#COVID19 pandemic

Largely through partial immune escape, lineage BA.5 viruses resulted in sizable epidemics throughout much of the world. However, in most countries these epidemics are now beginning to wind down. What do we expect after BA.5? 1/10 pic.twitter.com/zze4p5ebEJ

— Trevor Bedford (@trvrb) August 16, 2022

Based on the experience in winter 2020/2021, seasonal influence on SARS-CoV-2 transmission is quite clear, but much of the Northern Hemisphere is currently experiencing large summer epidemics driven the spread of evolved BA.5 viruses. 1/11 pic.twitter.com/P6bQ6DZhcF

— Trevor Bedford (@trvrb) August 3, 2022

There seems to be a worry that telling people we've exited the "pandemic phase" will lead to further reduced precautions. As always however, I think it's best not to conduct messaging for intended behavioral effect and just try to make scientifically accurate statements. 1/5

— Trevor Bedford (@trvrb) July 20, 2022

The @US_FDA VRBPAC committee will be meeting tomorrow to discuss variant-specific COVID-19 vaccines (https://t.co/Dm62X28f2K). Based on present observations, I would argue that the most important metric to optimize are titers against BA.4/BA.5 viruses. 1/10

— Trevor Bedford (@trvrb) June 27, 2022

Global monkeypox confirmed and suspected cases compiled by @globaldothealth show initial rapid increase as case-based surveillance comes online, followed by slower continued growth. 1/10 pic.twitter.com/I4sGz66jMj

— Trevor Bedford (@trvrb) June 3, 2022

We now have enough co-circulation of Omicron sub-lineages BA.4, BA.5 and BA.2.12.1 in the US to make an assessment of relative fitness between these viruses. 1/12

— Trevor Bedford (@trvrb) May 28, 2022

Non-travel related monkeypox cases were announced by @UKHSA just 10 days ago on May 14 and first viral genome shared by @irj_pt 5 days later on May 19. It's remarkable how far pathogen genomic sequencing has come, in part spurred by the pandemic. 1/9https://t.co/Rli8Y1h5pY

— Trevor Bedford (@trvrb) May 25, 2022

We're now starting to see the evolution of new potentially impactful sublineages of Omicron with particular focus on mutations at spike residue 452. Here, I'd like to highlight lineages B.2.12.1 in New York, as well as BA.4 and BA.5 in South Africa. 1/17

— Trevor Bedford (@trvrb) April 18, 2022

Today, I presented to @US_FDA VRBPAC with an overview of SARS-CoV-2 evolution up to this point and a brief perspective for what to expect going forward. Slides are here: https://t.co/QnzOctVCSN and my slot in the full recording is viewable here: https://t.co/n5rlgOvtEg. 1/13

— Trevor Bedford (@trvrb) April 7, 2022

Omicron viruses can be divided into two major groups, referred to as PANGO lineages BA.1 and BA.2 or @nextstrain clades 21K and 21L. The vast majority of globally sequenced Omicron have been 21K (~630k) compared a small minority of 21L (~18k), but 21L is gaining ground. 1/15

— Trevor Bedford (@trvrb) January 28, 2022

Case counts for the US appear to have peaked at a 7-day average of 806k on Jan 14. Omicron grew from approximately 35k daily cases on Dec 14 to ~800k daily cases in ~4 weeks. 1/9 pic.twitter.com/D1Y6R58SjN

— Trevor Bedford (@trvrb) January 20, 2022

With Omicron, case counts in the US and many other countries have skyrocketed. The US 7-day average is now ~680k cases per day, or 0.2% of the population recorded as confirmed cases each day. 1/15 pic.twitter.com/adTzjiNUQA

— Trevor Bedford (@trvrb) January 10, 2022

The impact of Omicron on case counts in the US is now abundantly obvious with 885k reported cases yesterday alone. Figure using @CDCgov data and showing daily reported cases with 7-day smoothing on log scale. 1/12 pic.twitter.com/ikK9bzaggo

— Trevor Bedford (@trvrb) January 5, 2022

An update on Omicron epidemic dynamics and where we stand today. Exponential growth cannot go on forever, but predicting when a wave will crest ahead of observing slowing in case growth is very difficult. 1/17

— Trevor Bedford (@trvrb) December 23, 2021

I fully agree that the single best action individuals (and governments) can be taking to reduce impact of the Omicron wave is to get booster dose if already vaccinated and to get vaccinated if not. 1/14

— Trevor Bedford (@trvrb) December 20, 2021

The extremely rapid rate of spread of Omicron clearly visible since the beginning of December will now be acutely felt in many geographies as local epidemics amplify to the point of eclipsing Delta circulation. 1/12https://t.co/nHfoybHE4d

— Trevor Bedford (@trvrb) December 17, 2021

It seems that the common assumption has been that Omicron will displace Delta, just as Delta displaced Alpha, Beta, Gamma, etc... before it. This may well be the case, but it's by no means definite. 1/15

— Trevor Bedford (@trvrb) December 13, 2021

There is now enough genomic data from the US and Germany to repeat this approach to estimating Omicron-specific rate of epidemic spread. Here, we observe similar initial rapid spread in the US and Germany. 1/10https://t.co/VOmgLy0rEy

— Trevor Bedford (@trvrb) December 11, 2021

We've seen exceptionally rapid spread of Omicron in South Africa. Although we should expect this rapid spread to follow in other geographies, we've mostly lacked data to confirm this until recently. 1/21https://t.co/nHfoybHE4d

— Trevor Bedford (@trvrb) December 10, 2021

As the Omicron epidemic continues to expand in South Africa and as case counts and sequencing data continues to come in, we can better estimate the current transmission rate of Omicron. 1/19

— Trevor Bedford (@trvrb) December 4, 2021

I'm re-upping an analogy from Feb 2020 for how to think about epidemic spatial spread as Omicron is detected across the world. 1/6https://t.co/wTLynzYgNM

— Trevor Bedford (@trvrb) December 2, 2021

Following up here with speculative estimates of the rate of spread of Omicron and a stab at how to apportion this rapid rate of spread between intrinsic transmissibility and immune escape. 1/18

— Trevor Bedford (@trvrb) December 1, 2021

I think there's perhaps been some confusion regarding transmissibility vs immune escape in Omicron. The apparent rapid increase in frequency of Omicron in Gauteng does not mean that Omicron is necessarily more intrinsically transmissible than Delta. 1/15

— Trevor Bedford (@trvrb) November 29, 2021

There have been a number of overview threads on the emerging variant designated as @PangoNetwork lineage B.1.1.529, @nextstrain clade 21K and @WHO Variant of Concern Omicron. I'm not going to attempt to be comprehensive here, but will highlight a few aspects of the data. 1/16

— Trevor Bedford (@trvrb) November 26, 2021

Did vaccination drive the evolution of variant (Alpha, Beta, etc...) SARS-CoV-2 viruses? This is a legitimate scientific question, but after looking into it I don't believe this to be the case. 1/19

— Trevor Bedford (@trvrb) November 22, 2021

Something is clearly wrong with @CDCGov vaccination coverage data. The dashboard at https://t.co/axIvRnKbwK reports that 99.7% (!) of those over 65 have received at least 1 dose. Given known vaccine hesitancy, having 997 out of 1000 in this cohort with 1 dose is unlikely. 1/3 pic.twitter.com/0S6TNr8igC

— Trevor Bedford (@trvrb) November 20, 2021

I support making boosters broadly available for those 18 and older. Even if breakthrough cases are generally mild in younger age groups, there is significant societal benefit to reducing circulation. 1/6https://t.co/FfrEPAU1lk

— Trevor Bedford (@trvrb) November 17, 2021

The evolution of SARS-CoV-2 in the past year has been remarkable with Delta increasing transmissibility by perhaps 2.2X over "non-variant" viruses. 1/14https://t.co/CGZN5jvQEF

— Trevor Bedford (@trvrb) November 15, 2021

I've meaning to write a "COVID endgame" thread for a while and I apologize this is somewhat delayed compared to media interviews like https://t.co/dQuo9i6ER7 and https://t.co/48MmCeq33g and to recent seminars like https://t.co/PGcgDinSNT. 1/17

— Trevor Bedford (@trvrb) October 13, 2021

New (not yet peer-reviewed) work by Katie Kistler and @huddlej in the lab assessing adaptive evolution in SARS-CoV-2 across the viral genome. 1/12 https://t.co/YGRDVnjHiO

— Trevor Bedford (@trvrb) September 13, 2021

New (not yet peer-reviewed) work by Katie Kistler and @huddlej in the lab assessing adaptive evolution in SARS-CoV-2 across the viral genome. 1/12 https://t.co/YGRDVnjHiO

— Trevor Bedford (@trvrb) September 13, 2021

It looks like we're about at the peak of the Delta SARS-CoV-2 wave in the US (figure based on @CDCGov data). A thread on current circulation patterns and the impact of Delta. 1/14 pic.twitter.com/gfy9iC8SqA

— Trevor Bedford (@trvrb) September 7, 2021

I'm not an immunologist, but I've been trying to read into the literature on waning immunity to SARS-CoV-2 and to understand the recent NIH, CDC, FDA booster recommendation (https://t.co/pDUJ7DOUJT). I'll share some takeaways here. 1/14

— Trevor Bedford (@trvrb) August 31, 2021

How big of a wave of #COVID19 do we expect in the US from the Delta variant? Here I describe a simple approach to this question and attempt a rough back-of-the-envelop estimate. 1/16

— Trevor Bedford (@trvrb) June 30, 2021

Jesse Bloom's preprint has, of course, caused quite a stir. I wanted to try to explain a bit about the "rooting issue" discussed in the manuscript and also provide some hopefully clarifying phylogenetic trees. 1/15https://t.co/WlhxLcBbzW

— Trevor Bedford (@trvrb) June 24, 2021

An update on genomic surveillance in the US and spread of the Delta variant (PANGO lineage B.1.617.2, Nextstrain clade 21A). At this point, 95% of viruses circulating in the US are "variant" viruses that have been designated as "Variant of Concern" or "Variant of Interest". 1/12 pic.twitter.com/A07HLaih01

— Trevor Bedford (@trvrb) June 22, 2021

With the publication of the Science letter, the Overton window for discussion of "lab leak" hypothesis has shifted dramatically. We now have mainstream scientific opinions that largely range between "lab leak can be dismissed" and "both zoonosis and lab leak are viable". 1/8

— Trevor Bedford (@trvrb) June 2, 2021

#COVID19 cases in the US reported by @CDCGov have continued their week-after-week exponential decline that began in mid-April. This is exceptionally welcome news, although I'm now watching closely for variants driving sub-epidemics despite overall cases falling. 1/10 pic.twitter.com/UQmYgx9wG0

— Trevor Bedford (@trvrb) May 25, 2021

The drivers of the #COVID19 epidemic in India are certainly multifactorial, but we have now seen the viral lineage B.1.617 linked to this epidemic continue to increase in frequency in India and spread rapidly outside of the country. 1/10

— Trevor Bedford (@trvrb) May 11, 2021

From Aug 2020 to Mar 2021, the lagged case fatality rate (CFR) of the US #COVID19 epidemic had remained largely constant at ~1.5% and provided a simple method to predict subsequent deaths from current cases. 1/6https://t.co/dzyCWrM1BI

— Trevor Bedford (@trvrb) May 7, 2021

Just as we can decompose the US #COVID19 epidemic into a B.1.1.7 epidemic and a non-B.1.1.7 epidemic, we can further partition by variants of concern B.1.1.7, B.1.351 and P.1, where it's clear that P.1 has been gaining ground. 1/13https://t.co/vl3l1JT3ZD

— Trevor Bedford (@trvrb) May 3, 2021

There are effectively two #COVID19 epidemics in the US at this moment; one largely resolving epidemic comprised of non-variant viruses and one growing epidemic of B.1.1.7. Together they have resulted in a near-plateau of cases throughout much of the spring. 1/10

— Trevor Bedford (@trvrb) April 26, 2021

When variants of concern were first identified in late Dec, the US was not where it needed to be in terms of genomic surveillance. However, with considerable ramp up by the CDC, state labs and academic groups, we now have a remarkable genomic surveillance system. 1/14

— Trevor Bedford (@trvrb) April 23, 2021

Since their recognition in the UK, South Africa and Brazil in Dec 2020 and Jan 2021, the variant of concern lineages B.1.1.7, B.1.351 and P.1 have continued to spread throughout the world with B.1.1.7 so far the most successful of the three. 1/15https://t.co/RtVLQPRUiV

— Trevor Bedford (@trvrb) April 14, 2021

After a ~2 month plateau from mid-Nov to mid-Jan, the US #COVID19 epidemic has undergone a steady week after week decline and is now back to daily case counts last seen in late October. A thread on what we might expect going forwards. 1/13 pic.twitter.com/M7vrdECUX2

— Trevor Bedford (@trvrb) February 18, 2021

With emerging variants of SARS-CoV-2 and initial evidence of antigenic evolution, I've seen comparisons here to seasonal influenza and its rate of evolution. In this thread, I want to ground these comparisons with some data. 1/18https://t.co/AMxT5lWOVR

— Trevor Bedford (@trvrb) February 3, 2021

Important new study by Wibmer et al (https://t.co/q6150ahSCz) of neutralization by convalescent sera on wildtype vs 501Y.V2 variant viruses circulating in South Africa. It shows that mutations present in 501Y.V2 result in reduced neutralization capacity. 1/10

— Trevor Bedford (@trvrb) January 20, 2021

At this point, the countries with most genomic data to analyze spread of the variant virus belonging to https://t.co/ImaHU6Jxdv B.1.1.7 lineage or @nextstrain clade 20I/501Y.V1 are the UK, Denmark and the USA. Here I compare growth rates of B.1.17 across these countries. 1/13

— Trevor Bedford (@trvrb) January 18, 2021

After ~10 months of relative quiescence we've started to see some striking evolution of SARS-CoV-2 with a repeated evolutionary pattern in the SARS-CoV-2 variants of concern emerging from the UK, South Africa and Brazil. 1/19

— Trevor Bedford (@trvrb) January 14, 2021

With data that has emerged in the last week, I'm now 80-90% convinced that infections by the UK variant virus (Pangolin lineage B.1.1.7, @nextstrain clade 20B/501Y.V1) result in, on average, more onward infections, ie are more transmissible. 1/10https://t.co/g8HKduGvqW

— Trevor Bedford (@trvrb) December 29, 2020

Given that the US has not detected SARS-CoV-2 variant viruses 501Y.V1 or 501Y.V2, what bounds can we place on their current frequency in the US based on sample counts? 1/12https://t.co/g8HKduoU2m

— Trevor Bedford (@trvrb) December 28, 2020

Given the large discrepancy in specimens collected in Dec that were sequenced and shared between the US and the UK, I wanted to follow up on the relative quality of genomic surveillance in the US and the UK. 1/12https://t.co/fmBArZHaIU

— Trevor Bedford (@trvrb) December 23, 2020

Following up on general thoughts on antigenic drift of #COVID19 from this weekend, I wanted to discuss what we know about the new variant of SARS-CoV-2 thats emerged in the UK. 1/17https://t.co/AMxT5lWOVR

— Trevor Bedford (@trvrb) December 22, 2020

With #COVID19 vaccine efficacy of ~95%, I'm looking forward to vaccine distribution in 2021 bringing the pandemic under control. However, I'm concerned that we'll see antigenic drift of SARS-CoV-2 and may need to update the strain used in the vaccine with some regularity. 1/18

— Trevor Bedford (@trvrb) December 19, 2020

There has been a significant question about the degree to which Thanksgiving holiday and associated travel and social gatherings may have contributed to transmission of #COVID19. Here I try to briefly address this question. 1/8

— Trevor Bedford (@trvrb) December 17, 2020

Although the US is continuing to hit records for daily #COVID19 cases reported, the rate of exponential growth has slowed. Mortality is still catching up to increased case loads and I expect daily deaths reported to further increase. 1/8https://t.co/zdDRM6WUAu

— Trevor Bedford (@trvrb) December 12, 2020

The US reported over 3000 deaths from #COVID19 today and the 7-day average of deaths has hit a record with today's average of 2276. Here, I dig into these grim mortality numbers and look at deaths across ages and across weeks in the epidemic. 1/14https://t.co/OW11EEmNke

— Trevor Bedford (@trvrb) December 10, 2020

The US is reporting over 2000 deaths per day from Dec 1 and I believe will do so consistently throughout December based on daily case loads above 120k starting early November. 1/4https://t.co/mDdBnci5zi

— Trevor Bedford (@trvrb) December 4, 2020

I don't think that this study by Basavaraju et al from @CDCgov can be taken as evidence that #COVID19 was circulating in the US in December 2019. 1/10https://t.co/yTjIwSvM4X

— Trevor Bedford (@trvrb) December 1, 2020

Another update on #COVID19 circulation in the US. With today's report we're seeing an average of ~172k daily cases reported compared to ~157k a week ago, and we're seeing ~1650 daily deaths reported compared to ~1200 a week ago. 1/10https://t.co/vq7Hs2zxLS

— Trevor Bedford (@trvrb) November 26, 2020

When I ran these simple lagged case fatality rate (CFR) calculations last week I was surprised and troubled at how big the predicted numbers of deaths in the coming weeks were. Since then #COVID19 daily case counts have continued to rise. 1/10https://t.co/NTG23jR0mp

— Trevor Bedford (@trvrb) November 19, 2020

The #COVID19 epidemic is rapidly growing throughout the US. What happens now? Here I try to make some predictions, but mostly try to explain how I think about the epidemic. 1/14https://t.co/B6C99061Ju

— Trevor Bedford (@trvrb) November 14, 2020

After posting about sharply rising #COVID19 cases Friday, there were multiple replies to the effect of "but deaths aren't going up". As should be obvious to most at this point, (reported) deaths lag (reported) cases. This thread investigates. 1/8https://t.co/5PStGbR5PJ

— Trevor Bedford (@trvrb) November 11, 2020

I know that everyone has been (justifiably) distracted by other things, but the #COVID19 epidemic in the US is looking pretty dire with 125,552 confirmed cases reported Friday by @COVID19Tracking. 1/10https://t.co/MdTqagsGsG

— Trevor Bedford (@trvrb) November 7, 2020

Our research group at @fredhutch, @UWMedicine and @BrotmanBaty has sequenced the viral genomes of two SARS-CoV-2 infections that were connected to the White House #COVID19 outbreak. The @nytimes reports here: https://t.co/k54FDzVag9. 1/16

— Trevor Bedford (@trvrb) November 1, 2020

Daily #COVID19 case counts are increasing in the US and we seem to hitting a third wave (or second surge if you'd prefer). Here I wanted to look at how case counts through time correlate across different states. 1/12

— Trevor Bedford (@trvrb) October 19, 2020

A follow up to yesterday's controversial thread on societal behavior, population immunity and Rt to specifically address issue of what fraction of the population in Florida, Texas and Arizona may have had COVID-19. 1/16https://t.co/bpLgRG3rdO

— Trevor Bedford (@trvrb) August 9, 2020

I wanted to discuss the degree to which population immunity may be contributing to curbing #COVID19 in Florida, Arizona and Texas, where recent surges have resulted in substantial epidemics. 1/16

— Trevor Bedford (@trvrb) August 7, 2020

With @CDCgov's update to their seroprevalence results across sites in the US, it's possible to see if with increased availability in testing whether we're catching a larger fraction of infections as confirmed cases. 1/13

— Trevor Bedford (@trvrb) July 23, 2020

A follow up to the thread two weeks ago on rising case counts and "reopening", looking at continued trajectories in states with large epidemics. 1/15https://t.co/EtlnnnPqFp

— Trevor Bedford (@trvrb) July 17, 2020

It's abundantly clear that societal behavior strongly impacts #COVID19 spread. We saw this early on where social distancing resulted in significant reductions to epidemic spread. With the surge of cases in the south, what can we expect going forward? 1/14https://t.co/Po4VuHOFks

— Trevor Bedford (@trvrb) July 3, 2020

A small follow up to the "long plateau" assessment of the #COVID19 epidemic. When I tweeted this on April 30, we had ~30k daily confirmed cases and ~2000 daily deaths. This last week, we had ~24k daily confirmed cases and ~700 daily deaths. 1/10https://t.co/SjLdYVZdhK

— Trevor Bedford (@trvrb) June 20, 2020

As many have noted, there has been an uptick in confirmed #COVID19 cases in multiple states starting roughly at the beginning of June. There is a major question surrounding how much "re-opening" efforts are contributing to increases in transmission. Figure from @nytimes. 1/10 pic.twitter.com/lwUyrWrSug

— Trevor Bedford (@trvrb) June 17, 2020

The simple model I was using here is perhaps worth thinking about in terms of how to mitigate impact from protests or other potential sources of transmission. 1/7https://t.co/NRpIHv959l

— Trevor Bedford (@trvrb) June 8, 2020

I appreciate the feedback I've gotten on these estimates (and whether it's even responsible to make them). A couple of things to emphasize here. 1/11 https://t.co/ZtEUtQOwTK

— Trevor Bedford (@trvrb) June 8, 2020

I appreciate the feedback I've gotten on these estimates (and whether it's even responsible to make them). A couple of things to emphasize here. 1/11 https://t.co/ZtEUtQOwTK

— Trevor Bedford (@trvrb) June 8, 2020

Excellent reporting by @AP outlining timeframe of release of #SARSCoV2 genetic data in early Jan as the #COVID19 outbreak unfolded in Wuhan. 1/6https://t.co/tf10gugfiJ

— Trevor Bedford (@trvrb) June 2, 2020

Slightly belated, but a response to the US cutting ties with the @WHO and a bit on my relationship with the organization. 1/8https://t.co/ftajYngtkH

— Trevor Bedford (@trvrb) June 2, 2020

On Feb 29, using the genetic sequence of the first community case of #COVID19 in Washington State, I made the claim that the Washington State outbreak descended directly from the Jan 15 arrival of the WA1 case with direct travel history to Wuhan. 1/18https://t.co/8wWxtiotE3

— Trevor Bedford (@trvrb) May 25, 2020

I wanted to take a moment to acknowledge the amazing team that have been responsible for @nextstrain and its work during the #COVID19 crisis. 1/11

— Trevor Bedford (@trvrb) May 17, 2020

We now have enough #SARSCoV2 genomic data from different states to make some broad conclusions about how the #COVID19 epidemic has unfolded in the US. 1/14

— Trevor Bedford (@trvrb) May 12, 2020

I'm seeing a bunch of talk about how the code behind the simulations for the March 16 @MRC_Outbreak report (https://t.co/xyMJL1Ejjs) was never previously released and is not well written. This is then taken to somehow mean that the "lockdown" policy was ill-founded. 1/11

— Trevor Bedford (@trvrb) May 8, 2020

I wanted to address the hypothesis put forward in Korber et al (https://t.co/ouM4IUyNrd) that the mutation in spike protein D614G causes an increase in transmissibility of SARS-CoV-2 virus. I find this hypothesis to be plausible, but far from proven. 1/16

— Trevor Bedford (@trvrb) May 6, 2020

I know all the discussion is about a possible "2nd wave", but I've found this odd given that we haven't finished the first one. I would think quite possible that, nationally, we're in for a scenario of a long plateau. 1/10

— Trevor Bedford (@trvrb) April 30, 2020

Given my statement that the US has 300k - 600k new infections per day, I've had a bunch of responses telling me that #TestTraceIsolate is futile and we should give up on it. This thread demonstrates the benefits of reducing transmission even if suppression is not attainable. 1/9

— Trevor Bedford (@trvrb) April 27, 2020

If we're going to manage a #TestTraceIsolate solution to the #COVID19 epidemic, we need a massive scale up in testing. There are some really exciting initiatives here. 1/9

— Trevor Bedford (@trvrb) April 25, 2020

Thoughts on seroprevalence in NYC. I'm not at all surprised by an estimate of 21% seropositive in NYC as discussed by @NYGovCuomo today (https://t.co/Bo9SwgdEmR). 1/6

— Trevor Bedford (@trvrb) April 23, 2020

I wanted to respond to news of #COVID19 death in Santa Clara County on Feb 6. This is an interesting, if slightly puzzling, data point. 1/9

— Trevor Bedford (@trvrb) April 22, 2020

Very interesting new preprint by Eran Bendavid and colleagues reports seroprevalence estimates from Santa Clara county. Great to have seroprevalence work start to emerge, but I'd be skeptical of the 2-4% seroprevalence result. 1/8 https://t.co/qzDd8ky1p0

— Trevor Bedford (@trvrb) April 18, 2020

I wanted to give a basic picture of why #TestTraceIsolate is so important to the control of the #COVID19 epidemic and why we need to move quickly when testing and contact tracing in order to create an effective intervention. 1/14

— Trevor Bedford (@trvrb) April 16, 2020

There is a lot of Twitter chatter surrounding a rumor that circulation of #COVID19 in California in fall 2019 has resulted in herd immunity. This is empirically not the case. COVID-19 was first introduced into the USA in Jan/Feb 2020. 1/18

— Trevor Bedford (@trvrb) April 12, 2020

In many ways, this should be entirely obvious, but we now have strong evidence that social distancing results in decreased #COVID19 transmission rates. 1/7

— Trevor Bedford (@trvrb) April 9, 2020

How can we assess the total number of #SARSCoV2 infections that have occurred up to this point? As others have noted, it's not easy to extrapolate from confirmed cases to total infections. Some thoughts here, but no real answers. 1/9

— Trevor Bedford (@trvrb) April 7, 2020

Today, we're standing up a project called NextTrace that aims to enable digital participatory contact tracing and guide #COVID19 surveillance efforts. See a full description here https://t.co/0jKDupUlVb or get the summary in this thread. 1/20

— Trevor Bedford (@trvrb) April 1, 2020

This article by @USATODAY misleadingly states that there are "8 strains of coronavirus" circulating. Because of this our @nextstrain inbox is today full of questions like "if you get one strain of Covid-19 and recover, do you have immunity to the other seven?". 1/13 pic.twitter.com/y9OW8Mdnsd

— Trevor Bedford (@trvrb) March 30, 2020

Genomic sequencing of viruses from the #COVID19 pandemic can help reveal transmission patterns. Thanks to data sharing through @GISAID from groups all over the world, @nextstrain is now showing 1882 #SARSCoV2 genomes. This is an update on a few aspects of what we're seeing. 1/14

— Trevor Bedford (@trvrb) March 28, 2020

A thread on #SARSCoV2 mutations and what they might mean for the #COVID19 vaccination and immunity, in which I predict it will take the virus a few years to mutate enough to significantly hinder a vaccine. 1/12

— Trevor Bedford (@trvrb) March 25, 2020

I've been mulling over the @MRC_Outbreak modeling report on #COVID19 mitigation and suppression strategies since it was posted on March 16. Although mitigation through social distancing may not solve things I believe we can bring this epidemic under control. 1/19

— Trevor Bedford (@trvrb) March 19, 2020

This is a thread about how to interpret the seemingly sudden appearance of #COVID19 across the much of the US in the past week with some back-of-the-envelop calculations for number of current infections. 1/13 pic.twitter.com/QbzRbRVheS

— Trevor Bedford (@trvrb) March 14, 2020

There is continued interest in "L" vs "S" strains of #SARSCoV2 proposed in the manuscript https://t.co/FU1AIaxyY2. Please consider this thread to be a public peer review of this work. 1/8

— Trevor Bedford (@trvrb) March 7, 2020

(This analysis and tweet thread in collaboration with @famulare_mike) The existence of a community transmission cluster of #COVID19 in Snohomish and King Counties is now supported by 8 confirmed and sequenced cases (https://t.co/2efDbQrW1v). 1/7

— Trevor Bedford (@trvrb) March 7, 2020

The team at the @seattleflustudy have sequenced the genome the #COVID19 community case reported yesterday from Snohomish County, WA, and have posted the sequence publicly to https://t.co/tbVb4MAGpy. There are some enormous implications here. 1/9

— Trevor Bedford (@trvrb) March 1, 2020

A few thoughts on where we stand on #COVID19.
1. It appears there aren't massive undercounts of cases in China (https://t.co/MRXH6eu9Bb). This fits as with both my own phylodynamic analyses (https://t.co/fMUyNJdxJ6) and those of @erikmvolz (https://t.co/F0bbvNMdxg). 1/6

— Trevor Bedford (@trvrb) February 26, 2020

I've written before that #COVID19 has no evidence of genetic engineering and the "bioweapon" theory has no grounds. See, for example https://t.co/aR5NfTJzYq. In this thread I wanted to directly address the theory of escape from lab in Wuhan. 1/21

— Trevor Bedford (@trvrb) February 20, 2020

One of the most important unknowns in the #nCoV2019 epidemic is the total number of _infections_ as opposed to _cases_, as there may be many mild infections that do not rise to case definition. I sought to address this with phylodynamic methods here: https://t.co/iRqMpQ87ql 1/9

— Trevor Bedford (@trvrb) February 10, 2020

Insight into the spatial behavior of epidemics from @ohallats and colleagues. An initial outbreak will grow in its highly connected environment and subsequently seed outbreaks in other locations. These other outbreaks resemble a transposed copy of the first. 1/4 pic.twitter.com/0pbtf2ZCOz

— Trevor Bedford (@trvrb) February 8, 2020

I thought to examine signal of natural evolution in #nCoV2019 by looking at distribution of mutations in the lineage leading to nCoV and compare this distribution to mutations occurring in other SARS-like bat viruses 1/9

— Trevor Bedford (@trvrb) February 3, 2020

Based on the content of my mentions, I feel like I need to further debunk crazy #nCoV2019 / HIV conspiracy preprint. This is a thread doing so. 1/9

— Trevor Bedford (@trvrb) February 1, 2020

Thanks to rapid and open data sharing by China CDC, Wuhan Institute of Virology, Institute of Pathogen Biology and Fudan University, we know genomes from 6 of the novel coronaviruses isolated in Wuhan. I've posted a tree of these viruses here: https://t.co/Qz2zmZD5yS 1/4 pic.twitter.com/ErafWRioog

— Trevor Bedford (@trvrb) January 12, 2020

As others have already said, we see the novel coronavirus from Wuhan grouping with sampled SARS-related bat coronaviruses. We thank Professor Zhang and colleagues for amazingly rapid data sharing. A full interactive phylogeny of beta-CoV diversity is here: https://t.co/koZGMWy0hI pic.twitter.com/ozYLnFsF7o

— Trevor Bedford (@trvrb) January 11, 2020