Open letter: Urgent need for expanded surveillance and forecasting of novel SAR-CoV-2 variants

Much like the start of 2020, when we were unaware of the extent of the spread of SARS-CoV-2 due to inadequate diagnostic testing, we are beginning 2021 almost totally in the dark about the newly identified SARS-CoV-2 mutations that have come to light. Many countries are in the dark about the extent of spread of the novel SARS-CoV-2 variants — some of which are likely significantly more transmissible and others of which may evade vaccine-induced immune responses. We are urging for a massive increase in genomic surveillance and increased forecasting of these variants. We encourage you to read our open letter to policy makers and public health officials on this subject, and if you agree with our recommendations, please sign it and share it widely. The full letter is below.

Open letter: Urgent need for expanded surveillance and forecasting of novel SAR-CoV-2 variants

Friday, 8 January 2021

To all who care about saving lives and livelihoods during the COVID-19 pandemic:

As of the time of writing, there have been over 88 million confirmed cases of SARS-CoV-2 and more than 1.9 million confirmed COVID-19 deaths. Many more millions of cases and deaths have gone unrecorded. Millions more are out of work and have had their lives upended. But an end is in sight — multiple vaccine candidates have demonstrated astoundingly impressive safety and efficacy results and thus it is only a matter of time before we can bring an end to the pandemic.

However, new developments regarding novel SAR-CoV-2 variants have threatened to prolong the destruction wrought by this pandemic. SARS-CoV-2 lineage B.1.1.7, otherwise known as Variant of Concern 202012/01 (VOC), is a novel strain that is almost certainly significantly more transmissible than preexisting variants. A recent study estimates B.1.1.7 to be 56% more transmissible (95% Crl: 50%-74%) compared to preexisting variants, and a second study finds that the new variant has “an additive increase in R that ranged between 0.4 and 0.7, and alternatively as a multiplicative increase in R that ranged between 50% and 75%." There is also concern that a new variant detected in South Africa, the 501.V2 variant, may be similarly more transmissible. According to the consensus of Metaculus forecasters, there is a 90% chance that one of these new variants has an increased transmissibility of over 30%, and a 74% chance of a greater than 50% increase in transmissibility. Moreover, the 501.V2 variant appears to have a mutation that raises concern about immune escape — a relevant Metaculus question currently finds a 66% chance that production will have to start on an updated vaccine before 2022. Taken together, these developments are nothing short of catastrophic for efforts to use nonpharmaceutical interventions and widespread vaccine administration to blunt the spread of SARS-CoV-2.

Efforts are already being made to characterize and understand the infectivity properties and immunological consequences of these new variants. However, as was the case at the start of the pandemic, most countries remain extraordinarily uncertain as to (1) the extent to which these novel variants are spreading and (2) the likelihood as to whether and when these new variants will become predominant. Unfortunately, these issues do not appear as if they will be extensively addressed in the immediate future. The U.S. CDC, for instance, is currently only planning on having each state send it "at least 10 samples” on a biweekly basis for sequencing and further characterization. This is woefully inadequate genomic surveillance — we are in the dark.

We are calling for a massive increase in genomic sequencing, monitoring, data sharing, and probabilistic forecasting so we can have a detailed understanding of where these new variants are circulating and how rapidly they are increasing as a proportion of all cases. More specifically, we are calling on policy makers, public health officials, and infectious disease scientists to support:

  • Increased genomic sequencing — specifically, the creation of random sequencing programs so as to avoid potential sampling and sequencing biases (for instance, to avoid the overrepresentation of S-gene-dropout sequences)
  • Timely and publicly accessible genomic sequence data sharing on open access platforms like GISAID and Nextstrain, so that public health officials and forecasters can provide up-to-date estimations of key metrics
  • Collaborative forecasting by subject matter experts and forecasters on relevant questions that are actionable and informative to public health experts and the general public, as well as interdisciplinary collaboration and input into new relevant and important questions
  • The use of up-to-date forecasts to inform policy decisions and public health measures so as to delay and eliminate the spread of these new variants

Together, we can slow the transmission of these new variants and improve decision-making so as to save most lives and livelihoods possible. Add your signature to the letter here.

Signed (last updated 01 February 3:30PM EST),

Juan Cambeiro, Metaculus

Tamay Besiroglu, Metaculus

Gaia Dempsey, Metaculus

Anthony Aguirre, Metaculus and Future of Life Institute

Christian Williams, Metaculus

Carroll Wainwright, Metaculus and Partnership on AI

Sylvain Chevalier, Metaculus

William Richardson, University of Nottingham

Kyle Greene, Lawyer

Doug Urbanus, Forecaster

Gabriel Recchia, Winton Centre for Risk and Evidence Communication at the University of Cambridge

Eliza Passell

Vinney Cavallo, exnilio

Robi Rahman, Harvard University

Mikk Wilson, Forecaster

Nathan Young, Newspeak House

Steven Schkolne, Metaculus

Gary Mindlin Miguel, Google

Alex Lawsen, KCL

Justin Otto, Forecaster

Shahar Avin, Centre for the Study of Existential Risk at the University of Cambridge

Galen Cuthbertson, Australian National University

Adrian Regenfuß, Forecaster

Josh Curtis

David Blank, Forecaster

Andrew Kirk, The University of Edinburgh

Michał Dubrawski, Forecaster

Thomas Balbach, KU Leuven

Alyssa Stevens, Metaculus

Pavel D Atanasov, Pytho LLC

Jenella Loye, Carroll-Loye Biological Research

Sean Kucer, University of California, Berkeley

Matej Vrzala, Metaculus

Thomas McAndrew, Lehigh University

Armando di Matteo, Istituto Nazionale di Fisica Nucleare, sezione di Torino

J J Flattery

Linchuan Zhang, Rethink Priorities

Peter Hurford, Rethink Priorities

Jared Leibowich

Janique Behman, Rethink Priorities

Siebe Rozendal, Effective Altruism Netherlands

Gregory Laughlin, Metaculus

Nuño Sempere, Forecaster

Institutions listed for identification purposes only; unless otherwise noted, individuals are signing in their personal capacity, and not on behalf of institutions.