我读不懂内行话 就只能看看summary 和twitter上的interpretation 这版上不少生化的MM估计读得懂 https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/ Report 42 - Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data Summary The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases. Twitter以及媒体上上的interoperation挺多的。这里有个玛丽皇后学院的。 https://twitter.com/dgurdasani1/status/1344774555718590464
https://twitter.com/dgurdasani1/status/1344774576371335175 It's clear that the variant is more dominant (1.2x) in children aged 0-9 yrs and 0-19 yrs. There could be many reasons for this - including transmission dynamics - due to high levels of unmitigated transmission in schools during lockdown - which has favoured the variant. It could also mean that children with the variant are more likely to develop symptoms and therefore be tested. Given these are not random samples from healthy people, but results based on pillar 2 testing, we need to interpret these cautiously. This also does not necessarily mean increased biological susceptibility in children vs adults, & shouldn't be interpreted as such. Irrespective of the relative prominence of the variant among children the prevalence of the variant is greatest among 10-19 yrs among those tested.
BB的评论 https://www.bloomberg.com/news/articles/2020-12-31/faster-spreading-covid-strain-affects-young-the-most-study-says Faster-Spreading Covid Strain Affects Young the Most, Study Says The new coronavirus variant that emerged in the U.K. is more transmissible and appears to affect a higher proportion of people under 20, according to a report from Imperial College London and other science groups. The mutation of concern has “a substantial transmission advantage” and is linked to “epidemic growth in nearly all areas,” the scientists wrote. It can raise the virus’s reproduction rate, which indicates how many people one patient infects, by as much as 0.7, the researchers found. “This will make control more difficult and further accentuates the urgency of rolling out vaccination as quickly as possible,” said Neil Ferguson, a professor at Imperial who has worked on modeling the outbreak. Social distancing measures that worked against earlier strains of the virus were insufficient to control the spread of the new variant, the study found. The government had previously said the new strain was as much as 70% more transmissible than other versions, without providing documentation. The researchers used statistical tools to evaluate the link between transmission and frequency of the new variant across the U.K. The data have informed the government’s pandemic planning in recent weeks, Ferguson said. It’s possible the new variant appears to infect the young the most because the research was conducted at a time when there were lockdowns but schools remained opened, the scientists said.
The study finds that individuals under 20 years old make up a higher proportion of VOC cases than non-VOC cases. However, it is too early to determine the mechanism behind this change according to the researchers. They explain that it may partly have been influenced by the variants spread coinciding with a period where lockdown was in force but schools were open. Further research is ongoing on the specific nature of any changes in how the virus affects this age group.
又去看了一下ORF8是干嘛的 https://www.biorxiv.org/content/10.1101/2020.05.24.111823v1 Zhang et al. hypothesized that one possible mechanism used by SARS-CoV-2 to participate in efficacious viral spread is an evasion of the immune response by interfering with antigen presentation by infected cells via MHC-I. Of note, this behavior has been previously characterized in other viruses, including HIV-1 and HSV.
西班牙流感怎么消失的真不知道。我估计是易感的人都死完了，其他的人有免疫了（可能是变异株）。 目前挖冻土挖出来的西班牙流感毒株，致病性非常强。以下引自cdc网页： https://www.cdc.gov/flu/pandemic-resources/reconstruction-1918-virus.html#learning “For example, four days after infection, the amount of 1918 virus found in the lung tissue of infected mice was 39,000 times higher than that produced by one of the comparison recombinant flu viruses.” “The 1918 virus was at least 100 times more lethal than one of the other recombinant viruses tested.”
回复 1楼梅干茶泡饭的帖子 The authors reported "We examined the time and location of sampling of 1,904 VOC whole genomes collected between October and 5 December 2020, combined with a genetic background of 48,128 genomes collected over the same period". From Oct 1st to Dec 5th, the positive cases in the UK is close to 1 million based on JHU's data. The conclusion is drawn from ~5% cases, not sure if the remaining 95% cases support the conclusion or not. Has to raise the doubt that if the authors only "selected" data that support their conclusion... No bio-medical background, but really cannot agree with the philosophy/approach that the authors used...
昨天有伦敦的护士到BBC电台说儿童医院有满病房的儿童新冠住院的 然后引起轩然大波 今天政府在辟谣 BBC上有报道 可以去看看 其实读下来挺有意思的 说的是儿童重症并没有增加 绝大多数年轻的还是无症状或者极为轻症 Worry more about the elderly than the young - exact worlds they used
昨天有伦敦的护士到BBC电台说儿童医院有满病房的儿童新冠住院的 然后引起轩然大波 今天政府在辟谣 BBC上有报道 可以去看看 其实读下来挺有意思的 说的是儿童重症并没有增加 绝大多数年轻的还是无症状或者极为轻症 Worry more about the elderly than the young - exact worlds they used
Summary The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK in late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases.
Twitter以及媒体上上的interoperation挺多的。这里有个玛丽皇后学院的。 https://twitter.com/dgurdasani1/status/1344774555718590464
It's clear that the variant is more dominant (1.2x) in children aged 0-9 yrs and 0-19 yrs. There could be many reasons for this - including transmission dynamics - due to high levels of unmitigated transmission in schools during lockdown - which has favoured the variant. It could also mean that children with the variant are more likely to develop symptoms and therefore be tested. Given these are not random samples from healthy people, but results based on pillar 2 testing, we need to interpret these cautiously. This also does not necessarily mean increased biological susceptibility in children vs adults, & shouldn't be interpreted as such. Irrespective of the relative prominence of the variant among children the prevalence of the variant is greatest among 10-19 yrs among those tested.
https://www.bloomberg.com/news/articles/2020-12-31/faster-spreading-covid-strain-affects-young-the-most-study-says
Faster-Spreading Covid Strain Affects Young the Most, Study Says The new coronavirus variant that emerged in the U.K. is more transmissible and appears to affect a higher proportion of people under 20, according to a report from Imperial College London and other science groups. The mutation of concern has “a substantial transmission advantage” and is linked to “epidemic growth in nearly all areas,” the scientists wrote. It can raise the virus’s reproduction rate, which indicates how many people one patient infects, by as much as 0.7, the researchers found.
“This will make control more difficult and further accentuates the urgency of rolling out vaccination as quickly as possible,” said Neil Ferguson, a professor at Imperial who has worked on modeling the outbreak. Social distancing measures that worked against earlier strains of the virus were insufficient to control the spread of the new variant, the study found. The government had previously said the new strain was as much as 70% more transmissible than other versions, without providing documentation.
The researchers used statistical tools to evaluate the link between transmission and frequency of the new variant across the U.K. The data have informed the government’s pandemic planning in recent weeks, Ferguson said. It’s possible the new variant appears to infect the young the most because the research was conducted at a time when there were lockdowns but schools remained opened, the scientists said.
https://www.imperial.ac.uk/news/211793/new-covid19-variant-growing-rapidly-england/
Greater transmission Under 20s more affected
The study finds that individuals under 20 years old make up a higher proportion of VOC cases than non-VOC cases. However, it is too early to determine the mechanism behind this change according to the researchers. They explain that it may partly have been influenced by the variants spread coinciding with a period where lockdown was in force but schools were open. Further research is ongoing on the specific nature of any changes in how the virus affects this age group.
谢谢！我开着两个tab就看花眼了。
No virulence measure ?
所以南非和uk同时测出快速变异也是说得通的
也说明了为啥最早有人讲就是一big flu。。。
edit 我看的是这篇 https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563
12/20/2020出的
Outside of spike, the ORF8 Q27stop mutation truncates the ORF8 protein or renders it inactive and thus allows further downstream mutations to accrue.
貌似ORF8被early terminate了，然后更多的变异就开始快速积累了
这次uk变异让我觉得最诡异的地方是，为嘛uk和南非都可以仔细监控病毒变异，疫情一点不比他们好的美国却听之任之了？
再加两点
3.变异发生在某个检测试剂盒的目标区间，所以PCR结果有可能不可靠。
4.目前个人防护是戴口罩，保持社交距离，勤洗手。然而这些措施下，新变异的R值是大于1. 就是说普通的个人防护已经防不住。
这个就有点糟糕了。reddit上说现在儿童医院里病人不少。如果这个新变异的致病性也高的话，那真的是奔着西班牙流感去了。
南非的人用得到瑞德西韦？
https://www.biorxiv.org/content/10.1101/2020.05.24.111823v1
Zhang et al. hypothesized that one possible mechanism used by SARS-CoV-2 to participate in efficacious viral spread is an evasion of the immune response by interfering with antigen presentation by infected cells via MHC-I. Of note, this behavior has been previously characterized in other viruses, including HIV-1 and HSV.
https://www.pnas.org/content/118/2/e2021785118
这个蛋白貌似在sars1和sars2之间并不是conserved的，那sars2有那么多无症状和长期带毒的cases也能解释了，因为免疫反应被suppress了
https://advances.sciencemag.org/content/6/27/eabb9153.full
（via recombination and purification）
true
西班牙流感后来是怎么消失的？
还有一个问题，
mRNA的疫苗还是否有效？
bbc说有效性和之前主流传播的strain相比应该差不多
但是 这次uk变异里包含关键的变异会造成免疫抑制 所以流传下去就是朝着escape vaccine的道路去的 （目前看加州和科罗拉多都是社区传染了）
并不是说这次在spike protein上的变异本身有多可怕，而是打开了今后继续高速变异的一扇门
西班牙流感怎么消失的真不知道。我估计是易感的人都死完了，其他的人有免疫了（可能是变异株）。
目前挖冻土挖出来的西班牙流感毒株，致病性非常强。以下引自cdc网页： https://www.cdc.gov/flu/pandemic-resources/reconstruction-1918-virus.html#learning “For example, four days after infection, the amount of 1918 virus found in the lung tissue of infected mice was 39,000 times higher than that produced by one of the comparison recombinant flu viruses.” “The 1918 virus was at least 100 times more lethal than one of the other recombinant viruses tested.”
Better to be the worst year than the last
他的意思是欧美的这种current social distance measurement
那在英国的变异株中orf8 因 truncation 而失活是好消息，这样 immune suppression 就没有了。
The authors reported "We examined the time and location of sampling of 1,904 VOC whole genomes collected between October and 5 December 2020, combined with a genetic background of 48,128 genomes collected over the same period". From Oct 1st to Dec 5th, the positive cases in the UK is close to 1 million based on JHU's data. The conclusion is drawn from ~5% cases, not sure if the remaining 95% cases support the conclusion or not. Has to raise the doubt that if the authors only "selected" data that support their conclusion... No bio-medical background, but really cannot agree with the philosophy/approach that the authors used...
你更应该问，现在的灭活疫苗是否有效，或者腺病毒疫苗明年是否有用！
3 是什么意思，试剂盒才能测出？
possible
ORF7自己单个是不是就没用了？
我想知道腺病毒载体疫苗明年还能用吗？
"如果这个新变异的致病性也高的话，那真的是奔着西班牙流感去了。"
不是一个概念。如果新变种致病死高那也是冲sars去，而不是1918-20流感，可以搜fatality rate - r0对比图以及各种病毒致病机理来看。虽然这波covid貌似更易感染孩子，而1918流感对青壮年，看起来都是对年轻人不利，但注意是两个年龄段的年轻群体，而且感染后致病机理不同。1918 influenza第二波更易致死抵抗力强的青壮年，老人和孩子反而问题小。而且发病快只有1-4天，发病到病死也是1-2天，所以后来才会消失。这些covid比不了，所以不可能很快消失，走不了1918流感老路。covid现在只是表现出来孩子易感染，但其实目前看并不是因为年龄，而是学校的人口密度和不利防护在变种的高感染力下缺点放大。而且感染后并没有说少年儿童（或青壮年）比其它年龄段更致死，和1918流感不同。所以covid19消失遥遥无期。
昨天有伦敦的护士到BBC电台说儿童医院有满病房的儿童新冠住院的
然后引起轩然大波
今天政府在辟谣 BBC上有报道 可以去看看 其实读下来挺有意思的 说的是儿童重症并没有增加 绝大多数年轻的还是无症状或者极为轻症 Worry more about the elderly than the young - exact worlds they used
明年应该还好，再过两年不好说，冠状病毒靠突变形成vaccine escape需要几年的时间，而且这是个渐进的过程，不是说一个突变就让疫苗全部失效了。
这是指腺病毒载体疫苗。那请问mRNA疫苗呢？
好奇这个几年是怎么估的？
还有免疫逃逸和vaccine escape是两回事吧？
有人拿普通感冒的冠状病毒做过实验，早期保存下来的康复患者血清可以中和几年后流行的毒株，但是再长了不行
嗯，已修改
哪里那么多关键几年。
你这说的跟我不是一个意思吗。covid还是更担心老人，不像1918更致死青壮年。你说辟谣是指什么，是英国政府说儿童医院没有住满？如果只是说儿童重症率没明显增加，也没错啊，不算辟谣。你觉得有意思是指英国政府downplay儿童感染吧。美国政客也差不多，都是inept.