We updated the situation report. It would be great if this update was reflected in the translations in a timely manner: @fzhang12 @alvinxhan @wdingx (Wei was a PhD student/post-doc with me and offered to help as well).
The list of changes seems long, but the biggest chunks of text are completely touched. many are mainly updated numbers.
Thank you very much for your work!
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< title: Genomic analysis of nCoV spread. Situation report 2020-01-30.
---
> title: Genomic analysis of nCoV spread. Situation report 2020-01-25.
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< date: "2020 Jan 30"
< dataset: "https://nextstrain.org/ncov/2020-01-30?d=map"
---
> date: "2020 Jan 25"
> dataset: "https://nextstrain.org/ncov/2020-01-25?d=map"
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< # [Executive summary](https://nextstrain.org/ncov/2020-01-30/2020-01-30)
---
> # [Executive summary](https://nextstrain.org/ncov/2020-01-25)
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< Using 42</tag> publicly shared novel coronavirus (nCoV) genomes, we examined genetic diversity to infer date of common ancestor and rate of spread.
---
> Using 27 publicly shared novel coronavirus (nCoV) genomes, we examined genetic diversity to infer date of common ancestor and rate of spread.
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< * the 42</tag> sampled genomes are very similar, differing from the consensus by 0-7 mutations
---
> * 27 sampled genomes are very similar, differing by 0-5 mutations
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< # [Coronaviruses](https://nextstrain.org/ncov/2020-01-30)
---
> # [Coronaviruses](https://nextstrain.org/ncov/2020-01-25)
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< * General information on coronaviruses on [Wikipedia](https://en.wikipedia.org/wiki/Coronavirus) _2020-01-30_
< * Summary of the nCov outbreak on [Wikipedia](https://en.wikipedia.org/wiki/2019%E2%80%9320_Wuhan_coronavirus_outbreak) _2020-01-30_
< * Material provided by the [US CDC](https://www.cdc.gov/coronavirus/index.html) _2020-01-29_
---
> * General information on coronaviruses on [Wikipedia](https://en.wikipedia.org/wiki/Coronavirus) _2020-01-25_
> * Summary of the nCoV outbreak on [Wikipedia](https://en.wikipedia.org/wiki/2019%E2%80%9320_Wuhan_coronavirus_outbreak) _2020-01-25_
> * Material provided by the [US CDC](https://www.cdc.gov/coronavirus/index.html) _2020-01-23_
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< * Interactive risk analysis by [MOBS-lab](https://datastudio.google.com/reporting/3ffd36c3-0272-4510-a140-39e288a9f15c/page/U5lCB) _2010-01-29_
< * Interactive risk analysis by [ROCS-lab](http://rocs.hu-berlin.de/corona/) _2010-01-29_
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< # [Novel coronavirus (nCoV) 2019-2020](https://nextstrain.org/ncov/2020-01-30)
---
> # [Novel coronavirus (nCoV) 2019-2020](https://nextstrain.org/ncov/2020-01-25)
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< As of January 30th over 7,914 cases and 170 deaths [have been reported](https://en.wikipedia.org/wiki/2019%E2%80%9320_outbreak_of_novel_coronavirus_(2019-nCoV)).
---
> As of January 25th, 2020 over 1400 cases and 42 deaths [have been reported](https://en.wikipedia.org/wiki/2019%E2%80%9320_outbreak_of_novel_coronavirus_(2019-nCoV)).
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< While the outbreak seems to be centered in Wuhan, which is now [under quarantine](https://twitter.com/PDChina/status/1220060879112282117), the virus has spread throughout China and abroad, including Hong Kong, Singapore, Japan, and Thailand, as well as Europe, North America, South Asia, the Middle East, and Australia. Limited local transmission outside of China has been reported.
---
> While the outbreak seems to be centered in Wuhan, which is now [under quarantine](https://twitter.com/PDChina/status/1220060879112282117), the virus has spread throughout China and abroad, including Hong Kong, Macau, Thailand, Japan, South Korea, USA, and France. Limited local transmission outside of China has been reported.
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< # [How to interpret the phylogenetic trees](https://nextstrain.org/ncov/2020-01-30)
---
> # [How to interpret the phylogenetic trees](https://nextstrain.org/ncov/2020-01-25)
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< <img alt="cartoon of phylogenetic tree and corresponding alignment, with samples labelled A-E" width="500" src="https://data.nextstrain.org/toy_alignment_tree.png"/>
---
> <img alt="cartoon of phylogenetic tree and corresponding alignment, with samples labelled A-E" width="500" src="https://nextstrain-data.s3.amazonaws.com/toy_alignment_tree.png"/>
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< # [Phylogenetic analysis](https://nextstrain.org/ncov/2020-01-30?m=div&d=tree)
---
> # [Phylogenetic analysis](http://localhost:4000/ncov/2020-01-25?m=div&d=tree)
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< Here we present a phylogeny of 42</tag> strains of nCoV that have been publicly shared.
---
> Here we present a phylogeny of 27 strains of nCoV that have been publicly shared.
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< The colours represent the within-country region or US-state of isolation, with the x-axis representing nucleotide divergence.
---
> The colours represent the city/US-state of isolation, with the x-axis representing nucleotide divergence.
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< Other viruses have between one and seven mutations.
---
> Other viruses have between one and five mutations.
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< # [Phylogenetic Interpretation](https://nextstrain.org/ncov/2020-01-30?m=div&d=tree)
---
> # [Phylogenetic Interpretation](https://nextstrain.org/ncov/2020-01-25?m=div&d=tree)
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< We currently see little genetic diversity across the nCoV sequences, with 11</tag> out of 42</tag> sequences having no unique mutations.
---
> We currently see little genetic diversity across the nCoV sequences, with 8 out of 27 sequences having no unique mutations.
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< We are starting to see groups of sequences that share mutations.
< One cluster contains sequences from Guangdong and four isolates from the US.
< Other clusters contain two to four isolates.
< Sequences in these clusters tend to be from more recent samples, suggesting that the virus has started to accumulate mutations as it spread in Wuhan and subsequently to other cities.
< There is currently no evidence that these mutations change how the virus behaves -- it is expected that RNA viruses mutate.
---
> At the moment, most mutations that can be observed are singletons – they are unique to individual genomes. Only the sequences that form the two clusters from Guangdong and the sequence form the USA share mutations – we will explore these in later slides.
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< # [Within-family transmission 1](https://nextstrain.org/ncov/2020-01-30?m=div&d=tree&f_location=Zhuhai)
---
> # [Within-family transmission 1](https://nextstrain.org/2020-01-25/ncov?m=div&d=tree&f_location=Zhuhai)
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< There are three genetically-identical isolates from Zhuhai (Southeastern China, Guangdong Province) which form a cluster, sharing one unique mutation seen in no other isolate (you can hover your mouse over the branches to see which mutations are present).
---
> There are two genetically-identical isolates from Zhuhai (Southeastern China, Guangdong Province) which form a cluster, sharing one unique mutation seen in no other isolate (you can hover your mouse over the branches to see which mutations are present).
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< Two of these cases (ending 028 and 040) are [known to come from a single family](https://twitter.com/JingLu_LuJing/status/1220143773532880896), again indicating human-to-human transmission.
< We don't have information about the third case.
---
> These two cases are [known to come from a single family](https://twitter.com/JingLu_LuJing/status/1220143773532880896), again indicating human-to-human transmission.
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< # [Within-family transmission 2](https://nextstrain.org/ncov/2020-01-30?m=div&d=tree&f_location=Shenzhen)
---
> # [Within-family transmission 2](https://nextstrain.org/ncov/2020-01-25?m=div&d=tree&f_location=Shenzhen)
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< Of the six isolates from Guangdong Province (which includes the city of Shenzhen) we see four isolates which are genetically identical.
---
> Of the six isolates from Shenzhen (Southeastern China, Guangdong Province) we see four isolates which are genetically identical.
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> Two of these mutations are also found in the sequence of the case in Washington, USA (more below).
> One sequence from Shenzhen has two additional mutations.
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< Three of the sequences from Guangdong (ending F025, F013, and F012) are [known to come from a single family](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext), and almost certainly represent human-to-human transmission.
<
---
> The sequences form Shenzhen are [known to come from a single family](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext), and almost certainly represent human-to-human transmission.
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< # [Within-family transmission 2 - shared mutations](https://nextstrain.org/ncov/2020-01-30?m=div&d=tree&f_location=Shenzhen,Los%20Angeles,Orange%20County,Seattle,Chicago,Phoenix)
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< The three mutations found in this cluster are also present in the Arizona, USA isolate, and two of the mutations are found in three other USA isolates.
---
> # [Cases outside China](https://nextstrain.org/ncov/2020-01-25?c=country&d=tree&m=div)
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> There are reported diagnostically confirmed nCoV cases in many East and South-East Asian countries, USA, Australia, and Europe.
> Vietnam has reported a case without travel history to Wuhan who possibly got infected from a [relative visiting from Wuhan](https://www.aljazeera.com/news/2020/01/china-coronavirus-outbreak-latest-updates-200123133559818.html).
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< # [Within-family transmission 3](https://nextstrain.org/ncov/2020-01-30?m=div&d=tree&f_location=Paris)
<
< Finally, the two sequences from France are identical, sharing one unique mutation, and one mutation also found in one of the USA isoaltes and the Taiwanese isolate.
---
> The only currently available sequence data for cases outside of China are the two cases from Thailand and one case from the USA, which are coloured here in yellow and red, respectively.
> The Thai samples are genetically identical to six Chinese sequences, including five isolated in Wuhan.
> The sequence from Washington, US, shares two mutations with the cluster of sequences from Shenzhen.
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< The two french sequences are [known to be from the same family](https://www.thelocal.fr/20200129/coronavirus-in-france-what-you-need-to-know) - a Chinese couple from Wuhan.
<
<
< # [Cases outside China](https://nextstrain.org/ncov/2020-01-30?c=country&d=tree&m=div)
<
< There are reported diagnostically confirmed nCoV cases in many East and South-East Asian countries, USA, Australia, the Middle East, and Europe.
< Vietnam, Japan, and Germany have reported transmission within the country, albeit always with a known link to Wuhan, China.
<
< <br>
---
> The case from Washington, USA, had travelled to Wuhan.
> The most parsimonious explanation for the observed pattern of mutation sharing is the virus variant with the two shared mutations was circulating in Wuhan and was independently exported to Shenzhen and to the USA.
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< The only currently available sequence data for cases outside of China are the two cases from Thailand, five from the USA, two from France, and one from Taiwan.
< The Thai samples are genetically identical to nine Chinese sequences, including seven isolated in Wuhan.
< Four sequences from the US share two mutations with the cluster of sequences from Shenzhen.
< The remaining sequence from the US shares a mutation with the sequence from Taiwan and the two from France.
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< <br>
<
< The most parsimonious explanation for the observed pattern of mutation sharing between the US and Shenzhen sequences is a virus variant with the two shared mutations was circulating in Wuhan and was independently exported to Shenzhen and multiple times to the USA.
< There is no evidence for a link between US sequences other than a link to Wuhan.
<
< # [Dating the time of the most recent common ancestor](https://nextstrain.org/ncov/2020-01-30?d=tree)
---
> # [Dating the time of the most recent common ancestor](https://nextstrain.org/ncov/2020-01-25?d=tree)
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< With the additional sequences shared during the past week, the tree now shows several distinct clusters such that our analysis from 2020-01-25 assuming a star-like topology is no longer appropriate.
<
< We reproduce here our analysis based on data available up to 2020-01-25
< assuming a star-like phylogeny structure along with a Poisson distribution of mutations through time to estimate the time of the most recent common ancestor ('TMRCA') of sequenced viruses.
< **We found that the common ancestor most likely existed between mid-Nov and the beginning of Dec 2019. The biggest source of uncertainty is the substitution rate.**
---
> Here, we assume a star-like phylogeny structure along with a Poisson distribution of mutations through time to estimate the time of the most recent common ancestor ('TMRCA') of sequenced viruses.
> **We find that the common ancestor most likely existed between mid-Nov and the beginning of Dec 2019.**
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< <img alt="graph of TMRCA estimates based on different mutation rates" width="500" src="https://data.nextstrain.org/ncov_poisson-tmrca.png"/>
---
> <img alt="graph of TMRCA estimates based on different mutation rates" width="500" src="https://nextstrain-data.s3.amazonaws.com/ncov_poisson-tmrca.png"/>
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< Using the entire data set, the nextstrain analysis pipeline estimates that the common ancestor most likely existed between late-Nov and the beginning of Dec 2019.
<
< There is a [confirmed case in Wuhan with onset date of Dec 1, 2019](https://twitter.com/trvrb/status/1220749265380593664), which would put an upper bound on the date of most recent common ancestor.
< The common ancestor of viruses sequenced to date might be later than this date though.
---
> As the more samples are sequenced, we expect the tree to show more structure, such that the star-like phylogeny topology is no longer a good assumption.
> At this point, phylodynamic estimates of the age of the epidemic will become feasible.
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< More detailed modeling of the onset of the outbreak are onging.
< Despite considerable uncertainty, our best guess is remains late November/early December.
---
> There is a [confirmed case in Wuhan with onset date of Dec 1, 2019](https://twitter.com/trvrb/status/1220749265380593664), which would put an upper bound on the date of most recent common ancestor. And strongly suggests evolutionary rates of ~3.0 x 10^-4 are more plausible.
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< # [Estimating the growth rate](https://nextstrain.org/ncov/2020-01-30?d=tree)
---
> # [Estimating the growth rate](https://nextstrain.org/ncov/2020-01-25?d=tree)
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< Scientists at Imperial College London have used the number of cases observed outside of China to estimate the [total number of cases](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/news--wuhan-coronavirus/) and suggested that there have been at least several thousand cases by 2020-01-22.
< With the additional exported cases since and the continued growth of confirmed cases in China, we currently have to expect at least 50000 cases to date.
---
> Scientists at Imperial College London have used the number of cases observed outside of China to estimate the [total number of cases](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/news--wuhan-coronavirus/) and suggested that there have been at least several thousand cases.
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< **We find plausible estimates of R0 between 1.8 and 3.5.**
---
> **We find plausible estimates of R0 between 1.5 and 3.5.**
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< If we assume the outbreak started at the beginning of November 2019 (12 weeks ago), we find that R0 should range between 1.8 and 2.5, depending on how large ('n') the outbreak is now.
---
> If we assume the outbreak started at the beginning of November 2019 (12 weeks ago), we find that R0 should range between 1.5 and 2.5, depending on how large ('n') the outbreak is now.
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< <img alt="graph of R0 estimates with epidemic start 12 weeks ago" width="500" src="https://data.nextstrain.org/ncov_branching-R0-early_2020-01-29.png"/>
---
> <img alt="graph of R0 estimates with epidemic start 12 weeks ago" width="500" src="https://nextstrain-data.s3.amazonaws.com/ncov_branching-R0-early.png"/>
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< If we assume a more recent start, at the beginning of December 2019 (8 weeks ago), the estimates for R0 range between 2.2 and 3.5:
---
> If we assume a more recent start, at the beginning of December 2019 (8 weeks ago), the estimates for R0 range between 1.8 and 3.5:
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< <img alt="graph of R0 estimates with epidemic start 8 weeks ago" width="500" src="https://data.nextstrain.org/ncov_branching-R0-recent_2020-01-29.png"/>
---
> <img alt="graph of R0 estimates with epidemic start 8 weeks ago" width="500" src="https://nextstrain-data.s3.amazonaws.com/ncov_branching-R0-recent.png"/>
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< This estimates are broadly consistent with those by other scientists which mostly fall between R0=2-3, see for example <a href="https://www.biorxiv.org/content/10.1101/2020.01.25.919787v1">this preprint</a>.
< Importantly, R0 is a quantitity that depends strongly on the socio-economic context and infection control measures.
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< # [Scientific credit](https://nextstrain.org/ncov/2020-01-30?d=map&c=author)
---
> # [Scientific credit](https://nextstrain.org/ncov/2020-01-25?d=map&c=author)
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< * Centers for Disease Control, R.O.C., Taipei, Taiwan
< * Institut Pasteur, Paris, France
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< # [Detailed scientific credit](https://nextstrain.org/ncov/2020-01-30?d=map&c=author)
---
> # [Detailed scientific credit](https://nextstrain.org/ncov/2020-01-25?d=map&c=author)
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< - Guangdong/20SF001/2020
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< - Guangdong/20SF174/2020
< - Guangdong/20SF206/2020
< - Guangdong/20SF207/2020
< - Foshan/20SF207/2020
< - Foshan/20SF210/2020
< - Foshan/20SF211/2020
<
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< - USA/AZ1/2020
< - USA/IL1/2020
< - USA/CA1/2020
< - USA/CA2/2020
< * Centers for Disease Control, R.O.C., Taipei, Taiwan
< - Taiwan/2/2020
< * Institut Pasteur, Paris, France
< - France/IDF0372/2020
< - France/IDF0373/2020
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