Thanks to rapid global data sharing of #SARSCoV2 genomic data via gisaid.org, we can reconstruct large and small scale patterns of #COVID19 spread. This is a thread discussing this intersection of large and small. 1/7
At this point, a decent fraction (10/43) of sequenced viruses sampled after Feb 1 belong to a particular genetic lineage. This lineage has mutations unique to it that differentiate it from other #SARSCoV2 lineages. nextstrain.org/ncov?c=gt-nuc_… 2/7 
This lineage contains viruses sampled from Germany, Switzerland, Finland, Italy, Brazil and Mexico. The Italian sample is from Lombardy, further suggesting this lineage is responsible for a sizable portion of the Italian epidemic. 3/7
At the base of this lineage lies the sample Germany/BavPat1/2020. This was "patient 1" in Bavaria who was infected by a business colleague visiting from China. This cluster was investigated via contact tracing and an analysis written here: nejm.org/doi/full/10.10… 4/7
Incredibly, it appears that this cluster containing Germany/BavPat1/2020 is the direct ancestor of these later viruses and thus led directly to some fraction of the widespread outbreak circulating in Europe today. 5/7
Thus, I believe, similar to the case in Washington State (), we had a situation in which a cluster was identified via intensive screening of travelers, but containment failed shortly thereafter and a sustained transmission chain was initiated. 6/7
An extremely important take home message here is that just because a cluster has been identified and "contained" doesn't actually mean this case did not seed a transmission chain that went undetected until it grew to be sizable outbreak. 7/7
I'm sorry. I should have been more clear in the thread. This is not a definitive finding. More sampling of cases from China could show that the Lombardy case was a distinct introduction. I would say this is highly suggestive, but not definitive.
