO/USAID/CDC).  Since Jan. 6, 2020 he has contributed over 75 posts to Science Speaks on COVID-19 and traveled to China in February 2020. He initially proposed, then fundraised and helped design the content for 2018-2022 Smithsonian Exhibition on Epidemics due to zoonotic viruses. From 1982-1988 he trained at University of California San Francisco and Harvard and was an attending physician at the NIH (NIAID) in the 1990s while in the US Public Health Service.

 

2 thoughts on “The COVID Archipelago: Volcanoes and variants

  1. John Bruch

    What is the connection between the ability to rapidly identify a virus’ genome and the ability to prevent or curtail outbreaks?

    Let’s imagine that we could, at the point of testing, immediately identify the genome of a virus and share that information. How would this help, as compared to the current situation?

    We’ve known about the variants for quite some time. That has not prevented them becoming a problem, even in places where they’ve been rapidly identified. The lead time between identification and vaccine modification is where the time is spent, no? And it takes time to determine the effect of any change in the genome, right? Will speeding-up genome identification really help much?

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  2. Rae Trinity

    According to Dr. Michael Yeadon, former Pfizer Chief Science Office and VP, among the approximately 4,000 viruses in our domain, no variant deviates more than .3% from the original virus. In other words, he said variants are 99.7% the same as the original virus and immunity, whether naturally derived or from a vaccine, will handle “ALL variants.” He said viruses mutate and may become more infectious, but less virulent because they do not want to kill the host. He is against mass vaccination with the new mRNA gene therapy ‘vaccines’ because in his co-petition to the European Medicines Agency with Dr. Wolfgang Wodarg, he cited risks, including blood clot risks from all Covid19 vaccines and female infertility. He warned any mention about “dangerous variants” is a strategy to push boosters and because the health safety agencies have stepped aside during this process, the boosters will not be tested for safety. In the U.S., any booster shots will fall under the Emergency Use Authorization and not be subject to further safety tests.

    Reply

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