Beijing's new coronavirus sequence released

The sequences of three new coronavirus samples recently collected in Beijing are not the same, suggesting that the new coronavirus may have been spreading quietly in Beijing communities as early as 1-2 months ago.

Written by | Shi Jun

The number of confirmed cases worldwide is 8,242,999

Global death toll: 445,535

(Latest data as of press time, source | WHO)

In a diary entry on April 21, "Detailed Explanation of the Virus Gene Sequence Tracking and Epidemic Investigation Method", I mentioned the virus sequence sharing and the Nextstrain program.

After an epidemic breaks out, scientists from all over the world will sequence the newly collected virus samples. Because the epidemic is urgent, many scientists will upload the unpublished virus gene sequences to some shared databases (such as GISAID) and share them with the world.

Trevor Bedford and other virus evolution experts at the Fred Hutchinson Cancer Research Center in Seattle organized a project called Nextstrain. Scientists will download the shared virus sequences to the backend of Nextstrain as soon as possible, incorporate these sequences into the global spread map, and publish the latest information on the genomic epidemiology of the new coronavirus on nextstrain.org and update the virus family tree.

Nextstrain, a software platform that has been developed over the past few years and used to tackle outbreaks such as Ebola, Zika and seasonal flu, aims to make genomic epidemiology work as quickly as possible during an outbreak. This year, it is also updating the spread of the new coronavirus.

Today, Nextstrain's Twitter account released three new coronavirus gene sequences, all from virus samples from the recent outbreak in Beijing. These three samples were collected on June 11, 2020, two from infected people and one from the environment. They were rapidly sequenced by the National Institute for Viral Disease Control and Prevention (NIVDC) of the Chinese Center for Disease Control and Prevention and shared on GISAID.

These three sequences fall into an evolutionary cluster that includes many samples from Europe (Figure 1, upper and lower panels), and are very different from the genetic sequences of the three viruses imported into Beijing sampled on March 19-20, 2020.

Figure 1 Global coronavirus family tree. The upper graph uses the sampling time as the horizontal axis, and the lower graph uses the number of mutations as the horizontal axis. (Click to see the larger image)

In the global framework, the sequences closest to the three Beijing sequences come from the Czech Republic, Taiwan, China, Greece and Portugal (Figure 2). Because Nextstrain recently streamlined many repeated sequences in the database, it is still unclear where the Beijing virus came from.

Figure 2 (click to enlarge)

If we look at the regional distribution, in the Asian framework (Figure 3), Beijing's sequence is very close to those from the Czech Republic, Taiwan, Denmark, Colombia, Israel and Austria.

Figure 3 (click to enlarge)

In the European framework (Figure 4), Beijing's sequence is very close to sequences from many European countries such as the Czech Republic and Denmark, and only differs by one mutation from the genetic sequences from Portugal and Sweden.

Figure 4 (click to enlarge)

Therefore, from the perspective of gene sequence analysis, the new coronavirus that has recently spread in Beijing is related to the virus prevalent in Europe. However, because it is similar to the sequences in many countries/regions, it is still unclear where it may have originated and when it was introduced to Beijing.

Finally, the most important point is that although the three virus gene sequences in Beijing are close, they are not the same. There are already two mutations between sample (1) and samples (2, 3) (Figure 5). The first mutation (A29694C) is present in samples (2 and 3), but the second mutation is different (C12085T and A11910G). This suggests that before the outbreak, the new coronavirus may have been spreading quietly in the Beijing community for some time. Because the mutation rate of the new coronavirus is not fast, it mutates twice a month on average. If it is an outbreak in a short period of time at a single point (Xinfadi Market), the virus gene sequence is likely to be the same.

Figure 5 (click to enlarge)

I have mentioned in my previous diary (see "Opening the Coffin and Autopsy: When Did the Coronavirus Infection Appear in Various Countries | 117 Epidemic Observation") that in many parts of the world, such as Seattle and New York in the United States, and Paris in France, the coronavirus spread silently in the community without people noticing for 1-2 months before causing a full-scale outbreak. The community spread of the coronavirus in Beijing may have started 1-2 months ago.

References

https://mobile.twitter.com/nextstrain/status/1273642115826880512