严重急性呼吸综合症冠状病毒2变异株
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,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。
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。
變異株對照表
编辑最初檢出 | 代號 | 重要突变 | 传播 | 相对于武汉首次发现变体的临床变化 | ||||||
---|---|---|---|---|---|---|---|---|---|---|
地區 | 日期 | WHO标签[2] | PANGO谱系 | PHE变种[3] | Nextstrain分化枝 | 传播力 | 致命性 | 抗原性 | ||
2020年8月[4] | — | B.1.1.207 | — | — | P681H[5] | 多国[6] | 无变化[5] | 无变化[5] | ||
2020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≈ ( 82%– 43 130%) [13] | 正在调查 | 抗体中和效力略降低[14] | |
2021年1月[3] | B.1.1.7#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 | ||
2020年9月[16] | — | B.1.1.298[17] | — | — | Y453F, 69–70deltaHV[18] | 可能灭绝[19] | ||||
2020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≈ ( 50%– 20 113%) | 无变化[27] | 显著降低抗体中和效力 | |
2020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≈ ( 161%– 145 174%) |
致命性增高≈ ( 50%– 20 90%) |
抗体中和效力降低 | |
2020年10月[2] | Delta[A] | B.1.617.2[39] | VOC-21APR-02 | 21A[40] | T478K, L452R, P681R | 多国 | 增高≈ 198% |
正在调查[F] | 抗体中和效力降低[46][30] | |
2020年3月[2][47] | Epsilon | B.1.427,B.1.429[47][48] | — | 21C[49] | L452R[48] | 多国[48] | 增高≈ ( 20%) 18.6%–24.2% |
恢复期和疫苗接种后血清中和效力降低 | ||
2020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 | |||
2020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 | |||
2021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] | ||||
2020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] | |||
2020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] | ||||
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 | ||||
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: ( −63%– 69 74%) [67] | 疫苗对有症状疾病的免疫效果降低 |
- ^ 1.0 1.1 1.2 1.3 1.4 被世界卫生组织列为高關注變異株
- ^ 2.0 2.1 The reported confidence or credible interval has a low probability, so the estimated value can only be understood as possible, not certain nor likely.
- ^ Another study[37] has estimated that P.1 may be ≈ (50% CrI, 100%– 70) more transmissible. 140%[B]
- ^ Preliminary results from a study in the Southern Region of Brazil found P.1 much more lethal for healthy young people. In groups without pre-existing conditions, the variant was found to be ≈ ( 490%– 220 985%) more lethal for men in the 20-39 age group, ≈ ( 465%– 190 1003%) more lethal for women in the 20-39 age group and ≈ ( 670%– 401 1083%) for women in the 40-59 age group.[38]
- ^ About ( 64%– 26 113%) more transmissible than the Alpha variant,[41] so 1.64 × 1.82 ≈ 2.98.
- ^ 相对2020年初参考病毒株,Delta變異株症状发展更快、更严重[42];相對Alpha變異株,感染者住院率增加约一倍[43][44]。但根據英格蘭公共衛生署6月份報告,Delta變異株病例死亡率累計0.2%(如只計無注射疫苗則0.13%),而舊有Alpha變異株則為1.9%[45]
命名法
编辑目前严重急性呼吸综合征冠状病毒2之變異株有三个常用的命名系统,分别由GISAID、Nextstrain和PANGO建立。[2]
2021年5月31日,世界卫生组织宣布为重要變種病毒提供希臘字母标签,為免首先發現變種病毒的國家遭受歧視及汙名化。[68]其中,命名規則在Mu變異株後跳過了希臘字母「Nu」和「Xi」這兩個字母。據俄羅斯官方電視台《RT》報導,有不具名的WHO官員透露跳過「Nu」是為避免與發音相同的「New」混淆,至於跳過「Xi」則是由於這個字母的姓氏很普遍,為了避免「對區域的汙名化」[69][70][71][72]。
支序演化树
编辑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]
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關注度之基準
编辑現階段的主流變異株
编辑需要關注的變異株(VOC)
编辑病毒变异是一个自然随机过程,並引发关切的程度取决于其导致的传染性、发病率、死亡率,及逃避检测、免疫与治疗的风险。目前在世界的主要變異株为最早发现于非洲南部由希腊字母「Omicron」标记。
Omicron(B.1.1.529谱系)
编辑B.1.1.529變異株(WHO命名為Omicron[109][110][111])是目前變異最多的嚴重特殊傳染性肺炎病毒。據媒體簡報會上發佈:這個變異株有超過50個突變[112],而單單在刺突蛋白的突變也有32種[110][113][112]。
- 於2021年11月,在非洲南部的波札那和南非發現[112][114][111]。
- 2021年11月24日,升級為「VUM」等級。
- 2021年11月26日,再升級為「VOC」等級。
- 目前變種分支亞型:BA.1(標準亞型)、BA.2、BA.3、BA.4、BA.5,總共超過千種以上的「次分支」、「子代」及「重組」變異株。
目前「VOC-VOI」等級(需要留意)變異株
编辑- BA.2.86:被稱為「皮羅拉」(Pirola)
- JN.1
目前「VOC-VUM」等級(監視)變異株
编辑- KP.2
- KP.3
- KP.3.1.1
- JN.1.7
- JN.1.18
- LB.1
過去的主流變異株
编辑需要关注的变异株(Previous VOC)
编辑Alpha(B.1.1.7谱系)
编辑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。
- 在2020年9月,首次从英国東南方的肯特郡(Kent)所發現采集的样本中发现[115]。
- 2020年12月18日,升級為「VOC」等級。
- 2022年3月9日,降級為「Previous VOC」等級。
Beta(B.1.351谱系)
编辑B.1.351谱系,WHO命名為「Beta」,又称501Y.V2变种。與「N501Y」、「K417N」、「E484K」突變有關,与先前的新冠病毒变种相比,501Y.V2变种的传染率增加约50%。[116]有证据表明,501Y.V2变种的刺突蛋白突变E484K可能会影响一些多克隆抗体和单克隆抗体的中和作用。当前尚未有证据表明该变种影響嚴重特殊傳染性肺炎的嚴重程度[117]。。
- 2020年5月,在南非东开普省的纳尔逊·曼德拉湾发现。
- 2020年12月18日,被南非科学家和卫生官员报道。[118][119]
- 2020年12月18日,升級為「VOC」等級。
- 2022年3月9日,降級為「Previous VOC」等級。
Gamma(P.1谱系)
编辑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」。
- 2020年11月,在巴西发现。
- 2021年1月2日,在东京国际机场从四名巴西飞抵日本的旅客发现,由日本国立感染症研究所报道[117]。
- 2021年1月11日,升級為「VOC」等級。
- 2022年3月9日,降級為「Previous VOC」等級。
Delta(B.1.617.2谱系)
编辑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)、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]
英国公共卫生部于5月7日将B.1.617.2列为“高關注變異株”,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]
- 2021年4月4日,為升級為「VOI」等級。
- 2021年5月11日,為升級為「VOC」等級。
- 2022年6月7日,降級為「Previous VOC」等級。
需要留意的变异株(Previous VOI)
编辑Epsilon(B.1.427譜系、B.1.429譜系)
编辑B.1.427譜系、B.1.429譜系,WHO命名為「Epsilon」,於2020年3月在美國加州首次發現。
- 2021年3月5日,升級為「VOI」等級。
- 2021年7月6日,降級為「Previous VOI」等級。
Zeta(P.2譜系)
编辑P.2譜系,WHO命名為「Zeta」,於2020年4月在巴西里約熱內盧首次發現。
- 2021年3月17日,升級為「VOI」等級。
- 2021年7月6日,降級為「Previous VOI」等級。
Eta(B.1.525譜系)
编辑B.1.525譜系,WHO命名為「Eta」,於2020年12月在奈及利亞首次發現。
- 2021年3月17日,升級為「VOI」等級。
- 2021年9月20日,降級為「Previous VOI」等級。
Iota(B.1.526譜系)
编辑B.1.526譜系,WHO命名為「Iota」,於2020年11月在美國紐約首次發現。
- 2021年3月20日,升級為「VOI」等級。
- 2021年9月20日,降級為「Previous VOI」等級。
Theta(P.3譜系)
编辑P.3譜系,WHO命名為「Theta」,於2021年1月在菲律賓首次發現。
- 2021年3月24日,升級為「VOI」等級。
- 2021年7月6日,降級為「Previous VOI」等級。
Kappa(B.1.617.1)
编辑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。
- 2021年4月4日,升級為「VOI」等級。
- 2021年9月20日,降級為「Previous VOI」等級。
Lambda(C.37谱系)
编辑C.37譜系,WHO命名為「Lambda」,於2020年8月在秘魯首次發現。
- 2021年6月14日,升級為「VOI」等級。
- 2022年3月9日,降級為「Previous VOI」等級。
Mu(B.1.621譜系)
编辑B.1.621譜系,WHO命名為「Mu」,於2021年1月在哥倫比亞首次發現。
- 2021年8月30日,升級為「VOI」等級。
- 2022年3月9日,降級為「Previous VOI」等級。
备注
编辑- ^ 臺灣疾管署按美國CDC定義分三類,稱為:需留意變異株(Variants of Interest, VOI)、高關注變異株(Variants of Concern, VOC)、高衝擊變異株(Variant of High Consequence)。
参见
编辑参考文献
编辑- ^ SARS CoV-2 spike variants exhibit differential infectivity and neutralization resistance to convalescent or post-vaccination sera. [2021-03-24]. (原始内容存档于2021-12-08).
- ^ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 追踪SARS-CoV-2变体. 世界卫生组织. [2021-06-18]. (原始内容存档于2021-12-14).
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- ^ Lineage B.1.1.207. cov-lineages.org. [2021-07-15]. (原始内容存档于2021-07-18).
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本文含有此來源中屬於公有领域的内容。
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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")
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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.
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- ^ 30.0 30.1 Wall, Emma C; Wu, Mary; Harvey, Ruth; Kelly, Gavin; Warchal, Scott; Sawyer, Chelsea; Daniels, Rodney; Hobson, Philip; Hatipoglu, Emine; Ngai, Yenting; Hussain, Saira; Nicod, Jerome; Goldstone, Robert; Ambrose, Karen; Hindmarsh, Steve; Beale, Rupert; Riddell, Andrew; Gamblin, Steve; Howell, Michael; Kassiotis, George; Libri, Vincenzo; Williams, Bryan; Swanton, Charles; Gandhi, Sonia; Bauer, David LV. Neutralising antibody activity against SARS-CoV-2 VOCs B.1.617.2 and B.1.351 by BNT162b2 vaccination. The Lancet. 2021-06, 397 (10292): 2331–2333. doi:10.1016/S0140-6736(21)01290-3.
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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.
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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.
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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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外部链接
编辑- WHO: Tracking SARS-CoV-2 variants (页面存档备份,存于互联网档案馆)
- Science Brief: Emerging SARS-CoV-2 Variants (CDC) (页面存档备份,存于互联网档案馆)
- SARS-CoV-2 Variant Classifications and Definitions (CDC) (页面存档备份,存于互联网档案馆)
- Variants of concern or under investigation: data up to 5 May 2021 (PHE) (页面存档备份,存于互联网档案馆)
- SARS-CoV-2 variants of concern as of 11 May 2021 (ECDC) (页面存档备份,存于互联网档案馆)
- Living Evidence - SARS-CoV-2 variants (页面存档备份,存于互联网档案馆)
- Coronavirus Variants and Mutations (页面存档备份,存于互联网档案馆)