严重急性呼吸综合症冠状病毒2变异株

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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

變異株對照表

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英语Public Health England变种[3] Nextstrain英语Nextstrain分化枝 传播力 致命性 抗原性
 奈及利亞 2020年8月[4] B.1.1.207 P681H[5] 多国[6] 无变化[5] 无变化[5]
 英国 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% (43130%) [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
 丹麥 2020年9月[16] B.1.1.298英语Cluster 5[17] Y453F, 69–70deltaHV[18] 可能灭绝[19]
 南非 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% (20113%) 无变化[27] 显著降低抗体中和效力[28][29][14][30]
 日本
 巴西
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% (145174%)[36][C] 致命性增高≈50% (2090%) [37][B][D] 抗体中和效力降低[10]
 印度 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%[E] 正在调查[F] 抗体中和效力降低[46][30]
 美國 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%)[50] 恢复期和疫苗接种后血清中和效力降低
 巴西 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
 英国
 奈及利亞
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
 菲律賓 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]
 印度 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]
 秘魯 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]
 哥伦比亚 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
 博茨瓦纳 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% (6974%) [67] 疫苗对有症状疾病的免疫效果降低[66]
  1. ^ 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英语Variant of concern
  2. ^ 2.0 2.1 The reported confidence or credible interval英语credible interval has a low probability, so the estimated value can only be understood as possible, not certain nor likely.
  3. ^ Another study[37] has estimated that P.1 may be ≈100% (50% CrI, 70140%) more transmissible.[B]
  4. ^ 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% (220985%) more lethal for men in the 20-39 age group, ≈465% (1901003%) more lethal for women in the 20-39 age group and ≈670% (4011083%) for women in the 40-59 age group.[38]
  5. ^ About 64% (26113%) more transmissible than the Alpha variant,[41] so 1.64 × 1.82 ≈ 2.98.
  6. ^ 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

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GISAIDNextstrain英语NextstrainPANGO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

PANGO命名系统的SARS-CoV-2谱系图
随疫情发展,D614G变异英语Variants of SARS-CoV-2#D614G(属B.1演化支[73])逐渐成为目前全球主要传播的严重急性呼吸综合征冠状病毒2类型。[74]

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
A.1–A.6

WIV04/2019(参考基因组[76]

B.1[74]
B.1.1[94]
B.1.1.1
C.1

C.1.2 (B.1.1.1.1.2)[73][77]

C.36書面挪威語C.36 (B.1.1.1.36)[73]

Lambda變異株 (C.37谱系, B.1.1.1.37) [62][78][73]

Alpha變異株(B.1.1.7谱系) [A]

VOC-21FEB-02 (B.1.1.7#E484K)書面挪威語Lineage B.1.1.7 with E484K [3][A]

B.1.1.28

Gamma變異株 (P.1谱系) [A]

P.2谱系英语SARS-CoV-2 Zeta variant (Zeta) [79]

P.3谱系英语SARS-CoV-2 Theta variant (Theta)

B.1.1.207書面挪威語Lineage B.1.1.207

B.1.1.318 (AZ.1 - AZ.5)[73][80]

Omicron變異株(B.1.1.529谱系)[95][73][87][A]

BA.1[81]

BA.2[81]

BA.2.12 (BA.2.12.1)[82][83]

BA.2.75

BA.2.75.2 [84][85][86]

XBB (与 BA2.10.1 重组而形成) [87][88][89]

CH.1.1 [90]

BA.2.86

JN.1

BA.3[87]

BA.4[87]

BA.4.6 [87][91][92]

BA.5

BA.5.1[87]

BA.5.2 (BF.7, BA.5.2.1.7) [87][93]

BA.5.3 (BQ.1, BA.5.3.1.1.1.1.1) [87][94][86][89]

Beta變異株 (Beta, B.1.351谱系) [A]

CAL.20C書面挪威語California-koronavarianten (Epsilon, B.1.427書面挪威語Lineage B.1.427B.1.429書面挪威語Lineage B.1.429) [B]

B.1.525英语SARS-CoV-2 Eta variant (Eta)

B.1.526英语SARS-CoV-2 Iota variant (Iota)

B.1.617谱系[39][106][107]

B.1.617.1英语SARS-CoV-2 Kappa variant (Kappa)

Delta變異株 (B.1.617.2) [96][A]

B.1.617.2.1德语B.1.617#B.1.617.2.1 (Delta Plus, AY.1) [97]

B.1.617.2.4.2 (Delta Plus, AY.4.2) [73][98]

B.1.617.3

B.1.618書面挪威語Lineage B.1.618 [99][100]

Mu變異株(B.1.621譜系)[101][102][103][104]

B.1.640 [105][87]

  1. ^ 1.0 1.1 1.2 1.3 1.4 1.5 高關注變異株英语Variant of concern
  2. ^ 美国疾病控制与预防中心宣布的引发关切的变种英语Variant of concern

關注度之基準

  1. 需要关注的变异株英语Variant of concern(英語:variant of concern,VOC[108]
  2. 需要留意的变异株英语Variant of interest(英語:variant of interest,VOI[108]
  3. 监视下的变异株英语Variant under monitoring(英語:variant under monitoring,VUM[108]

現階段的主流變異株

需要關注的變異株(VOC)

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)

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
  • XBB.1.5:被稱為「海怪克拉肯」(Kraken)
  • XBB.1.16:被稱為「大角星」(Arcturus)
  • EG.5:被稱為「艾里斯」(Eris)
  • BA.2.86:被稱為「皮羅拉」(Pirola)
  • JN.1

過去的主流變異株

需要关注的变异株(Previous VOC)

Alpha(B.1.1.7谱系)

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)

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]。。

Gamma(P.1谱系)

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)

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]

  • 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)

Epsilon(B.1.427譜系、B.1.429譜系)

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)

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)

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)

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)

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)

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)

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)

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

  1. ^ 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

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  21. ^ Lowe, Derek. The New Mutations. In the Pipeline. American Association for the Advancement of Science. 2020-12-22 [2020-12-23]. (原始内容存档于2021-01-29). 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. ^ 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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