劍橋大學昨天發(fā)表論文，認為新冠病毒A類是病毒爆發(fā)的根源，而A類集中出現(xiàn)在美國和澳洲，出現(xiàn)于武漢的病毒屬于B類，是從A類變異而來。

這篇論文發(fā)表于美國科學院院刊，如果結(jié)論屬實，對中國和全球華人都是一件幸事。

劍橋大學發(fā)表關于新冠病毒的幾個變種和傳播路徑的研究報告。

報告指出，新冠病毒分三個變種：A、B、C。A類病毒更多發(fā)現(xiàn)于美國和澳洲的受感染者。A類在武漢只有極少案例，且來源于在武漢生活過的美國人。A類和從蝙蝠、穿山甲身上提取的病毒最為相似。研究人員稱A類病毒為“爆發(fā)根源”（ “the root of the outbreak” ）。

B類毒株是中國境內(nèi)（即武漢）主要類型，且并沒有傳播出東亞地區(qū)。

C類病毒是歐洲主要類型。亞洲地區(qū)的香港，新加坡，韓國皆有此類型。且沒有在中國大陸發(fā)現(xiàn)。

研究人員認為，A類毒株，C類型演化自B，B類型演化自A。

研究人員采用的研究方法，此前主要被運用于通過研究DNA來追蹤史前人類的人口流動。此次是首次運用在追蹤新冠病毒的傳播路徑。

原文地址:https://www./research/news/covid-19-genetic-network-analysis-provides-snapshot-of-pandemic-origins

論文今天發(fā)表在PNAS （美國科學院院刊），論文鏈接：https://www./content/early/2020/04/07/2004999117

Researchers from Cambridge, UK, and Germany have reconstructed the early “evolutionary paths” of COVID-19 in humans – as infection spread from Wuhan out to Europe and North America – using genetic network techniques.

By analysing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

“There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously,” said geneticist Dr Peter Forster, lead author from the University of Cambridge.  

“These techniques are mostly known for mapping the movements of prehistoric human populations through DNA. We think this is one of the first times they have been used to trace the infection routes of a coronavirus like COVID-19.” 

The team used data from virus genomes sampled from across the world between 24 December 2019 and 4 March 2020. The research revealed three distinct “variants” of COVID-19, consisting of clusters of closely related lineages, which they label 'A’, 'B’ and 'C’.

Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats – type 'A’, the “original human virus genome” – was present in Wuhan, but surprisingly was not the city’s predominant virus type.

Mutated versions of 'A’ were seen in Americans reported to have lived in Wuhan, and a large number of A-type viruses were found in patients from the US and Australia.

Wuhan’s major virus type, 'B’, was prevalent in patients from across East Asia. However, the variant didn’t travel much beyond the region without further mutations – implying a "founder event" in Wuhan, or “resistance” against this type of COVID-19 outside East Asia, say researchers.

The 'C’ variant is the major European type, found in early patients from France, Italy, Sweden and England. It is absent from the study’s Chinese mainland sample, but seen in Singapore, Hong Kong and South Korea.

The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a “Singapore cluster”.

Importantly, the researchers say that their genetic networking techniques accurately traced established infection routes: the mutations and viral lineages joined the dots between known cases.

As such, the scientists argue that these “phylogenetic” methods could be applied to the very latest coronavirus genome sequencing to help predict future global hot spots of disease transmission and surge.

“Phylogenetic network analysis has the potential to help identify undocumented COVID-19 infection sources, which can then be quarantined to contain further spread of the disease worldwide,” said Forster, a fellow of the McDonald Institute of Archaeological Research at Cambridge, as well as the University’s Institute of Continuing Education.

The findings are published today in the journal Proceedings of the National Academy of Sciences (PNAS). The software used in the study, as well as classifications for over 1,000 coronavirus genomes and counting, is available free at www..   

Variant 'A’, most closely related to the virus found in both bats and pangolins, is described as “the root of the outbreak” by researchers. Type 'B’ is derived from 'A’, separated by two mutations, then 'C’ is in turn a “daughter” of 'B’.

Researchers say the localisation of the 'B’ variant to East Asia could result from a “founder effect”: a genetic bottleneck that occurs when, in the case of a virus, a new type is established from a small, isolated group of infections.

Forster argues that there is another explanation worth considering. “The Wuhan B-type virus could be immunologically or environmentally adapted to a large section of the East Asian population. It may need to mutate to overcome resistance outside East Asia. We seem to see a slower mutation rate in East Asia than elsewhere, in this initial phase.”

He added: “The viral network we have detailed is a snapshot of the early stages of an epidemic, before the evolutionary paths of COVID-19 become obscured by vast numbers of mutations. It’s like catching an incipient supernova in the act.”

Since today’s PNAS study was conducted, the research team has extended its analysis to 1,001 viral genomes. While yet to be peer-reviewed, Forster says the latest work suggests that the first infection and spread among humans of COVID-19 occurred between mid-September and early December. 

The phylogenetic network methods used by researchers – allowing the visualisation of hundreds of evolutionary trees simultaneously in one simple graph – were pioneered in New Zealand in 1979, then developed by German mathematicians in the 1990s.

These techniques came to the attention of archaeologist Professor Colin Renfrew, a co-author of the new PNAS study, in 1998. Renfrew went on to establish one of the first archaeogenetics research groups in the world at the University of Cambridge.