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title authors authorLinks affiliations license licenseLink date dataset abstract
Genomic analysis of COVID-19 spread. Situation report 2020-03-13.
Emma Hodcroft
Nicola Müller
Cassia Wagner
Misja Ilcisin
James Hadfield
Sidney M. Bell
Richard Neher
Trevor Bedford
Fred Hutch, Seattle, USA; Biozentrum, Basel, Switzerland; CZI, CA, USA
CC-BY
2020 March 13
This report uses publicly shared genomic data to track the spread of COVID-19. These reports are updated weekly.

Table of Contents

# Executive summary

Here, we analyzed 410</tag> publicly shared COVID-19 genomes. By comparing these viral genomes to each other, we can characterize how COVID-19 is evolving and moving around the world.

For a current snapshot of the number of coronavirus cases around the world, see [Our World In Data](https://ourworldindata.org/coronavirus).

In this report, we show that the virus is widely circulating across the globe, with evidence of local transmission on multiple continents.
At this time, we urge focus on efforts to slow the spread within communities; travel bans are less likely to be effective.

In this week's updates, we report:  

* COVID-19 is circulating widely across Europe, with significant movement between countries.  

* We identify at least 4 introductions to the UK, some with onward community transmission.  

* There have been a number of travel-related cases linking Iran with other parts of the world.  

* There have been many introductions into the U.S. to date, resulting in local transmission chains in multiple states.  

* The outbreak continues to grow in Washington state; some cases are closely related to those from the Grand Princess cruise ship.  

* There is local circulation of COVID-19 in California.  

* Social distancing measures should be enacted swiftly to ease the burden on healthcare systems and protect the vulnerable.

COVID-19 Resources

We've prepared some resources that are worth reading to familiarize yourself with COVID-19 and the virus that causes it, SARS-CoV-2. This information will make interpreting the data we present in this narrative easier; if you aren't familiar with phylogenetic trees, we encourage you to check out the 'How to Read Phylogenies' narrative and come back when you're ready.


## Background

<div>
  <a href="https://nextstrain.org/help/coronavirus/human-CoV"><img alt="microscopy image of coronaviruses" width="100" src="https://nextstrain.org/static/ncov_narrative-76cfd610d11ef708d213a3170de9519f.png"/> Background on Coronaviruses </a>

  <a href="https://nextstrain.org/help/coronavirus/SARS-CoV-2"><img alt="illustration of a coronavirus" width="100" src="http://data.nextstrain.org/img_nCoV-CDC.jpg"/> Recent COVID-19 Outbreak Background </a>

  <a href="https://nextstrain.org/narratives/trees-background/"><img alt="cartoon of a phylogenetic tree" width="100" src="http://data.nextstrain.org/img_toy_alignment_mini.png"/> How to Read Phylogenies</a>
</div>

## Further Reading

* Summary of the SARS-CoV-2 outbreak on [Wikipedia](https://en.wikipedia.org/wiki/2019%E2%80%9320_Wuhan_coronavirus_outbreak).
* Material provided by the [US CDC](https://www.cdc.gov/coronavirus/index.html).

## Nextstrain narratives

The following pages contain analysis performed using [Nextstrain](https://nextstrain.org).
Scrolling through will reveal paragraphs of text with a corresponding visualization of the genomic data.

To have full genomes of a novel and large RNA virus this quickly is a remarkable achievement.
These analyses have been made possible by the rapid and open sharing of genomic data and interpretations by scientists all around the world (see the final slide for a visualization of sequencing authorship).

A note about sampling

We currently have sequences from samples taken in 30 countries across 5 continents. This is an incredible feat -- sequencing an unknown, large RNA virus in the midst of a pandemic is difficult, and is only possible through the incredible work and timely sharing of data by scientists and physicians around the world.

While this data enables us to infer many useful characteristics of the outbreak and track its spread in real time, it's important to emphasize that our conclusions are limited by the available data.

For example, the map shows very few sequences from the global south. This is NOT because COVID-19 isn't circulating in these areas, or that these cases are not as crucial to understand; rather, we just don't have much data available from these areas. The size of each circle on the map indicates how much data is currently available from that area, rather than the true size of the outbreak.

Circulation across Europe

Here, we see a large clade of sequences from Europe. Notably, sequences from many different countries intercalate, indicating that COVID-19 is already circulating quite widely across Europe.

Zooming in on the map, we see that there are many links between Italy and other areas; however, it is important to keep in mind that the directionality of these links can't always be confidently inferred. Other hypotheses can also explain these data (e.g., if an unsampled case infected both a secondary case sequenced in Italy and a secondary case sequenced elsewhere).

Local transmission in the British Isles & Ireland

Looking at the British Isles & Ireland as an example, we can see several instances where viruses that are closely related to samples from other countries appear in the British Isles & Ireland.

This is consistent with 4 or more introductions from other locations.

We also see instances where after an introduction, there are several closely-related cases from the same location. This is consistent with local community transmission from more than one of these introductions.

Spread of SARS-CoV-2 from Iran

A number of genomes have been sequenced from patients reporting travel history to Iran. These genomes are all extremely similar, and indicate that the outbreak in Iran may be the result of a single transmission which has subsequently been transmitted to many other places.

Note that there are no full genomes available from patients in Iran.

Introductions to the U.S.

Here, we can see that the virus has been introduced to the U.S. on multiple independent occasions.

Most of these introductions aren't associated with any other sampled cases from the U.S., so we're not sure if these introductions led to local outbreaks. However, given that testing capacity is not yet ramped up in most areas, we expect there are many unreported cases.

For Washington and California, though, we do see clusters of cases that are closely related. This suggests ongoing transmission and local spread within these two states.

Spread of SARS-CoV-2 in Washington state

Here, we see a large cluster of cases from Washington that are all closely related. From this, we conclude that there is extensive local spread within Washington state.

Interestingly, the Washington samples intercalate with samples from the Grand Princess cruise ship. We aren't sure yet whether the virus spread from the cruise ship to Washington or the other way around; as we get more data, we'll update our analysis.

Spread of SARS-CoV-2 in California

Looking at samples from California, we see evidence for multiple introductions. More importantly, we see at least one cluster of closely related cases, all sampled in California over a short time period (click on 'Explore the Data' and search for 'CA9' to see on example).

This strongly suggests that there is ongoing local transmission within California.

Takeaways

  • The virus has been introduced to many parts of the globe multiple times. Not all introductions result in local transmission.


  • We see evidence of local transmission across Europe, parts of the United States, China, and Southeast Asia.


  • Controlling local outbreaks through social distancing is crucial to protect the vulnerable.
# What you can do  

Social distancing -- that is, decreasing the number of people you encounter each day -- can be challenging, but is hugely beneficial to the public good.  
 If everyone decreased their daily contacts by 25%, we would expect to see a 50% decrease in the cumulative number of cases over the next month ([Klein et al., 2020-03-13](https://institutefordiseasemodeling.github.io/COVID-public/reports/Working%20paper%20%E2%80%93%20model-based%20estimates%20of%20COVID-19%20burden%20in%20King%20and%20Snohomish%20counties%20through%20April%207.pdf)). Not sure what social distancing means? [Check out this helpful guide](https://www.theatlantic.com/family/archive/2020/03/coronavirus-what-does-social-distancing-mean/607927/).
<div>
  <img src="https://github.com/nextstrain/narratives/raw/master/figures/social-distancing-efficacy.png" width="70%">
</div>

## Steps individuals can take
* Reduce the number of people you are in contact with each day, especially if you are in a vulnerable group (e.g., seniors and those with pre-existing conditions).
* Remember that even if you are not super vulnerable, many people around you are; follow these practices to protect others.
* Wash your hands "like you just chopped a jalapeno and have to change a contact lens".  
* Stay home if you are sick; be prepared with a few extra supplies in case you need to self-quarantine.  
* If you are an employer, encourage your employees to stay home when sick (and financially support them to do so).  

## Steps officials can take  
* Make testing free and broadly available.  
* Put social distancing measures in place.  
* Financially support those impacted by social distancing measures (e.g., hourly workers, those with elder or childcare responsibilities, small businesses, etc.).

FAQs & Misconceptions

We know that a lot of people have questions about COVID-19.

We've set up a guide to try and answer the most frequently asked questions.

The Federation of American Scientists also maintains a great resource for FAQs.

# Further reading  

* "Don't believe the conspiracy theories you hear about coronavirus & HIV" [article](https://massivesci.com/notes/wuhan-coronavirus-ncov-sars-mers-hiv-human-immunodeficiency-virus/) _2020-01-31_

* "Baseless Conspiracy Theories Claim New Coronavirus Was Bioengineered" [article](https://www.factcheck.org/2020/02/baseless-conspiracy-theories-claim-new-coronavirus-was-bioengineered/) _2020-02-07_

* "No, The Wuhan Coronavirus Was Not Genetically Engineered To Put Pieces Of HIV In It" [article](https://www.forbes.com/sites/victoriaforster/2020/02/02/no-coronavirus-was-not-bioengineered-to-put-pieces-of-hiv-in-it/#5d339e8e56cb) _2020-02-02_

* "Busting coronavirus myths" [AFP Fact Check](https://factcheck.afp.com/busting-coronavirus-myths) _2020-02-19_


# Misconceptions

A number of misconceptions have been circulated about the origins of the novel coronavirus.
During outbreaks like this one, the spread of information that's known to be incorrect can lead to more panic, and cause people not to trust scientists and governments, meaning they are less likely to follow advisories and take appropriate precautions.

In an effort to try and explain why these views are incorrect, scientists have addressed these theories at the pages below:

<div>

  <a href="http://virological.org/t/ncovs-relationship-to-bat-coronaviruses-recombination-signals-no-snakes-no-evidence-the-2019-ncov-lineage-is-recombinant/331"><img alt="picture of a snake" width="100" src="http://data.nextstrain.org/img_snake-freeToUse.jpg"/> 'Snake' Origins of SARS-CoV-2 (Technical) </a>
  <a href="https://twitter.com/trvrb/status/1223666856923291648"><img alt="illustration of HIV" width="100" src="http://data.nextstrain.org/img_HIV-wiki.jpg"/> 'HIV Engineering' Idea (Twitter thread)</a>


</div>

Scientific credit

We would like to acknowledge the amazing and timely work done by all scientists involved in this outbreak, and particularly those working in China. Only through the rapid sharing of genomic data and metadata are analyses such as these possible.


We also gratefully acknowledge GISAID for providing the platform through which these data can be uploaded and shared.


We are grateful for the data gathered by these originating labs:

* Arizona Department of Health Services
* Auckland Hospital
* BCCDC Public Health Laboratory
* Bamrasnaradura Hospital
* Bundeswehr Institute of Microbiology
* CNR Virus des Infections Respiratoires - France SUD
* CR&WISCO GENERAL HOSPITAL
* California Department of Health
* California Department of Public Health
* Center of Medical Microbiology, Virology, and Hospital Hygiene
* Center of Medical Microbiology, Virology, and Hospital Hygiene, University of Duesseldorf
* Centers for Disease Control, R.O.C. (Taiwan)
* Centre for Human and Zoonotic Virology (CHAZVY), College of Medicine University of Lagos/Lagos University Teaching Hospital (LUTH), part of the Laboratory Network of the Nigeria Centre for Disease Control (NCDC)
* Centre for Infectious Diseases and Microbiology - Public Health
* Centre for Infectious Diseases and Microbiology Laboratory Services
* Centro Hospital do Porto, E.P.E. - H. Geral de Santo Antonio
* Centro Hospitalar e Universitario de Sao Joao, Porto
* Charite Universitatsmedizin Berlin, Institute of Virology; Institut fur Mikrobiologie der Bundeswehr, Munich
* Department of Infectious Diseases, Istituto Superiore di Sanita, Roma , Italy
* Department of Infectious and Tropical Diseases, Bichat Claude Bernard Hospital, Paris
* Department of Internal Medicine, Triemli Hospital
* Department of Laboratory Medicine, National Taiwan University Hospital
* Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University
* Department of Pathology, Toshima Hospital
* Department of Virology III, National Institute of Infectious Diseases
* Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Huslab Finland
* Department of microbiology laboratory,Anhui Provincial Center for Disease Control and Prevention
* Dept. of Pathology, National Institute of Infectious Diseases
* Dept. of Virology III, National Institute of Infectious Diseases
* Dienst Gezondheid & Jeugd Zuid-Holland Zuid
* Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine
* Division of Infectious Diseases, University Hospital Zurich
* Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Diseases Control and Prevention
* Dutch COVID-19 response team
* ErasmusMC
* Foundation Elisabeth-Tweesteden Ziekenhuis
* Foundation Pamm
* Fujian Center for Disease Control and Prevention
* General Hospital of Central Theater Command of People's Liberation Army of China
* Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Public Health
* Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provinical Public Health
* Guangdong Provincial Center for Diseases Control and Prevention;Guangdong Provincial Institute of Public Health
* Guangdong Provincial Institution of Public Health, Guangdong Provinical Center for Disease Control and Prevention
* HUS Diagnostiikkakeskus, Hallinto
* Hangzhou Center for Disease Control and Prevention
* Hangzhou Center for Disease and Control Microbiology Lab
* Harborview Medical Center
* Hong Kong Department of Health
* Hospital Israelita Albert Einstein
* IL Department of Public Health Chicago Laboratory
* INMI Lazzaro Spallanzani IRCCS
* Indian Council of Medical Research - National Institute of Virology
* Indian Council of Medical Research-National Institute of Virology
* Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
* Institute of Viral Disease Control and Prevention, China CDC
* Instituto Nacional de Enfermedades Respiratorias
* KU Leuven, Clinical and Epidemiological Virology
* Klinik Hirslanden Zurich
* Korea Centers for Disease Control & Prevention (KCDC) Center for Laboratory Control of Infectious Diseases Division of Viral Diseases
* Laboratoire National de Sante
* Laboratoire de Virologie, HUG
* Laboratorio di Microbiologia e Virologia, Universita Vita-Salute San Raffaele, Milano
* Laboratory Medicine
* Lapland Central Hospital
* MHC Brabant Zuidoost
* MHC Drente
* MHC Flevoland
* MHC Gooi & Vechtstreek
* MHC Haaglanden
* MHC Kennemerland
* MHC Rotterdam-Rijnmond
* MHC Utrecht
* MHC West-Brabant
* MSHS Clinical Microbiology Laboratories
* Massachusetts Department of Public Health
* Monash Medical Centre
* NHC Key laboratory of Enteric Pathogenic Microbiology, Institute of Pathogenic Microbiology
* National Centre for Infectious Diseases
* National Influenza Center - National Institute of Hygiene and Epidemiology (NIHE)
* National Influenza Centre, National Public Health Laboratory, Kathmandu, Nepal
* National Institute for Viral Disease Control and Prevention, China CDC
* National Public Health Laboratory
* National Public Health Laboratory, National Centre for Infectious Diseases
* Pathology Queensland
* Providence Regional Medical Center
* Public Health Ontario Laboratory
* RIVM
* Respiratory Virus Unit, Microbiology Services Colindale, Public Health England
* Seattle Flu Study
* Serology, Virology and OTDS Laboratories (SAViD), NSW Health Pathology Randwick
* Servicio Microbiologia. Hospital Clinico Universitario. Valencia.
* Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
* Singapore General Hospital
* Sorbonne Universite, Inserm et Assistance Publique-Hopitaux de Paris (Pitie Salpetriere)
* State Health Office Baden-Wuerttemberg
* Taiwan Centers for Disease Control
* Texas Department of State Health Services
* The Central Hospital Of Wuhan
* The National Institute of Public Health Center for Epidemiology and Microbiology
* The University of Hong Kong - Shenzhen Hospital
* Tianmen Center for Disease Control and Prevention
* UCD National Virus Reference Laboratory
* University of Washington Virology Lab
* Union Hospital of Tongji Medical College, Huazhong University of Science and Technology
* Valley Medical Center
* Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust
* Virology Unit, Institut Pasteur du Cambodge.
* Wales Specialist Virology Centre
* Washington State Department of Health
* Washington State Public Health Lab
* Weifang Center for Disease Control and Prevention
* West of Scotland Specialist Virology Centre, NHSGGC
* Wisconsin Department of Health Services
* Wuhan Fourth Hospital
* Wuhan Jinyintan Hospital
* Wuhan Lung Hospital
* Yongchuan District Center for Disease Control and Prevention
* Zhejiang Provincial Center for Disease Control and Prevention
* Zhongxian Center for Disease Control and Prevention

Detailed scientific credit

These data were shared via GISAID. We gratefully acknowledge their contributions.


To the right we give specific sequences shared by each lab.


The SARS-CoV-2 genomes were generously shared by scientists at these submitting labs:
* Arizona Department of Health Services
	* USA/AZ1/2020

* Auckland Hospital
	* NewZealand/01/2020

* BCCDC Public Health Laboratory
	* Canada/BC_37_0-2/2020

* Bamrasnaradura Hospital
	* Nonthaburi/61/2020
	* Nonthaburi/74/2020

* Beijing Institute of Microbiology and Epidemiology
	* pangolin/Guangdong/P2S/2019
	* pangolin/Guangxi/P1E/2017
	* pangolin/Guangxi/P2V/2017
	* pangolin/Guangxi/P3B/2017
	* pangolin/Guangxi/P4L/2017
	* pangolin/Guangxi/P5E/2017
	* pangolin/Guangxi/P5L/2017

* Bundeswehr Institute of Microbiology
	* Germany/BavPat2/2020
	* Germany/BavPat3/2020

* CNR Virus des Infections Respiratoires - France SUD
	* France/RA739/2020

* CR&WISCO GENERAL HOSPITAL
	* Wuhan/HBCDC-HB-05/2020

* California Department of Health
	* USA/CA3/2020
	* USA/CA4/2020
	* USA/CA5/2020

* California Department of Public Health
	* USA/CA-CDPH-UC1/2020
	* USA/CA-CDPH-UC2/2020
	* USA/CA-CDPH-UC3/2020
	* USA/CA-CDPH-UC4/2020
	* USA/CA-CDPH-UC5/2020
	* USA/CA-CDPH-UC6/2020
	* USA/CA-CDPH-UC7/2020
	* USA/CA-CDPH-UC8/2020
	* USA/CA-CDPH-UC9/2020
	* USA/CA1/2020
	* USA/CA2/2020
	* USA/CA6/2020
	* USA/CA7/2020
	* USA/CA8/2020
	* USA/CA9/2020
	* USA/UC-CDPH-UC11/2020

* Center of Medical Microbiology, Virology, and Hospital Hygiene
	* Germany/NRW-01/2020
	* Germany/NRW-02-1/2020
	* Germany/NRW-03/2020
	* Germany/NRW-04/2020

* Center of Medical Microbiology, Virology, and Hospital Hygiene, University of Duesseldorf
	* Germany/NRW-011/2020
	* Germany/NRW-05/2020
	* Germany/NRW-06/2020
	* Germany/NRW-07/2020
	* Germany/NRW-08/2020
	* Germany/NRW-09/2020
	* Germany/NRW-10/2020

* Centers for Disease Control, R.O.C. (Taiwan)
	* Taiwan/2/2020

* Centre for Human and Zoonotic Virology (CHAZVY), College of Medicine University of Lagos/Lagos University Teaching Hospital (LUTH), part of the Laboratory Network of the Nigeria Centre for Disease Control (NCDC)
	* Nigeria/Lagos01/2020

* Centre for Infectious Diseases and Microbiology - Public Health
	* Australia/NSW10/2020
	* Australia/NSW12/2020
	* Australia/NSW13/2020
	* Australia/NSW14/2020

* Centre for Infectious Diseases and Microbiology Laboratory Services
	* Australia/NSW01/2020
	* Australia/NSW05/2020
	* Australia/NSW06/2020
	* Australia/NSW07/2020
	* Australia/NSW08/2020
	* Australia/NSW09/2020
	* Sydney/2/2020

* Centre for Infectious Diseases and Microbiology- Public Health
	* Australia/NSW11/2020

* Centro Hospital do Porto, E.P.E. - H. Geral de Santo Antonio
	* Portugal/CV62/2020

* Centro Hospitalar e Universitario de Sao Joao, Porto
	* Portugal/CV63/2020

* Charite Universitatsmedizin Berlin, Institute of Virology; Institut fur Mikrobiologie der Bundeswehr, Munich
	* Germany/BavPat1/2020

* Department of Infectious Diseases, Istituto Superiore di Sanita, Roma , Italy
	* Italy/CDG1/2020

* Department of Infectious Diseases, Istituto Superiore di Sanita, Rome, Italy
	* Italy/SPL1/2020

* Department of Infectious and Tropical Diseases, Bichat Claude Bernard Hospital, Paris
	* France/IDF0372-isl/2020
	* France/IDF0372/2020
	* France/IDF0373/2020
	* France/IDF0386-islP1/2020
	* France/IDF0386-islP3/2020
	* France/IDF0515-isl/2020
	* France/IDF0515/2020
	* France/IDF0571/2020

* Department of Internal Medicine, Triemli Hospital
	* Switzerland/1000477102/2020
	* Switzerland/1000477377/2020

* Department of Laboratory Medicine, National Taiwan University Hospital
	* Taiwan/NTU01/2020
	* Taiwan/NTU02/2020
	* Taiwan/NTU03/2020

* Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University
	* SouthKorea/KUMC01/2020
	* SouthKorea/KUMC02/2020
	* SouthKorea/KUMC04/2020
	* SouthKorea/KUMC06/2020

* Department of Pathology, Toshima Hospital
	* Japan/TK/20-31-3/2020

* Department of Virology III, National Institute of Infectious Diseases
	* Japan/AI/I-004/2020

* Department of Virology and Immunology, University of Helsinki and Helsinki University Hospital, Huslab Finland
	* Finland/FIN01032020/2020
	* Finland/FIN03032020A/2020
	* Finland/FIN03032020B/2020
	* Finland/FIN03032020C/2020

* Department of microbiology laboratory,Anhui Provincial Center for Disease Control and Prevention
	* Anhui/SZ005/2020

* Dept. of Pathology, National Institute of Infectious Diseases
	* Japan/NA-20-05-1/2020
	* Japan/OS-20-07-1/2020

* Dept. of Virology III, National Institute of Infectious Diseases
	* Japan/KY-V-029/2020
	* Japan/TY-WK-012/2020
	* Japan/TY-WK-501/2020
	* Japan/TY-WK-521/2020

* Dienst Gezondheid & Jeugd Zuid-Holland Zuid
	* Netherlands/Hardinxveld_Giessendam_1364806/2020

* Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine
	* SouthKorea/KUMC03/2020
	* SouthKorea/KUMC05/2020

* Division of Infectious Diseases, University Hospital Zurich
	* Switzerland/1000477796/2020
	* Switzerland/1000477797/2020
	* Switzerland/1000477806/2020

* Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Diseases Control and Prevention
	* SouthKorea/KCDC05/2020
	* SouthKorea/KCDC06/2020
	* SouthKorea/KCDC07/2020
	* SouthKorea/KCDC12/2020
	* SouthKorea/KCDC24/2020

* Dutch COVID-19 response team
	* Netherlands/Gelderland_1/2020
	* Netherlands/Limburg_2/2020
	* Netherlands/Limburg_3/2020
	* Netherlands/Limburg_4/2020
	* Netherlands/Limburg_5/2020
	* Netherlands/Limburg_6/2020
	* Netherlands/NoordBrabant_1/2020
	* Netherlands/NoordBrabant_10/2020
	* Netherlands/NoordBrabant_11/2020
	* Netherlands/NoordBrabant_12/2020
	* Netherlands/NoordBrabant_13/2020
	* Netherlands/NoordBrabant_14/2020
	* Netherlands/NoordBrabant_15/2020
	* Netherlands/NoordBrabant_16/2020
	* Netherlands/NoordBrabant_17/2020
	* Netherlands/NoordBrabant_18/2020
	* Netherlands/NoordBrabant_19/2020
	* Netherlands/NoordBrabant_2/2020
	* Netherlands/NoordBrabant_20/2020
	* Netherlands/NoordBrabant_21/2020
	* Netherlands/NoordBrabant_22/2020
	* Netherlands/NoordBrabant_23/2020
	* Netherlands/NoordBrabant_24/2020
	* Netherlands/NoordBrabant_25/2020
	* Netherlands/NoordBrabant_26/2020
	* Netherlands/NoordBrabant_27/2020
	* Netherlands/NoordBrabant_28/2020
	* Netherlands/NoordBrabant_29/2020
	* Netherlands/NoordBrabant_3/2020
	* Netherlands/NoordBrabant_30/2020
	* Netherlands/NoordBrabant_31/2020
	* Netherlands/NoordBrabant_32/2020
	* Netherlands/NoordBrabant_33/2020
	* Netherlands/NoordBrabant_34/2020
	* Netherlands/NoordBrabant_35/2020
	* Netherlands/NoordBrabant_36/2020
	* Netherlands/NoordBrabant_37/2020
	* Netherlands/NoordBrabant_38/2020
	* Netherlands/NoordBrabant_39/2020
	* Netherlands/NoordBrabant_4/2020
	* Netherlands/NoordBrabant_5/2020
	* Netherlands/NoordBrabant_6/2020
	* Netherlands/NoordHolland_1/2020
	* Netherlands/NoordHolland_2/2020
	* Netherlands/Overijssel_1/2020
	* Netherlands/Overijssel_2/2020
	* Netherlands/Utrecht_1/2020
	* Netherlands/Utrecht_10/2020
	* Netherlands/Utrecht_11/2020
	* Netherlands/Utrecht_12/2020
	* Netherlands/Utrecht_13/2020
	* Netherlands/Utrecht_14/2020
	* Netherlands/Utrecht_15/2020
	* Netherlands/Utrecht_16/2020
	* Netherlands/Utrecht_2/2020
	* Netherlands/Utrecht_3/2020
	* Netherlands/Utrecht_4/2020
	* Netherlands/Utrecht_5/2020
	* Netherlands/Utrecht_6/2020
	* Netherlands/Utrecht_7/2020
	* Netherlands/Utrecht_8/2020
	* Netherlands/ZuidHolland_1/2020
	* Netherlands/ZuidHolland_10/2020
	* Netherlands/ZuidHolland_11/2020
	* Netherlands/ZuidHolland_13/2020
	* Netherlands/ZuidHolland_14/2020
	* Netherlands/ZuidHolland_15/2020
	* Netherlands/ZuidHolland_16/2020
	* Netherlands/ZuidHolland_17/2020
	* Netherlands/ZuidHolland_18/2020
	* Netherlands/ZuidHolland_19/2020
	* Netherlands/ZuidHolland_2/2020
	* Netherlands/ZuidHolland_20/2020
	* Netherlands/ZuidHolland_21/2020
	* Netherlands/ZuidHolland_22/2020
	* Netherlands/ZuidHolland_23/2020
	* Netherlands/ZuidHolland_24/2020
	* Netherlands/ZuidHolland_5/2020
	* Netherlands/ZuidHolland_6/2020
	* Netherlands/ZuidHolland_7/2020
	* Netherlands/ZuidHolland_8/2020
	* Netherlands/ZuidHolland_9/2020

* ErasmusMC
	* Netherlands/Nieuwendijk_1363582/2020
	* Netherlands/Rotterdam_1363790/2020

* Foundation Elisabeth-Tweesteden Ziekenhuis
	* Netherlands/Tilburg_1363354/2020
	* Netherlands/Tilburg_1364286/2020

* Foundation Pamm
	* Netherlands/Berlicum_1363564/2020

* Fujian Center for Disease Control and Prevention
	* Fujian/13/2020
	* Fujian/8/2020

* General Hospital of Central Theater Command of People's Liberation Army of China
	* Wuhan/WH01/2019
	* Wuhan/WH02/2019
	* Wuhan/WH03/2020
	* Wuhan/WH04/2020

* Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provincial Public Health
	* Foshan/20SF207/2020
	* Foshan/20SF210/2020
	* Foshan/20SF211/2020
	* Guangdong/20SF012/2020
	* Guangdong/20SF013/2020
	* Guangdong/20SF014/2020
	* Guangdong/20SF025/2020
	* Guangdong/20SF028/2020
	* Guangdong/20SF040/2020

* Guangdong Provincial Center for Diseases Control and Prevention; Guangdong Provinical Public Health
	* Guangdong/20SF174/2020
	* Guangzhou/20SF206/2020

* Guangdong Provincial Center for Diseases Control and Prevention;Guangdong Provincial Institute of Public Health
	* Guangdong/20SF201/2020

* Guangdong Provincial Institution of Public Health, Guangdong Provinical Center for Disease Control and Prevention
	* Guangdong/2020XN4239-P0034/2020
	* Guangdong/2020XN4243-P0035/2020
	* Guangdong/2020XN4273-P0036/2020
	* Guangdong/2020XN4276-P0037/2020
	* Guangdong/2020XN4291-P0038/2020
	* Guangdong/2020XN4373-P0039/2020
	* Guangdong/2020XN4433-P0040/2020
	* Guangdong/2020XN4448-P0002/2020
	* Guangdong/2020XN4459-P0041/2020
	* Guangdong/2020XN4475-P0042/2020
	* Guangdong/DG-S2-P0054/2020
	* Guangdong/DG-S41-P0056/2020
	* Guangdong/DG-S6-P0055/2020
	* Guangdong/DG-S9-P0045/2020
	* Guangdong/FS-S29-P0051/2020
	* Guangdong/FS-S30-P0052/2020
	* Guangdong/FS-S34-P0015/2020
	* Guangdong/FS-S42-P0046/2020
	* Guangdong/FS-S48-P0047/2020
	* Guangdong/FS-S50-P0053/2020
	* Guangdong/GD2020012-P0022/2020
	* Guangdong/GD2020016-P0011/2020
	* Guangdong/GD2020080-P0010/2020
	* Guangdong/GD2020085-P0043/2020
	* Guangdong/GD2020086-P0021/2020
	* Guangdong/GD2020087-P0008/2020
	* Guangdong/GD2020115-P0009/2020
	* Guangdong/GD2020134-P0031/2020
	* Guangdong/GD2020139-P0007/2020
	* Guangdong/GD2020227-P0029/2020
	* Guangdong/GD2020233-P0027/2020
	* Guangdong/GD2020234-P0023/2020
	* Guangdong/GD2020241-P0013/2020
	* Guangdong/GD2020246-P0028/2020
	* Guangdong/GD2020258-P0018/2020
	* Guangdong/GDFS2020052-P0025/2020
	* Guangdong/GDFS2020054-P0005/2020
	* Guangdong/GDFS2020056-P0044/2020
	* Guangdong/GDFS2020127-P0026/2020
	* Guangdong/GDSZ202004-P0004/2020
	* Guangdong/GDSZ202008-P0020/2020
	* Guangdong/GDSZ202009-P0032/2020
	* Guangdong/GDSZ202013-P0014/2020
	* Guangdong/GDSZ202015-P0019/2020
	* Guangdong/GZ-S6-P0050/2020
	* Guangdong/JM-S1-P0062/2020
	* Guangdong/MM-S1-P0048/2020
	* Guangdong/SZ-N128-P0057/2020
	* Guangdong/SZ-N59-P0049/2020
	* Guangdong/ZH-N22-P0059/2020
	* Guangdong/ZH-S33-P0058/2020
	* Guangdong/ZQ-S2-P0061/2020
	* Guangdong/ZS-S6-P0060/2020

* HUS Diagnostiikkakeskus, Hallinto
	* Finland/FIN-25/2020

* Hangzhou Center for Disease Control and Prevention
	* Hangzhou/HZCDC0001/2020

* Hangzhou Center for Disease and Control Microbiology Lab
	* Hangzhou/HZ-1/2020

* Harborview Medical Center
	* USA/WA3-UW1/2020
	* USA/WA9-UW6/2020

* Hong Kong Department of Health
	* HongKong/VB20024950/2020
	* HongKong/VB20026565/2020
	* HongKong/VM20001061/2020
	* HongKong/case42_VM20002493/2020
	* HongKong/case48_VM20002507/2020
	* HongKong/case52_VM20002582/2020
	* HongKong/case78_VM20002849/2020
	* HongKong/case85_VM20002868/2020
	* HongKong/case90_VM20002907/2020
	* canine/HongKong/20-02756/2020

* Hospital Israelita Albert Einstein
	* Brazil/SPBR-01/2020
	* Brazil/SPBR-02/2020
	* Brazil/SPBR-03/2020

* Hospital Sao Joaquim Beneficencia Portuguesa
	* Brazil/SPBR-04/2020
	* Brazil/SPBR-05/2020
	* Brazil/SPBR-06/2020

* IL Department of Public Health Chicago Laboratory
	* USA/IL1/2020
	* USA/IL2/2020

* INMI Lazzaro Spallanzani IRCCS
	* Italy/INMI1-cs/2020
	* Italy/INMI1-isl/2020

* Indian Council of Medical Research - National Institute of Virology
	* India/1-27/2020

* Indian Council of Medical Research-National Institute of Virology
	* India/1-31/2020

* Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College
	* Wuhan/IPBCAMS-WH-01/2019
	* Wuhan/IPBCAMS-WH-02/2019
	* Wuhan/IPBCAMS-WH-03/2019
	* Wuhan/IPBCAMS-WH-04/2019
	* Wuhan/IPBCAMS-WH-05/2020

* Institute of Viral Disease Control and Prevention, China CDC
	* Wuhan/IVDC-HB-envF13-20/2020
	* Wuhan/IVDC-HB-envF13-21/2020
	* Wuhan/IVDC-HB-envF13/2020
	* Wuhan/IVDC-HB-envF54/2020

* Instituto Nacional de Enfermedades Respiratorias
	* Mexico/CDMX/InDRE_01/2020

* Jingzhou Center for Disease Control and Prevention
	* Jingzhou/HBCDC-HB-01/2020

* KU Leuven, Clinical and Epidemiological Virology
	* Belgium/GHB-03021/2020

* Klinik Hirslanden Zurich
	* Switzerland/1000477757/2020

* Korea Centers for Disease Control & Prevention (KCDC) Center for Laboratory Control of Infectious Diseases Division of Viral Diseases
	* SouthKorea/KCDC03/2020

* Laboratoire National de Sante
	* Luxembourg/Lux1/2020

* Laboratoire de Virologie, HUG
	* Switzerland/AG0361/2020
	* Switzerland/BL0902/2020
	* Switzerland/GE3121/2020
	* Switzerland/GE3895/2020
	* Switzerland/GE5373/2020
	* Switzerland/GE9586/2020
	* Switzerland/TI9486/2020
	* Switzerland/VD5615/2020

* Laboratorio di Microbiologia e Virologia, Universita Vita-Salute San Raffaele, Milano
	* Italy/UniSR1/2020

* Laboratory Medicine
	* Taiwan/CGMH-CGU-01/2020

* Lapland Central Hospital
	* Finland/1/2020

* MHC Brabant Zuidoost
	* Netherlands/Eindhoven_1363782/2020

* MHC Drente
	* Netherlands/Dalen_1363624/2020

* MHC Flevoland
	* Netherlands/Zeewolde_1365080/2020

* MHC Gooi & Vechtstreek
	* Netherlands/Blaricum_1364780/2020
	* Netherlands/Naarden_1364774/2020

* MHC Haaglanden
	* Netherlands/Nootdorp_1364222/2020

* MHC Hart voor Brabant
	* Netherlands/Oisterwijk_1364072/2020

* MHC Kennemerland
	* Netherlands/Haarlem_1363688/2020

* MHC Rotterdam-Rijnmond
	* Netherlands/Rotterdam_1364040/2020

* MHC Utrecht
	* Netherlands/Utrecht_1363564/2020
	* Netherlands/Utrecht_1363628/2020
	* Netherlands/Utrecht_1364066/2020

* MHC West-Brabant
	* Netherlands/Andel_1365066/2020
	* Netherlands/Helmond_1363548/2020

* MSHS Clinical Microbiology Laboratories
	* USA/NY1-PV08001/2020

* Massachusetts Department of Public Health
	* USA/MA1/2020

* Monash Medical Centre
	* Australia/VIC01/2020

* NHC Key laboratory of Enteric Pathogenic Microbiology, Institute of Pathogenic Microbiology
	* Jiangsu/JS01/2020
	* Jiangsu/JS02/2020
	* Jiangsu/JS03/2020

* National Centre for Infectious Diseases
	* Singapore/12/2020
	* Singapore/13/2020
	* Singapore/14/2020
	* Singapore/3/2020
	* Singapore/4/2020

* National Influenza Center - National Institute of Hygiene and Epidemiology (NIHE)
	* Vietnam/VR03-38142/2020

* National Influenza Centre, National Public Health Laboratory, Kathmandu, Nepal
	* Nepal/61/2020

* National Institute for Viral Disease Control and Prevention, China CDC
	* Beijing/IVDC-BJ-005/2020
	* Chongqing/IVDC-CQ-001/2020
	* Henan/IVDC-HeN-002/2020
	* Jiangsu/IVDC-JS-001/2020
	* Jiangxi/IVDC-JX-002/2020
	* Shandong/IVDC-SD-001/2020
	* Shanghai/IVDC-SH-001/2020
	* Sichuan/IVDC-SC-001/2020
	* Wuhan/IVDC-HB-01/2019
	* Wuhan/IVDC-HB-04/2020
	* Wuhan/IVDC-HB-05/2019
	* Yunnan/IVDC-YN-003/2020

* National Public Health Laboratory
	* Singapore/11/2020

* National Public Health Laboratory, National Centre for Infectious Diseases
	* Singapore/10/2020
	* Singapore/7/2020
	* Singapore/8/2020
	* Singapore/9/2020

* Pathology Queensland
	* Australia/QLD01/2020
	* Australia/QLD02/2020
	* Australia/QLD03/2020
	* Australia/QLD04/2020
	* Australia/QLD09/2020

* Providence Regional Medical Center
	* USA/WA1/2020

* Public Health Ontario Laboratory
	* Canada/ON-PHL2445/2020
	* Canada/ON-VIDO-01/2020

* RIVM
	* Netherlands/Delft_1363424/2020
	* Netherlands/Diemen_1363454/2020
	* Netherlands/Loon_op_zand_1363512/2020
	* Netherlands/Oss_1363500/2020
	* NetherlandsL/Houten_1363498/2020

* Respiratory Virus Unit, Microbiology Services Colindale, Public Health England
	* England/01/2020
	* England/02/2020
	* England/09c/2020
	* England/200641094/2020
	* England/200690245/2020
	* England/200690300/2020
	* England/200690306/2020
	* England/200690756/2020
	* England/200940527/2020
	* England/200960041/2020
	* England/200960515/2020
	* England/200981386/2020
	* England/200990002/2020
	* England/200990006/2020
	* England/200990660/2020
	* England/200990723/2020
	* England/200990724/2020
	* England/200990725/2020
	* England/200991076/2020
	* England/201000003/2020
	* England/201040081/2020
	* England/201040141/2020

* Seattle Flu Study
	* USA/WA-S2/2020
	* USA/WA-S3/2020

* Second Hospital of Anhui Medical University
	* Hefei/2/2020

* Serology, Virology and OTDS Laboratories (SAViD), NSW Health Pathology Randwick
	* Sydney/3/2020

* Servicio Microbiologia. Hospital Clinico Universitario. Valencia.
	* Spain/Valencia1/2020
	* Spain/Valencia2/2020

* Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital
	* Shenzhen/SZTH-002/2020
	* Shenzhen/SZTH-003/2020
	* Shenzhen/SZTH-004/2020

* Shenzhen Third People's Hospital
	* Shenzhen/SZTH-001/2020

* Singapore General Hospital
	* Singapore/1/2020
	* Singapore/2/2020

* Singapore General Hospital, Molecular Laboratory, Division of Pathology
	* Singapore/5/2020
	* Singapore/6/2020

* Sorbonne Universite, Inserm et Assistance Publique-Hopitaux de Paris (Pitie Salpetriere)
	* France/IDF0626/2020

* South China Agricultural University
	* pangolin/Guandong/1/2019

* State Health Office Baden-Wuerttemberg
	* Germany/Baden-Wuerttemberg-1/2020

* Taiwan Centers for Disease Control
	* Taiwan/3/2020
	* Taiwan/4/2020

* Texas Department of State Health Services
	* USA/TX1/2020

* The Central Hospital Of Wuhan
	* Wuhan/HBCDC-HB-02/2020

* The National Institute of Public Health Center for Epidemiology and Microbiology
	* CzechRepublic/951/2020

* The University of Hong Kong - Shenzhen Hospital
	* Shenzhen/HKU-SZ-002/2020
	* Shenzhen/HKU-SZ-005/2020

* Tianmen Center for Disease Control and Prevention
	* Tianmen/HBCDC-HB-07/2020

* UCD National Virus Reference Laboratory
	* Ireland/COR-20134/2020

* UW Virology Lab
	* USA/WA-UW15/2020
	* USA/WA-UW16/2020
	* USA/WA-UW17/2020
	* USA/WA-UW18/2020
	* USA/WA-UW19/2020
	* USA/WA-UW20/2020
	* USA/WA-UW21/2020
	* USA/WA11-UW7/2020
	* USA/WA12-UW8/2020
	* USA/WA13-UW9/2020
	* USA/WA14-UW10/2020
	* USA/WA15-UW11/2020
	* USA/WA16-UW12/2020
	* USA/WA17-UW13/2020
	* USA/WA18-UW14/2020

* Union Hospital of Tongji Medical College, Huazhong University of Science and Technology
	* Wuhan/HBCDC-HB-03/2020
	* Wuhan/HBCDC-HB-04/2020

* Unknown
	* Netherlands/Coevorden_1363618/2020

* Valley Medical Center
	* USA/WA8-UW5/2020

* Virology Department, Sheffield Teaching Hospitals NHS Foundation Trust
	* England/Sheff01/2020
	* England/Sheff02/2020

* Virology Unit, Institut Pasteur du Cambodge.
	* Cambodia/0012/2020

* WA State Department of Health
	* USA/WA1-A12/2020

* Wales Specialist Virology Centre
	* Wales/PHW03/2020
	* Wales/PHW05/2020
	* Wales/PHW1/2020
	* Wales/PHW2/2020

* Washington State Department of Health
	* USA/WA1-F6/2020
	* USA/WA2/2020

* Washington State Public Health Lab
	* USA/WA4-UW2/2020
	* USA/WA6-UW3/2020
	* USA/WA7-UW4/2020

* Weifang Center for Disease Control and Prevention
	* China/WF0001/2020
	* China/WF0002/2020
	* China/WF0003/2020
	* China/WF0004/2020
	* China/WF0006/2020
	* China/WF0009/2020
	* China/WF0012/2020
	* China/WF0014/2020
	* China/WF0015/2020
	* China/WF0016/2020
	* China/WF0017/2020
	* China/WF0018/2020
	* China/WF0019/2020
	* China/WF0020/2020
	* China/WF0021/2020
	* China/WF0023/2020
	* China/WF0024/2020
	* China/WF0026/2020
	* China/WF0028/2020
	* China/WF0029/2020

* West of Scotland Specialist Virology Centre, NHSGGC
	* Scotland/CVR01/2020
	* Scotland/CVR02/2020
	* Scotland/CVR03/2020
	* Scotland/CVR04/2020
	* Scotland/CVR05/2020

* Wisconsin Department of Health Services
	* USA/WI1/2020

* Wuhan Fourth Hospital
	* Wuhan/WH05/2020

* Wuhan Institute of Virology, Chinese Academy of Sciences
	* bat/Yunnan/RaTG13/2013

* Wuhan Jinyintan Hospital
	* Wuhan/HBCDC-HB-01/2019
	* Wuhan/HBCDC-HB-02/2019
	* Wuhan/HBCDC-HB-03/2019
	* Wuhan/HBCDC-HB-04/2019
	* Wuhan/WIV02/2019
	* Wuhan/WIV04/2019
	* Wuhan/WIV05/2019
	* Wuhan/WIV06/2019
	* Wuhan/WIV07/2019

* Wuhan Lung Hospital
	* Wuhan/HBCDC-HB-06/2020

* Yongchuan District Center for Disease Control and Prevention
	* Chongqing/YC01/2020

* Zhejiang Provincial Center for Disease Control and Prevention
	* Zhejiang/WZ-01/2020
	* Zhejiang/WZ-02/2020

* Zhongxian Center for Disease Control and Prevention
	* Chongqing/ZX01/2020