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本文主要讲述严重急性呼吸综合症冠状病毒2变异株及其发生的错义突变。
引发2019冠状病毒病的严重急性呼吸综合征冠状病毒2(SARS-CoV-2冠状病毒)容易发生突变而产生變異株(英语:Variant (biology)),关键病毒蛋白的突变即可能意味着其出现,目前已有多个变异株在世界各地形成并传播。由于病毒的核酸序列变异有可能导致抗原漂移,而使得病毒得以逃避宿主的免疫应答,并影响疫苗的效力[1],这种现象称为免疫逃避(英语:antigenic escape)。
已有五种被世界卫生组织認定为值得关注的变异株,它們分別為Alpha變異株、Beta變異株、Gamma變異株、Delta變異株以及Omicron變異株。
最初檢出 | 代號 | 重要突变 | 传播 | 相对于武汉首次发现变体的临床变化 | ||||||
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地區 | 日期 | WHO标签[2] | PANGO谱系 | PHE(英语:Public Health England)变种[3] | Nextstrain(英语:Nextstrain)分化枝 | 传播力 | 致命性 | 抗原性 | ||
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000000002020-08-01-00002020年8月[4] | — | B.1.1.207 | — | — | P681H[5] | 多国[6] | 无变化[5] | 无变化[5] | |
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000000002020-09-01-00002020年9月[2][7] | Alpha[A] | B.1.1.7[8] | VOC-20DEC-01 | 20I (V1)[9] | N501Y, 69–70del, P681H[5][10][11][12] | 全球[7] | 增高≈6999820000000000000♠82% (7001430000000000000♠43–7000130000000000000♠130%) [13] | 正在调查 | 抗体中和效力略降低[14] |
000000002021-01-01-00002021年1月[3] | B.1.1.7#E484K(書面挪威語:Lineage B.1.1.7 with E484K)[3] | VOC-21FEB-02 | 20I (V1) | N501Y, 69–70del, P681H,[5][15] E484K | 多國 | 正在调查 | 正在调查 | 正在调查 | ||
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000000002020-09-01-00002020年9月[16] | — | B.1.1.298(英语:Cluster 5)[17] | — | — | Y453F, 69–70deltaHV[18] | 可能灭绝[19] | |||
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000000002020-05-01-00002020年5月[2] | Beta[A] | B.1.351[5][8] | VOC-20DEC-02 | 20H (V2)[20] | N501Y, K417N, E484K[5][21][22][23][24][25] | 多国[26] | 增高≈6999500000000000000♠50% (7001200000000000000♠20–7000113000000000000♠113%) | 无变化[27] | 显著降低抗体中和效力 |
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000000002020-11-01-00002020年11月[2] | Gamma[A] | P.1譜系[10][8] | VOC-21JAN-02 | 20J (V3)[31] | N501Y, E484K, K417T[5][32][33][34] | 美国、巴西等68国[35] | 增高≈7000161000000000000♠161% (7002145000000000000♠145–7000174000000000000♠174%) |
致命性增高≈6999500000000000000♠50% (7001200000000000000♠20–6999900000000000000♠90%) |
抗体中和效力降低 |
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000000002020-10-01-00002020年10月[2] | Delta[A] | B.1.617.2[39] | VOC-21APR-02 | 21A[40] | T478K, L452R, P681R | 多国 | 增高≈7000198000000000000♠198% |
正在调查[F] | 抗体中和效力降低[46][30] |
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000000002020-03-01-00002020年3月[2][47] | Epsilon | B.1.427,B.1.429[47][48] | — | 21C[49] | L452R[48] | 多国[48] | 增高≈6999200000000000000♠20% (6999186000000000000♠18.6%–24.2%) |
恢复期和疫苗接种后血清中和效力降低 | |
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000000002020-04-01-00002020年4月[51] | Zeta | P.2 | VUI-21JAN-01 | 20B/S.484K[52] | E484K,D614G,V1176F[53] | 多国[51] | 单克隆抗体中和效力可能降低,疫苗接种后血清中和效力降低 | ||
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000000002020-12-01-00002020年12月[2][54] | Eta | B.1.525[55] | VUI-21FEB-03 | 21D[56] | E484K, F888L[55] | 加拿大、美国、德国等69国[54] | 单克隆抗体、恢复期和疫苗接种后血清中和效力可能降低 | ||
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000000002021-01-01-00002021年1月[2] | Theta | P.3[57] | VUI-21MAR-02 | 21E[58] | E484K,N501Y,P681H,141–143del[59] | 菲律宾、美国等17国[57] | |||
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000000002020-10-01-00002020年10月[2] | Kappa | B.1.617.1[39] | VUI-21APR-01 | 21B[60] | E484Q, L452R, P681R[61] | 多国 | 抗体中和效力降低[46] | ||
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000000002020-08-01-00002020年8月[62] | Lambda | C.37[63] | VUI-21JUN-01 | 21G[64] | G75V,T76I,247-253del,L452Q,F490S,D614G,T859N[65] | 智利、美国、祕魯等44國[63] | |||
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2021年1月 | Mu | B.1.621 | VUI-21JUL-1 | 21H | T95I、Y144S、Y145N、R346K、E484K N501Y、D614G、P681H、D950N |
哥倫比亞、美國等60國 | |||
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2021年11月 | Omicron[A] | B.1.1.529 | VUI-21NOV-1 | 21K | A67V、Δ69-70、T95I、G142D、Δ143-145、Δ211 L212I、ins214EPE、G339D、S371L、S373P、S375F K417N、N440K、G446S、S477N、T478K、E484A Q493K、G496S、Q498R、N501Y、Y505H、T547K D614G、H655Y、N679K、P681H、N764K |
博茨瓦纳、南非等数国 | 有可能提高[66] | 相对于 Delta:3000370000000000000♠−63% (7001690000000000000♠69–6999740000000000000♠74%) [67] | 疫苗对有症状疾病的免疫效果降低 |
以下为严重急性呼吸综合征冠状病毒2主要变种的支序演化树简化示意图。[75]
SARS-CoV-2 |
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B.1.1.7谱系,WHO命名为“Alpha”,又称VOC 202012/01,並称501Y.V1变种。部分與「N501Y」突變有關。有23個病毒基因變異點。
P.1谱系,WHO命名為「Gamma」,又称501Y.V3变种。包括三個相關突變:「N501Y」、「E484K」和「K417T」。
B.1.617谱系是2020年10月于印度发现的一种双突变變異株。直到2021年1月前,该變異株的感染人数都寥寥无几。4月时该變異株已经蔓延至超过20个国家,遍及南极洲和南美洲以外的所有大洲。[120][121][122]
在该變異株约15个谱系定义突变中包括刺突蛋白突变D111D(同义突变(英语:synonymous substitution))、G142D[123]、P681R、E484Q[107]、L452R[124],其中后两个突变可能会影响恢复期血浆和单克隆抗体的中和作用。[125]
英国公共卫生部(英语:Public Health England)于5月7日将B.1.617.2列为“高關注變異株(英语:Variant of concern)”,命名为VOC-21APR-02。[96][126]
5月10日WHO称,因为B.1.617较高的传染性,该变异正被列为全球范围内受关切变种[127]。6月1日WHO将受关切变种限定为B.1.617谱系当中的B.1.617.2(Delta)变种。[128] 稍后WHO將B.1.617.2命名為「Delta」。
5月21日,越南宣布发现一种传播性更高,由Delta變異株加上Alpha變異株上突变的病毒株。[129]6月3日,WHO澄清该病毒株不符合新混合变种的定义,并将其列为带有突变的Delta变种。[130]
据报道,Delta變異株基本传染数R0大约为6(有说法称其高达8或9)[131],是嚴重急性呼吸道症候群冠狀病毒2型原始毒株基本传染数的2倍以上。[132]
B.1.525譜系,WHO命名為「Eta」,於2020年12月在奈及利亞首次發現。
P.3譜系,WHO命名為「Theta」,於2021年1月在菲律賓首次發現。
B.1.617譜系的三個子譜系之一當中的「B.1.617.1」,WHO命名為「Kappa」,於2020年10月在印度首次發現。
C.37譜系,WHO命名為「Lambda」,於2020年8月在秘魯首次發現。
B.1.621譜系,WHO命名為「Mu」,於2021年1月在哥倫比亞首次發現。
Sekventeringen af de positive prøver viser samtidig, at der ikke er påvist yderligere tilfælde af minkvariant med cluster 5 siden den 15. september, hvorfor Statens Serums Institut vurderer, at denne variant med stor sandsynlighed er døet ud. ("With high probability [...] died out")
I should note here that there's another strain in South Africa that is bringing on similar concerns. This one has eight mutations in the Spike protein, with three of them (K417N, E484K and N501Y) that may have some functional role.
The new variant was found to be about 2.6 times more transmissible (95% Confidence Interval (CI): 2.4–2.8) than previous circulating variant(s). ... Table 1: Summary of the fitted parameters and respective confidence intervals considering the entire period, November 1 2020-January 31, 2021 maintaining the same pathogenicity of the previous variant. Parameter: Relative transmission rate for the new variant. Estimate: 2.61. 2.5%: 2.45. 97.5%: 2.76.
Within this plausible region of parameter space, P.1 can be between 1.7 and 2.4 times more transmissible (50% BCI, 2.0 median, with a 99% posterior probability of being >1) than local non-P1 lineages and can evade 21 to 46% (50% BCI, 32% median, with a 95% posterior probability of being able to evade at least 10%) of protective immunity elicited by previous infection with non-P.1 lineages, corresponding to 54 to 79% (50% BCI, 68% median) cross-immunity ... We estimate that infections are 1.2 to 1.9 times more likely (50% BCI, median 1.5, 90% posterior probability of being >1) to result in mortality in the period after the emergence of P.1, compared with before, although posterior estimates of this relative risk are also correlated with inferred cross-immunity. More broadly, the recent epidemic in Manaus has strained the city’s health care system, leading to inadequate access to medical care. We therefore cannot determine whether the estimated increase in relative mortality risk is due to P.1 infection, stresses on the Manaus health care system, or both. Detailed clinical investigations of P.1 infections are needed.
Female 20 to 39 years old, with no pre-existing risk conditions, were at risk of death 5.65 times higher in February (95% CI, 2.9-11.03; p <0.0001) and in the age group of 40 and 59 years old, this risk was 7.7 times higher (95% CI, 5.01-11.83; p <0.0001) comparing with November-December. ... The heterogeneity observed between the age groups was greater when we analyzed the subgroup of the population without preexisting risk conditions where we found that the CFR in the female sex in the second wave was 1.95 times (95% CI, 1.38-2.76) the CFR of the first wave in the population over 85 years old and was 7.7 times (95% CI, 5.01-11.83; p < 0.0001) in the population between 40 and 59 years old. In the male population without previous diseases, the CFR in the second wave was 2.18 (95% CI, 1.62-2.93) times the CFR of the first wave in the population over 85 years old and 5.9 (95% CI, 3.2-10.85; p < 0, 0001) higher in the range between 20 and 39 years old.
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