As we all know, a man died of coronavirus infection near Seattle in Washington state yesterday. There are 6 confirmed infections in the state, including three cases from people who contracted the illness within their community. Two people from a nursing facility in Kirkland have tested positive for the virus. Another 50 people from the nursing facility are being tested for the virus.

One of the burning questions has been why there are so few detected infections in the U.S., given that the virus must have entered the U.S. weeks ago with travelers from China. There is constant movement of tourists, family members and tech. workers between the U.S. and China and the travel bans did not go into effect until late January.

One reason some infections may be going unnoticed is because it’s the season for respiratory diseases. Flu and the common cold have similar symptoms as COVID-19 — and are the likely culprit in the majority of respiratory disease cases in the U.S. — which can make the new coronavirus harder to detect. www.sciencenews.org/...

A second reasons has been lack of testing and the protocol for not testing people who had not traveled recently to China. The man who died of coronavirus near Seattle would not have been diagnosed before last week — as someone who had not been traveling recently, the man didn’t meet the previous criteria for coronavirus testing. www.kuow.org/...

This raises the specter that there are lot more undetected infections lurking in the community, many asymptomatic or mildly asymptomatic. Left untreated, these infections will spread.

Scientists have also been sequencing the genomes of virus samples from the around the world at an unprecedented rate. The sequencing of a virus sample of a recent case in Washington state has enormous implications, because it matches very closely to a SARS-CoV-2 sample from the first case in WA state on Jan 19, implying that the virus has been present in the local population for over 6 weeks.

Take a look at this twitter chain from Trevor Bedford, a research scientist at the Bedford Lab at the Fred Hutch (Fred Hutchinson Cancer Research Center). The organization maintains real-time views of influenza evolution at nextflu.org and pathogen evolution and epidemic spread at nextstrain.org.

x 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: https://t.co/gxyo0PsJ7x 2/9 pic.twitter.com/LBH26A0AFC Ã¢ÂÂ Trevor Bedford (@trvrb) March 1, 2020

This strongly suggests that there has been cryptic transmission in Washington State for the past 6 weeks. 3/9

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

. 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 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

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

We will be working closely with @KCPubHealth and @WADeptHealth to investigate the full extent of the outbreak. 7/9

We're hoping to update soon with better estimates of the number of infections in Washington State using available data. 8/9

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

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.

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. Prof. Bedford offers his usual scientific caveat that this deduction may be incorrect, that the genetic similarity may be a coincidence, but other scientists have looked at the analysis and generally concur with the conclusion. All indications are that this has been happening around the U.S., since we have not been actively testing for the coronavirus, unlike other countries. Testing or lack thereof Compounding this problem has been the lack of testing and “surveillance testing” because of the policies and snafus of our government. E.g.. the CDC decided to develop its own Coronavirus test, which turned out to be faulty. x The U.S. insisted on developing its own Coronavirus test, even though the WHO already had one that worked.



Then the U.S.'s test didn't work. And now, it's dangerously behind in proactively testing for an outbreak.https://t.co/xn8BiCC7LF Ã¢ÂÂ ProPublica (@propublica) February 29, 2020 The federal agency shunned the World Health Organization test guidelines used by other countries and set out to create a more complicated test of its own that could identify a range of similar viruses. But when it was sent to labs across the country in the first week of February, it didn’t work as expected. The CDC test correctly identified COVID-19, the disease caused by the virus. But in all but a handful of state labs, it falsely flagged the presence of the other viruses in harmless samples. As a result, until Wednesday the CDC and the Food and Drug Administration only allowed those state labs to use the test — a decision with potentially significant consequences. The lack of a reliable test prevented local officials from taking a crucial first step in coping with a possible outbreak — “surveillance testing” of hundreds of people in possible hotspots. Epidemiologists in other countries have used this sort of testing to track the spread of the disease before large numbers of people turn up at hospitals. However, the FDA and the CDC are making headway on this front. Better late than never. x Coronavirus news moves at warp speed: FDA new rules announced today make thousands of more diagnostic tests potentially available in US soon. CDC also has new kits available. My latest update, which may be dated by time I hit Tweet button. https://t.co/Fu0lvHx5zK Ã¢ÂÂ Jon Cohen (@sciencecohen) February 29, 2020 Which means that case numbers are likely to dramatically rise soon - x As more labs gain the ability to test for the new coronavirus Ã¢ÂÂ and eligibility for that testing expands Ã¢ÂÂ "we are going to start to see more and more cases pop up across the country," an expert says. https://t.co/SOAWLLLB8A Ã¢ÂÂ NPR (@NPR) March 1, 2020 Related News Gov. Inslee has declared a state of emergency in WA state. x Washington governor Jay Inslee declares state of emergency over #coronavirus in response to new COVID19 cases and one death, directing state agencies to use Ã¢ÂÂall resources necessaryÃ¢ÂÂ The declaration also allows the use of the Washington National Guard. https://t.co/yKBqnn1FM7 Ã¢ÂÂ Max HowrouteÃ¢ÂÂ«Ã¯Â¸Â (@howroute) March 1, 2020 Quarantines are in place at the Life Care Center in WA. A senior care center is the last place we want to see this virus. x BREAKING: Resident and worker at Life Care Center of Kirkland diagnosed with #coronavirus. Center says residents and workers who were possibly exposed are being monitored closely and in some cases quarantined. All visits from family not allowed. Extra help on the way. #COVID19 pic.twitter.com/CEX2OaeDUL Ã¢ÂÂ Ted Land (@TedLandK5) February 29, 2020 Gene Sequencing Scientists have been sequencing the genomes of the virus at an unprecedented rate and making the results openly available to other researchers. As of Saturday evening, 134 samples have been sequenced. This enables tracing the origins of the virus, tracking its movement across the globe and developing treatments. x We've updated https://t.co/zRj0X72j64 with 5 new #SARSCoV2 genomes from the #COVID19 pandemic from Japan, China and Canada bringing the worldwide total up to 134(!). 1/4 pic.twitter.com/XSY0RVdwNp Ã¢ÂÂ Nextstrain (@nextstrain) February 29, 2020 Here is an example of the detective work done by scientists in tracing the spread of the virus - x "Preliminary Case Report on the #SARSCoV2 #COVID19 Cluster in the UK, France & Spain"

At least 21 Britons were exposed to #coronavirus in French Ski Resort - 13 were infected, w cases in England, France, & Spain.

I compiled all we know about the cases Ã¢Â¬ÂÃ¯Â¸ÂÃ°ÂÂ§Â¬https://t.co/KDn2GRZm4b pic.twitter.com/AiJGzSRy5L Ã¢ÂÂ Dr Emma Hodcroft (@firefoxx66) February 27, 2020 Corona virus in Brazil sequenced and analyzed within 48 hours after detection. Traced back to Italy and Bavaria. x Brazil/SPBR1/2020 genome of #coronavirus differs by 3 mutations to the Wuhan-Hu-1 strain. 2 of these mutations are shared with its closest sequence from a patient from Munich, Germany#covid19 https://t.co/12fZLZGqIK Ã¢ÂÂ Aleksandra StÃÂplowska (@stepelka) February 28, 2020 Here is a visualization of the workings of the COVID-19 virus - x It was great to work with @McLellan_Lab who recently mapped the first 3D atomic-scale map of the COVID-19 Spike protein (The part of the COVID-19 virus that attaches to and infects human cells) This image shows the initial step in COVID-19 infection #COVID2019 #SARSCoV2 pic.twitter.com/N0JwX7EAZb Ã¢ÂÂ NEXU Science Communication (@NEXUCreative) February 28, 2020 One of several vaccines under development is ready for testing. Gilead and NIH have also begun clinical testing of an antiviral drug called remdesivir that had been developed for Ebola. x Moderna Therapeutics, a biotech company based in Cambridge, Mass., has shipped the first batches of its COVID-19 vaccine https://t.co/lQQGaF97WD Ã¢ÂÂ TIME (@TIME) February 27, 2020 But it is still a long way (6-18 months) before vaccines will be ready for widespread use. Click on the tweet below to study the excellent illustration of the Coronavirus. x Vaccines against SARS-CoV-2 will be very important. But don't get fooled by press releases. To get them will take time. Here is the overview again that I posted some time ago. pic.twitter.com/9IvmPut9I1 Ã¢ÂÂ Florian Krammer (@florian_krammer) March 2, 2020 Epilogue The purpose of this diary is not to scare or to raise anxiety levels. It is meant to keep us informed so that we, as individuals and as communities, can make proper decisions, for ourselves and for others. The ineptness and callousness of the administration does not inspire much confidence, but there are plenty of scientists and health professionals working around the clock analyzing the virus and its spread, educating the public about procedures to avoid getting infected, guiding organizations and the public on what lies ahead, and developing novel treatments and vaccines. Also, take a look at the many excellent diaries at this site that cover day-to-day news of the virus and that have practical tips on precautions and preparedness. I will do a separate diary on preparedness and why it is important, not just for individuals but for society at large. As has been said many times — wash your hands frequently, practice how not to touch your face and avoid hand-shakes and close-contact with other people.

Updates

Snohomish Health District responds to the study -

x Statement on Seattle Flu Study preliminary findings: https://t.co/mJUWujemnl pic.twitter.com/jzWqUwB04z Ã¢ÂÂ SnoHD (@SnoHD) March 1, 2020

The Kirkland senior care center is now under lockdown.

x Coronavirus: Washington state nursing home placed on lockdown #COVID19https://t.co/nGNKZvdwhp Ã¢ÂÂ ÃÂªÃ¡Â´ÂÃÂ´ Ã¡Â´Â Ã¡Â´ÂÃ¡Â´ÂÃ¡Â´ÂÃ¡Â´ÂÃ¡Â´ÂÃÂ, Ã¡Â´ÂÃÂÃ¡Â´Â Ã°ÂÂ¦Â Ã°ÂÂ¤Â§Ã°ÂÂ§Â¬Ã°ÂÂ¥Â¼Ã°ÂÂ¦Â (@MackayIM) March 2, 2020

Firefighters, doctors, nurses, law enforcement — pay a heavier price than the rest of us.