Scientist @fredhutch, studying viruses, evolution and immunity. Collection of #COVID19 threads here: bedford.io/misc/twitter/
Seattle, WA
- Tweets 5,265
- Following 748
- Followers 401,824
- Likes 6,509
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 gisaid.org. There are some enormous implications here. 1/9
296
4,889
8,922
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
195
2,301
8,612
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
265
3,598
8,428
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
207
3,602
7,255
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
193
2,509
7,215
The world should be immensely grateful to @Tuliodna, @ceri_news, @nicd_sa, the Network for Genomics Surveillance in South Africa and the Botswana Harvard HIV Reference Laboratory for discovering this variant and immediately alerting to its existence. 16/16
70
822
4,553
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
108
1,866
4,657
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
136
2,095
4,551
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
103
1,914
4,410
I believe we're facing an already substantial outbreak in Washington State that was not detected until now due to narrow case definition requiring direct travel to China. 6/9
81
1,418
3,897
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
100
1,221
3,957
As #COVID19 spread, we continually heard "we're all in this together" as an expression of solidarity. This rings hollow when a fraction of our society faces state-sanctioned violence. We must fix this. #BlackLivesMatter
82
748
3,612
Together, I believe these (and other case-based) strategies can bring down the epidemic. This is the Apollo program of our times. Let's get to it. 19/19
163
581
3,541
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
89
1,671
3,449
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
74
1,181
3,289
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
82
1,026
3,323
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
58
878
3,126
Having ~40% of the population infected by a single pathogen in the span of 8 weeks is remarkable and I can't think of an obvious modern precedent. Flu seasons generally have perhaps 10% infected in the span of 16 weeks. 8/9
74
961
3,127
The appalling killing of George Floyd and video after video after video of police brutality cements the elemental *rightness* of the Black Lives Matter cause. 1/21
84
756
2,865
This strongly suggests that there has been cryptic transmission in Washington State for the past 6 weeks. 3/9
53
945
2,660
This was an emotional read for me. February is now a blur, but I remember being flabbergasted by the continued narrow case definition and restricted testing. Necessary perspective on how much was lost by @alexismadrigal and @yayitsrob. theatlantic.com/health/archi…
87
1,290
2,713
A small update on genomic epidemiology of the #COVID19 epidemic in Washington State (where we have lots of data) and elsewhere in the US (where data is sparse). 1/8
66
1,069
2,604
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
77
1,071
2,561
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
83
840
2,600
I wrote a blog post that details Saturday's finding of "cryptic transmission" of #SARSCoV2 in Washington State. Genomic evidence suggests that #COVID19 has been circulating here since Jan 15, but undetected due to lack of testing. bedford.io/blog/ncov-cryptic…
141
1,398
2,512
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
91
834
2,571
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. 1/18
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 gisaid.org. There are some enormous implications here. 1/9
70
699
2,411
This extremely long branch (>1 year) indicates an extended period of circulation in a geography with poor genomic surveillance (certainly not South Africa) or continual evolution in a chronically infected individual before spilling back into the population. 4/16
52
724
2,445
An update, because I see people overly speculating on total outbreak size. Our best current expectation is a few hundred current infections. Expect more analyses tomorrow.
75
506
2,184
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
56
895
2,375
I'm honored and completely overwhelmed by the recognition from @macfound and @HHMINEWS. Flexible funding with a multi-year commitment is the professional scientist's dream and I'm incredibly grateful for this opportunity. 1/4
111
119
2,219
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
61
1,298
2,288
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
56
584
2,147
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
63
1,144
2,213
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
145
851
2,217
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
57
681
2,137
Individuals who have serological evidence of recovery and are no longer shedding virus can fully return to the workforce and keep society functioning (especially important for those at the clinical front lines). 18/19
37
339
2,040
This strategy of massive testing has been a cornerstone in South Korea's response (sciencemag.org/news/2020/03/…) and we're now seeing their epidemic brought under control without the stringent policies put in place elsewhere. Case counts in South Korea via @covid2019app. 13/19
27
701
2,013
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
107
629
2,122
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
89
340
1,998
If growth continues unabated, this cluster alone may be responsible for 1100 (210, 2800) active infections by March 10 and 2000 (370, 5000) by March 15. 5/7
59
824
1,898
This case, WA2, is on a branch in the evolutionary tree that descends directly from WA1, the first reported case in the USA sampled Jan 19, also from Snohomish County, viewable here: nextstrain.org/ncov?f_divisi… 2/9
40
612
1,797
The second, related, strategy is using cell phone location data combined with data on known positive cases to alert possible exposures to self isolate and get tested. Figure from @ChristoPhraser and colleagues who've considered this in detail. 15/19
50
510
1,904
I've meaning to write a "COVID endgame" thread for a while and I apologize this is somewhat delayed compared to media interviews like science.org/content/article/… and statnews.com/2021/09/20/wint… and to recent seminars like piped.video/watch?v=VErVD_H1…. 1/17
71
697
1,942
Growth rate (in absolute terms and relative to Delta) will be become clearer in the following days, but at the moment, I believe we're looking at a variant that potentially has significant immune evasion and that appears to be spreading rapidly. 15/16
47
590
1,860
Thank you to the @seattleflustudy team, and particularly to @lea_starita, for exceptionally fast turnaround from diagnostic assay at @WADeptHealth to sequenced genome. 9/9
23
214
1,638
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
45
632
1,782
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
49
531
1,744
The seeming sudden appearance of outbreaks across the US are not due to a sudden influx of cases. Instead, transmission chains have been percolating for 4-8 weeks now and we're just now starting to see exponential growth pick up steam. 5/13
14
526
1,646
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
106
397
1,719
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 nexttrace.org/about or get the summary in this thread. 1/20
59
735
1,702
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. 1/8
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. 1/10
68
543
1,576
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. 1/10
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. 1/17
59
742
1,655
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
48
644
1,655
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
68
589
1,568
I've been hugely impressed by the thoughtful and deliberate actions taken to combat the #COVID19 outbreak in Seattle and Washington State by @JayInslee and @MayorJenny. Their perspective is fully science-based and I applaud their leadership here.
The health and well-being of Washingtonians during the COVID-19 outbreak remains our top priority.
Starting today, we will prohibit events of more than 250 people in King, Snohomish and Pierce Counties to slow the spread of this virus.
49
375
1,485
This rollout of testing could be achieved through at home delivery of swabs with centralized lab-based processing combined with drive-through testing facilities. There are logistics involved in getting a result quickly, but it's really just logistics, which can be solved. 14/19
22
318
1,497
The first strategy revolves around a massive rollout of testing capacity. We believe that a significant proportion of epidemic transmission is due to mild and maybe even asymptomatic infections (science.sciencemag.org/conte…). 10/19
19
383
1,477
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 (hhs.gov/about/news/2021/08/1…). I'll share some takeaways here. 1/14
55
518
1,575
Going forward, I suggest:
1. Emerging variants should be assayed against sera from recovered and vaccinated individuals to test for antigenic effects
2. Immunization records should be connected to genomic surveillance to identify variants involved in breakthrough infections
18/18
90
202
1,533
These transmission routes can be reduced by a huge rollout of testing capacity. If someone can be tested early in their illness before they show symptoms, they could effectively self isolate and reduce onward transmission compared to isolation when symptoms develop. 12/19
13
318
1,420
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
30
455
1,495
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
48
461
1,518
It's possible that this genetic similarity is a coincidence and these are separate introductions. However, I believe this is highly unlikely. The WA1 case had a variant at site 18060. This variant is only present in 2/59 viruses from China. 4/9
11
302
1,354
I very respectfully disagree with the estimate of 100k #COVID19 infections in Ohio put forth by the @OHdeptofhealth. As far as I can ascertain from the press coverage (news5cleveland.com/news/cont…), this number comes from extrapolating from 2 community cases detected. 1/5
106
535
1,457
We can compare #COVID19 1% infection fatality rate with an expected >80% attack rate (R0 of ~3) to seasonal influenza with 0.1% IFR and yearly attack rate of ~10%. Simple math would put unmitigated spread as >80X worse than a typical flu season.
Thoughts on seroprevalence in NYC. I'm not at all surprised by an estimate of 21% seropositive in NYC as discussed by @NYGovCuomo today (nitter.app/NYGovCuomo/status/1253…). 1/6
63
630
1,463
I'm of course concerned about the protests contributing to epidemic resurgence of #COVID19. They are outside, but close contact and large crowds are risk factors and if they continue day after day with the same group of people you risk amplification. 1/8
58
340
1,467
Work by colleagues at @IDMOD_ORG that takes current best estimate for number of active #COVID19 infections and simulates forward under different degrees of social distancing. A 25% reduction in mixing results in more than a 50% drop in cases after 1 month relative to baseline.
Grateful to support science-driven decision-making by Washington officials during this critical phase of the #COVID19 outbreak. Read about what generated today's graphic: bit.ly/2TYS0RL @GovInslee @KCPubHealth @WADeptHealth @MayorJenny @trvrb @famulare_mike @hagedornb
31
845
1,426
However, I'm not quite that pessimistic. Although I agree that basic mitigation efforts won't stop the epidemic, I have hope that we can solve this thing by doing traditional shoe leather epidemiology of case finding and isolation, but at scale, using modern technology. 8/19
11
266
1,408
We will be working closely with @KCPubHealth and @WADeptHealth to investigate the full extent of the outbreak. 7/9
8
210
1,295
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
32
666
1,484
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. 1/17
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
35
627
1,472
A third, supporting, strategy: as the epidemic proceeds get serological assays run on as many people as possible to systematically identify individuals who have recovered and are highly likely to possess immunity. 17/19
15
241
1,388
I could easily be off 2-fold in either direction, but my best guess is that we're currently in the 10,000 to 40,000 range nationally. 11/13
44
432
1,385
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
74
435
1,417
I'm sorry to have created confusion here. Although I do think that my original actions were warranted given available evidence at the time. 18/18
83
42
1,382
So, my prediction is that we should see occasional mutations to the spike protein of #SARSCoV2 that allow the virus to partially escape from vaccines or existing "herd" immunity, but that this process will most likely take years rather than months. 12/12
85
402
1,414
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. 1/21
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
46
542
1,418
Thanks to fast work by @UWVirology we now know that there are at least two #COVID19 transmission chains circulating in the greater Seattle area. We're working on revised prevalence estimates.
Updated with the 3rd #SARSCoV2 genome from Washington State sampled just 5 days ago on Feb 27. This looks like part of a transmission chain exported from Europe. Huge props to @UWVirology @pavitrarc @GreningerLab GISAID 👏 nextstrain.org/ncov
45
653
1,345
I wanted to address the hypothesis put forward in Korber et al (biorxiv.org/content/10.1101/…) 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
35
651
1,393
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
32
379
1,363
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? 1/14
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
71
496
1,300
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
35
417
1,354
Important new study by Wibmer et al (biorxiv.org/content/10.1101/…) 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
38
611
1,408
I'd assess the p-value for this coincidence at 2/59=0.03 and so is statistically significant. Additionally, these two cases are geographically proximal, both residing in Snohomish County. 5/9
18
216
1,229
One of the most powerful aspects of genomic data for #COVID19 is the ability to make connections between seemingly disparate outbreaks. This is a thread describing one such possible connection. Please keep in mind this is only a hypothesis and not proven fact. 1/9
30
439
1,311
I expect the US to be reporting over 2000 deaths per day in 3 weeks time. Importantly, this doesn't assume any further increases in circulation and is essentially "baked into" currently reported cases and represents conditions that take time to resolve and to be reported. 8/8
70
519
1,286
My big question now is to what extent will Omicron-like emergence events characterize "endemic" circulation of SARS-CoV-2? Given it occurred once, having it occur again would not be at all surprising, but I don't know whether to expect this every year or every ten. 9/9
63
214
1,300
One more update: my best guess at a p-value here is 0.03 as above based on shared mutations (still possible this pattern was chance). If we get another sequence or two from additional WA community cases this should clinch the matter one way or another.
62
150
1,177
Thanks to sequencing by @UWVirology, @CDCgov and @seattleflustudy we have genomes for 39 viruses sampled from WA. Importantly 35 of these 39 viruses (90%) fall into a single genetic cluster indicating a single ~Jan introduction from China and subsequent local spread. 3/8
27
596
1,218
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: bedford.io/talks/sars-cov-2-… and my slot in the full recording is viewable here: piped.video/x8rq247E80I?t=11572. 1/13
36
461
1,302
If Omicron Rt continues at around 3 this indicates a much larger threat in terms of case counts than Delta. I'm hoping that prior immunity protects against severe outcomes, but I'm very concerned about the size of the epidemic wave in the US and across the world. 18/19
33
456
1,282
(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 (nitter.app/trvrb/status/123567681…). 1/7
New #SARSCoV2 genomes from the #seattlecoronavirus outbreak have been shared by @UWVirology through GISAID. These group as part of the same emerging transmission chain. 1/3
45
596
1,226
These viruses are visible on @nextstrain as "21K (Omicron)" shown here in red (nextstrain.org/ncov/gisaid/a…). They do not descend from previously identified "variant" viruses and instead their closest evolutionary connection is to mid-2020 viruses. 3/16
16
342
1,289
We're hoping to update soon with better estimates of the number of infections in Washington State using available data. 8/9
7
181
1,122
I see #TestTraceIsolate as the only real solution to the problem we're facing (see recent thread from @firefoxx66 nitter.app/firefoxx66/status/1248…), alongside non-economically disruptive distancing and broad use of masks. 16/18
32
389
1,194
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. 1/12
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
36
463
1,233