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本文主要講述嚴重急性呼吸綜合症冠狀病毒2變異株及其發生的錯義突變。
引發2019冠狀病毒病的嚴重急性呼吸綜合徵冠狀病毒2(SARS-CoV-2冠狀病毒)容易發生突變而產生變異株(英語:Variant (biology)),關鍵病毒蛋白的突變即可能意味着其出現,目前已有多個變異株在世界各地形成並傳播。由於病毒的核酸序列變異有可能導致抗原漂移,而使得病毒得以逃避宿主的免疫應答,並影響疫苗的效力[1],這種現象稱為免疫逃避(英語:antigenic escape)。
已有五種被世界衛生組織認定為值得關注的變異株,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 | 重要突變 | 傳播 | 相對於武漢首次發現變體的臨床變化 | ||||||
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地區 | 日期 | WHO標籤[2] | PANGO譜系 | PHE(英語:Public Health England)變種[3] | Nextstrain(英語:Nextstrain)分化枝 | 傳播力 | 致命性 | 抗原性 | ||
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000000002020-08-01-00002020年8月[4] | — | B.1.1.207 | — | — | P681H[5] | 多國[6] | 無變化[5] | 無變化[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] | 正在調查 | 抗體中和效力略降低[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 | 正在調查 | 正在調查 | 正在調查 | ||
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000000002020-09-01-00002020年9月[16] | — | B.1.1.298(英語:Cluster 5)[17] | — | — | Y453F, 69–70deltaHV[18] | 可能滅絕[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] | 多國[26] | 增高≈6999500000000000000♠50% (7001200000000000000♠20–7000113000000000000♠113%) | 無變化[27] | 顯著降低抗體中和效力 |
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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] | 美國、巴西等68國[35] | 增高≈7000161000000000000♠161% (7002145000000000000♠145–7000174000000000000♠174%) |
致命性增高≈6999500000000000000♠50% (7001200000000000000♠20–6999900000000000000♠90%) |
抗體中和效力降低 |
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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 | 多國 | 增高≈7000198000000000000♠198% |
正在調查[F] | 抗體中和效力降低[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] | 多國[48] | 增高≈6999200000000000000♠20% (6999186000000000000♠18.6%–24.2%) |
恢復期和疫苗接種後血清中和效力降低 | |
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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] | 多國[51] | 單克隆抗體中和效力可能降低,疫苗接種後血清中和效力降低 | ||
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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、美國、德國等69國[54] | 單克隆抗體、恢復期和疫苗接種後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] | 菲律賓、美國等17國[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] | 多國 | 抗體中和效力降低[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、美國、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 |
博茨瓦納、南非等數國 | 有可能提高[66] | 相對於 Delta:3000370000000000000♠−63% (7001690000000000000♠69–6999740000000000000♠74%) [67] | 疫苗對有症狀疾病的免疫效果降低 |
以下為嚴重急性呼吸綜合徵冠狀病毒2主要變種的支序演化樹簡化示意圖。[75]
SARS-CoV-2 |
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B.1.1.7譜系,WHO命名為「Alpha」,又稱VOC 202012/01,並稱501Y.V1變種。部分與「N501Y」突變有關。有23個病毒基因變異點。
P.1譜系,WHO命名為「Gamma」,又稱501Y.V3變種。包括三個相關突變:「N501Y」、「E484K」和「K417T」。
B.1.617譜系是2020年10月於印度發現的一種雙突變變異株。直到2021年1月前,該變異株的感染人數都寥寥無幾。4月時該變異株已經蔓延至超過20個國家,遍及南極洲和南美洲以外的所有大洲。[120][121][122]
在該變異株約15個譜系定義突變中包括刺突蛋白突變D111D(同義突變(英語:synonymous substitution))、G142D[123]、P681R、E484Q[107]、L452R[124],其中後兩個突變可能會影響恢復期血漿和單克隆抗體的中和作用。[125]
英國公共衛生部(英語:Public Health England)於5月7日將B.1.617.2列為「高關注變異株(英語:Variant of concern)」,命名為VOC-21APR-02。[96][126]
5月10日WHO稱,因為B.1.617較高的傳染性,該變異正被列為全球範圍內受關切變種[127]。6月1日WHO將受關切變種限定為B.1.617譜系當中的B.1.617.2(Delta)變種。[128] 稍後WHO將B.1.617.2命名為「Delta」。
5月21日,越南宣布發現一種傳播性更高,由Delta變異株加上Alpha變異株上突變的病毒株。[129]6月3日,WHO澄清該病毒株不符合新混合變種的定義,並將其列為帶有突變的Delta變種。[130]
據報道,Delta變異株基本傳染數R0大約為6(有說法稱其高達8或9)[131],是嚴重急性呼吸道症候群冠狀病毒2型原始毒株基本傳染數的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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