[magnus]

for the covid outbreak.  

Seriously though,  if you're interested in tracing the spread of the virus around the US, nextstrain just released an analysis on their US findings. 

https://nextstrain.org/narratives/ncov/s...-04-17?n=1

The summary does include the finding that most of the CA cases can be traced back to WA or NYC.  I'm surprised there isn't a 3rd link directly to China given the likely number of travelers between CA and China (or Asia)

[magnus]

for the covid outbreak.  

Seriously though,  if you're interested in tracing the spread of the virus around the US, nextstrain just released an analysis on their US findings. 

https://nextstrain.org/narratives/ncov/s...-04-17?n=1

The summary does include the finding that most of the CA cases can be traced back to WA or NYC.  I'm surprised there isn't a 3rd link directly to China given the likely number of travelers between CA and China (or Asia)

[M T]

Regarding the nexstrain link you posted, dig deeper at this link.
Note the earlier California yellow circles at the bottom and about 1/3 the way up, that predate the NYC blue-green circles, and are split off from the orange WA branches

Since you started a thread on this topic, here's something I posted on April 4 in another thread.  Northern California SARS-CoV-2 is much wider than those 2 sources.   I dn't know of a similar workup of Southern California.

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Basically, it examines cases in northern California and decides that there have been a number of different introductions of the disease into the area.

Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. ...
In Santa Clara County, cases with onset dates within two weeks of each other were associated with a large facility with multiple employers, large areas of shared space, and heavy pedestrian traffic. ...
Consistent with this epidemiological data, the genomes (UC13-15) from the three workers in the large facility are distinct from each other.

[/quote]

and more detail...

These viruses included 2 viruses likely related to lineages from Wuhan or other regions of China, 4 viruses related to those circulating in Europe, 11 viruses positioned in small independent clusters and not part of a larger clade, and 13 viruses associated with the Washington State (WA1) clade

UC12 was a resident of San Mateo County with a travel history to Switzerland. The genome from UC12 fell within a large lineage containing many sequences from European residents or travelers from Europe  and therefore it is likely the infection was acquired there. The sequence from individual UC29 (MT027062 is from the same patient) was a returning traveler from China and has an identical COVID-19 sequence to a household contact (MT027063). Their viral genomes were more closely related to ancestral lineages from China. Interestingly, three further genomes (UC24, UC26 and UC27) also grouped within a viral lineage with widespread circulation in Europe. Individual UC27 was diagnosed after returning from a New York trip, raising the possibility of interstate transmission. Individual UC26 also reported domestic travel, while local resident UC24 had no known travel history, illustrating the existence of undetected virus transmission in the community.

Two patients from San Mateo County (UC18 and UC25) were close household contacts (a husband and wife), and their viruses comprised a separate cluster with a virus from an infected person from China.

[M T]

Regarding the nexstrain link you posted, dig deeper at this link.
Note the earlier California yellow circles at the bottom and about 1/3 the way up, that predate the NYC blue-green circles, and are split off from the orange WA branches

Since you started a thread on this topic, here's something I posted on April 4 in another thread.  Northern California SARS-CoV-2 is much wider than those 2 sources.   I dn't know of a similar workup of Southern California.

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

Basically, it examines cases in northern California and decides that there have been a number of different introductions of the disease into the area.

Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. ...
In Santa Clara County, cases with onset dates within two weeks of each other were associated with a large facility with multiple employers, large areas of shared space, and heavy pedestrian traffic. ...
Consistent with this epidemiological data, the genomes (UC13-15) from the three workers in the large facility are distinct from each other.

[/quote]

and more detail...

These viruses included 2 viruses likely related to lineages from Wuhan or other regions of China, 4 viruses related to those circulating in Europe, 11 viruses positioned in small independent clusters and not part of a larger clade, and 13 viruses associated with the Washington State (WA1) clade

UC12 was a resident of San Mateo County with a travel history to Switzerland. The genome from UC12 fell within a large lineage containing many sequences from European residents or travelers from Europe  and therefore it is likely the infection was acquired there. The sequence from individual UC29 (MT027062 is from the same patient) was a returning traveler from China and has an identical COVID-19 sequence to a household contact (MT027063). Their viral genomes were more closely related to ancestral lineages from China. Interestingly, three further genomes (UC24, UC26 and UC27) also grouped within a viral lineage with widespread circulation in Europe. Individual UC27 was diagnosed after returning from a New York trip, raising the possibility of interstate transmission. Individual UC26 also reported domestic travel, while local resident UC24 had no known travel history, illustrating the existence of undetected virus transmission in the community.

Two patients from San Mateo County (UC18 and UC25) were close household contacts (a husband and wife), and their viruses comprised a separate cluster with a virus from an infected person from China.

[magnus]

Thanks for the extra info/quotes, MT.

I've tried a couple times to figure out how to read those genome trees, but just when I think I've got it, I lose focus.  
What I am seeing now that you've pointed some things out, is that there aren't that many CA cases in this analysis in general and the majority of them appear to not be a part of the WA or NYC groupings.

[magnus]

Thanks for the extra info/quotes, MT.

I've tried a couple times to figure out how to read those genome trees, but just when I think I've got it, I lose focus.  
What I am seeing now that you've pointed some things out, is that there aren't that many CA cases in this analysis in general and the majority of them appear to not be a part of the WA or NYC groupings.

[M T]

Try this...
Go to  gisaid.org
Click on the genome tree image in the upper right to get to a page that is just the tree.  "Genomic epidemiology of hCoV-19"
When it comes up on my computer, the tree fills most of the screen. 
There is a little tab at the top of the left side.  Click on the tab to pop out a settings pane.
In that pane, under "ncov" select "North America" to limit to the genomes from North America.
Then change "Color by" to Admin Divisions (ie, state).

In what was the main window (now shifted right), find  "Phylogeny  v"  and click on the down arrow.  That will show all the states in US, Mexico, Canada.  If you place your cursor over "California", the icons belonging to California will get a little bigger. (sliding on/off the state name helps your eye detect them).

You can also adjust the date slider to watch as things arrive,

If you type "USA/CA" into "Search strains", you can see only 18 California genomes are in this database, with only two submitted for Santa Clara County (both essentially identical, submitted March 4 (I suspect for the case admitted Feb 27 with suspect community spread)

If you move your mouse over the circles, you'll see more info.

[M T]

Try this...
Go to  gisaid.org
Click on the genome tree image in the upper right to get to a page that is just the tree.  "Genomic epidemiology of hCoV-19"
When it comes up on my computer, the tree fills most of the screen. 
There is a little tab at the top of the left side.  Click on the tab to pop out a settings pane.
In that pane, under "ncov" select "North America" to limit to the genomes from North America.
Then change "Color by" to Admin Divisions (ie, state).

In what was the main window (now shifted right), find  "Phylogeny  v"  and click on the down arrow.  That will show all the states in US, Mexico, Canada.  If you place your cursor over "California", the icons belonging to California will get a little bigger. (sliding on/off the state name helps your eye detect them).

You can also adjust the date slider to watch as things arrive,

If you type "USA/CA" into "Search strains", you can see only 18 California genomes are in this database, with only two submitted for Santa Clara County (both essentially identical, submitted March 4 (I suspect for the case admitted Feb 27 with suspect community spread)

If you move your mouse over the circles, you'll see more info.

[2006alum]

CA can also thank a group of fast-acting SF doctors, the Association of Bay Area Health Officers, per SFGate:

SAN FRANCISCO (AP) — On the morning of March 15, as Italy became the epicenter of the global coronavirus pandemic, a half dozen high-ranking California health officials held an emergency conference call to discuss efforts to contain the spread of the virus in the San Francisco Bay Area. The tight-knit group of Bay Area doctors organized the call to discuss a consistent policy on public gatherings for the region's 7 million people, which then had fewer than 280 cases and just three deaths. Soon, though, the conversation focused on the potentially catastrophic emergency on their hands and how stay-at-home orders could slow the advance of the virus. . . .

“It was obviously spreading like wildfire under our noses and literally every minute we did not take aggressive action was going to mean more and more death,” said Dr. Scott Morrow, health director for San Mateo County, just south of San Francisco and home to Facebook. The doctors who met that day are members of the Association of Bay Area Health Officers, a group born out of the AIDS epidemic that ravaged San Francisco in the 1980s. The group usually meets a half-dozen times a year and has tackled other global threats such as Ebola and swine flu.

By mid-March, group members were alarmed by the spread of the virus since an initial case in the state was confirmed Jan. 26. Dr. Sara Cody, the top doctor in Santa Clara County, home to 2 million residents and the headquarters of Apple and Google, told her peers that COVID-19 cases were doubling every three days. In neighboring San Mateo County, every test conducted was coming back positive, shared Morrow. Across the bay in Alameda County, Dr. Erica Pan reported that cases were rising in areas bordering Santa Clara County.

A day later, the San Francisco Bay Area became the first place in the nation to order residents to stay home. At least 20 other California counties adopted the Bay Area order within hours. Two days later, Gov. Gavin Newsom ordered all 40 million Californians to stay home unless they had essential jobs.

[2006alum]

CA can also thank a group of fast-acting SF doctors, the Association of Bay Area Health Officers, per SFGate:

SAN FRANCISCO (AP) — On the morning of March 15, as Italy became the epicenter of the global coronavirus pandemic, a half dozen high-ranking California health officials held an emergency conference call to discuss efforts to contain the spread of the virus in the San Francisco Bay Area. The tight-knit group of Bay Area doctors organized the call to discuss a consistent policy on public gatherings for the region's 7 million people, which then had fewer than 280 cases and just three deaths. Soon, though, the conversation focused on the potentially catastrophic emergency on their hands and how stay-at-home orders could slow the advance of the virus. . . .

“It was obviously spreading like wildfire under our noses and literally every minute we did not take aggressive action was going to mean more and more death,” said Dr. Scott Morrow, health director for San Mateo County, just south of San Francisco and home to Facebook. The doctors who met that day are members of the Association of Bay Area Health Officers, a group born out of the AIDS epidemic that ravaged San Francisco in the 1980s. The group usually meets a half-dozen times a year and has tackled other global threats such as Ebola and swine flu.

By mid-March, group members were alarmed by the spread of the virus since an initial case in the state was confirmed Jan. 26. Dr. Sara Cody, the top doctor in Santa Clara County, home to 2 million residents and the headquarters of Apple and Google, told her peers that COVID-19 cases were doubling every three days. In neighboring San Mateo County, every test conducted was coming back positive, shared Morrow. Across the bay in Alameda County, Dr. Erica Pan reported that cases were rising in areas bordering Santa Clara County.

A day later, the San Francisco Bay Area became the first place in the nation to order residents to stay home. At least 20 other California counties adopted the Bay Area order within hours. Two days later, Gov. Gavin Newsom ordered all 40 million Californians to stay home unless they had essential jobs.