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新冠病毒Spike新型突变体

背景
2020年12月底,英国官员发出紧急报告,称一种具有高度传染性的新冠病毒突变株(B.1.1.7)正在英国传播。基因组的测序结果表明,B.1.1.7携带着多种基因突变,其中有些基因突变可能增强它的传播能力。最受科学家们关注的基因突变包括在新冠病毒S蛋白的受体结合域(RBD)上出现的N501Y突变。此前的动物研究显示,这一突变可以增强刺突蛋白与其受体ACE2的结合能力,从而可能提高病毒的感染能力。
根据美国疾控中心(CDC)报道,B.1.1.7病毒株具有23个突变,包括14个非同义突变 (氨基酸改变)、6个同义突变(非氨基酸改变)和3处氨基酸缺失。

>>> 点击查看新冠病毒与宿主细胞互作图

除了英国突变株B.1.1.7外,在南非也出现了新冠病毒的另一突变株,称为20C / 501Y.V2或B.1.351。南非突变株的RBD蛋白上发现有3个突变,其中N501Y突变与英国突变株一致。
ACROBiosystems提供覆盖N501Y、HV69-70del、D614G、P681H等B.1.1.7中包含的9个突变位点的一系列Spike蛋白,包括单点突变和多点突变,可应用于新冠病毒传染性和致病性机理、疫苗免疫应答、中和抗体作用等方面研究中。
产品列表
  • 重要新型蛋白突变
  • 所有新冠突变蛋白
分子 货号 标签 宿主 产品描述 来源 订购/预购
S protein SPN-C52Hc His Tag HEK293 SARS-CoV-2 S protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V), His Tag  B.1.351

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S protein SPN-C52Hk His Tag HEK293 SARS-CoV-2 (COVID-19) S protein (L18F, D80A, D215G, 242-244del, R246I, K417N, E484K, N501Y, D614G, A701V), His Tag B.1.351

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S protein SPN-C82E4 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (L18F, D80A, D215G, 242-244del, R246I, K417N, E484K, N501Y, D614G, A701V), His,Avitag™ B.1.351

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S protein SPN-C52H6 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein (HV69-70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), His Tag  B.1.1.7

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S protein SPN-C82E5 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (HV69-70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), His,Avitag™ B.1.1.7

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S protein SPN-C52Hg His Tag HEK293 SARS-CoV-2 (COVID-19) S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F), His Tag P.1

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S protein SPN-C82E6 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F), His,Avitag™ P.1

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S protein SPN-C52H3 His Tag HEK293 SARS-CoV-2 S protein (D614G), His Tag, Super stable trimer (MALS verified) B.1.1.7/B.1.351/P.1

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S protein SPN-C82E3 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (D614G), His,Avitag™, Super stable trimer (MALS verified) B.1.1.7/B.1.351/P.1

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S1 protein S1N-C52Hd His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (HV69-70del), His Tag  B.1.1.7

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S1 protein S1N-C52Hc His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (Y144del), His Tag  B.1.1.7

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S1 protein S1N-C52Hb His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (P681H), His Tag  B.1.1.7

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S1 protein S1N-C52Hk His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (HV69-70del, N501Y, D614G), His Tag  B.1.1.7

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S1 protein S1N-C52Hr His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (HV69-70del, Y144del, N501Y, A570D, D614G, P681H), His Tag B.1.1.7

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S1 protein S1N-C52Hm His Tag HEK293 SARS-CoV-2 S1 protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G), His Tag  B.1.351

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S1 protein S1N-C52Hg His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (N501Y), His Tag  B.1.1.7/B.1.351/P.1

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S1 protein S1N-C5256 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (D614G), His Tag  B.1.1.7/B.1.351/P.1

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S1 protein S1N-C52Hp His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y), His Tag P.1

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S1 protein S1N-C52Hn His Tag HEK293 SARS-CoV-2 S1 protein (E484K, D614G), His Tag B.1.351/P.1

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S1 protein S1N-C82E3 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 (COVID-19) S1 protein (D614G), His,Avitag™ B.1.1.7/B.1.351/P.1

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S1 protein S1N-C52H9 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (A570D), His Tag B.1.1.7

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S1 protein NTD S1D-C52Hd His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (HV69-70del, Y144del), His Tag B.1.1.7

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S1 protein NTD S1D-C52H9 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (L18F, D80A, D215G, R246I), His Tag  B.1.351

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S1 protein NTD S1D-C52Hc His Tag HEK293 SARS-CoV-2 (COVID-19) S protein NTD (L18F, D80A, D215G, 242-244del, R246I), His Tag B.1.351

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S1 protein NTD S1D-C52He His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (L18F, T20N, P26S, D138Y, R190S), His Tag P.1

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S protein RBD SPD-C82E6 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein RBD (N501Y), His,Avitag™ B.1.1.7/B.1.351/P.1

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S protein RBD SPD-C52Hs His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417N), His Tag B.1.351

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S protein RBD SRD-C52H3 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (E484K), His Tag B.1.351/P.1

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S protein RBD SPD-C52Hp His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417N, E484K, N501Y), His Tag  B.1.351

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S protein RBD SPD-C82E5 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein RBD (K417N,E484K,N501Y), His,Avitag™ B.1.351

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S protein RBD SPD-C52Hn His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (N501Y), His Tag  B.1.1.7/B.1.351/P.1

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S protein RBD SPD-C52Ht His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417T), His Tag P.1

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S protein RBD SPD-C52Hr His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417T, E484K, N501Y), His Tag P.1

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S protein RBD SPD-C82E7 His & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein RBD (K417T, E484K, N501Y), His,Avitag™ P.1

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S2 protein S2N-C52Hd His Tag HEK293 SARS-CoV-2 (COVID-19) S2 protein (T716I, S982A, D1118H), His Tag B.1.1.7

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S2 protein S2N-C52Hc His Tag HEK293 SARS-CoV-2 (COVID-19) S2 protein (A701V), His Tag B.1.351

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S2 protein S2N-C52He His Tag HEK293 SARS-CoV-2 (COVID-19) S2 protein (T1027I, V1176F), His Tag P.1

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Nucleocapsid protein NUN-C52H8 His Tag HEK293 SARS-CoV-2 Nucleocapsid protein (D3L, S235F), His Tag  B.1.1.7

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分子 货号 种属 标签 宿主 产品描述 订购/预购
S protein SPN-C52H6 SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein (HV69-70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), His Tag

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S protein SPN-C82E5 SARS-CoV-2 (B.1.1.7) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (HV69-70del, Y144del, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), His,Avitag™

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S protein SPN-C52H3 SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag HEK293 SARS-CoV-2 S protein (D614G), His Tag, Super stable trimer (MALS verified)

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S protein SPN-C82E3 SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (D614G), His,Avitag™, Super stable trimer (MALS verified)

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S protein SPN-C52Hc SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 S protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G, A701V), His Tag

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S protein SPN-C52Hk SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein (L18F, D80A, D215G, 242-244del, R246I, K417N, E484K, N501Y, D614G, A701V), His Tag

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S protein SPN-C82E4 SARS-CoV-2 (B.1.351) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (L18F, D80A, D215G, 242-244del, R246I, K417N, E484K, N501Y, D614G, A701V), His,Avitag™

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S protein SPN-C52Hg SARS-CoV-2 (P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F), His Tag

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S protein SPN-C82E6 SARS-CoV-2 (P.1) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y, T1027I, V1176F), His,Avitag™

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S protein SPN-C52Hd SARS-CoV-2 His Tag HEK293 SARS-CoV-2 S protein (F817P, A892P, A899P, A942P, K986P, V987P), His Tag

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S protein S1N-C52Hd SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (HV69-70del), His Tag

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S protein S1N-C52Hc SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (Y144del), His Tag

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S1 protein S1N-C52Hf SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (E583D), His Tag

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S1 protein S1N-C52Hn SARS-CoV-2 (B.1.351/P.1) His Tag HEK293 SARS-CoV-2 S1 protein (E484K, D614G), His Tag

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S1 protein S1N-C52Hr SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (HV69-70del, Y144del, N501Y, A570D, D614G, P681H), His Tag

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S1 protein S1N-C52Hp SARS-CoV-2 (P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, D614G, H655Y), His Tag

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S1 protein NTD S1D-C52H8 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (A222V), His Tag

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S1 protein NTD S1D-C52H7 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (N234Q), His Tag

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S1 protein NTD S1D-C52H5 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (A262S), His Tag

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S1 protein NTD S1D-C52H4 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (P272L), His Tag

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S1 protein NTD S1D-C52H9 SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 S1 protein NTD (L18F, D80A, D215G, R246I), His Tag

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S1 protein NTD S1D-C52Hd SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (HV69-70del, Y144del), His Tag

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S1 protein NTD S1D-C52Hc SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein NTD (L18F, D80A, D215G, 242-244del, R246I), His Tag

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S1 protein NTD S1D-C52He SARS-CoV-2 (P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein NTD (L18F, T20N, P26S, D138Y, R190S), His Tag

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S protein RBD SPD-S52H5 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (N354D), His Tag

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S protein RBD SPD-S52H4 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (V367F), His Tag

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S protein RBD SPD-S52H8 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (R408I), His Tag

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S protein RBD SPD-C52Hs SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417N), His Tag

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S protein RBD SPD-C52Ht SARS-CoV-2 (P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417T), His Tag

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S protein RBD SPD-S52H7 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (W436R), His Tag

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S protein RBD SPD-C52Hg SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (N439K), His Tag

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S protein RBD SRD-C52H2 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (N440K), His Tag

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S protein RBD SPD-C52He SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (L452R), His Tag

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S protein RBD SPD-C52Hk SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (Y453F), His Tag

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S protein RBD SPD-C52Hd SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (A475V), His Tag

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S protein RBD SPD-C52H4 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (G476S), His Tag

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S protein RBD SPD-C52Hm SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (S477N), His Tag

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S protein RBD SPD-C52H5 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (V483A), His Tag

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S protein RBD SRD-C52H3 SARS-CoV-2 (B.1.351/P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (E484K), His Tag

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S protein RBD SPD-C52Hf SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (F490L), His Tag

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S protein RBD SPD-C82E6 SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein RBD (N501Y), His,Avitag™

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S protein RBD SPD-C52Hn SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (N501Y), His Tag

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S protein RBD SPD-C52Hp SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417N, E484K, N501Y), His Tag

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S protein RBD SPD-C82E5 SARS-CoV-2 (B.1.351) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein RBD (K417N,E484K,N501Y), His,Avitag™

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S protein RBD SPD-C52Hr SARS-CoV-2 (P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S protein RBD (K417T, E484K, N501Y), His Tag

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S protein RBD SPD-C82E7 SARS-CoV-2 (P.1) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 S protein RBD (K417T, E484K, N501Y), His,Avitag™

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S1 protein S1N-C52Hg SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (N501Y), His Tag

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S1 protein S1N-C52H9 SARS-CoV-2 His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (A570D), His Tag

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S1 protein S1N-C5256 SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (D614G), His Tag

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S1 protein S1N-C82E3 SARS-CoV-2 (B.1.1.7/B.1.351/P.1) His Tag & Avi Tag HEK293 Biotinylated SARS-CoV-2 (COVID-19) S1 protein (D614G), His,Avitag™

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S1 protein S1N-C52Hb SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (P681H), His Tag

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S1 protein S1N-C52Hm SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 S1 protein (L18F, D80A, D215G, R246I, K417N, E484K, N501Y, D614G), His Tag

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S1 protein S1N-C52Hk SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S1 protein (HV69-70del, N501Y, D614G), His Tag

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S2 protein S2N-C52Hc SARS-CoV-2 (B.1.351) His Tag HEK293 SARS-CoV-2 (COVID-19) S2 protein (A701V), His Tag

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S2 protein S2N-C52Hd SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 (COVID-19) S2 protein (T716I, S982A, D1118H), His Tag

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S2 protein S2N-C52He SARS-CoV-2 (P.1) His Tag HEK293 SARS-CoV-2 (COVID-19) S2 protein (T1027I, V1176F), His Tag

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Nucleocapsid protein NUN-C52H8 SARS-CoV-2 (B.1.1.7) His Tag HEK293 SARS-CoV-2 Nucleocapsid protein (D3L, S235F), His Tag

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验证数据
高纯度经SDS-PAGE验证

SARS-CoV-2 (COVID-19) S protein RBD (N501Y), His Tag (Cat.No. SPD-C52Hn)on SDS-PAGE under reducing (R) condition. The gel was stained overnight with Coomassie Blue. The purity of the protein is greater than 90%.

SARS-CoV-2 (COVID-19) S1 protein (HV69-70del), His Tag (Cat.No. S1N-C52Hd)on SDS-PAGE under reducing (R) condition. The gel was stained overnight with Coomassie Blue. The purity of the protein is greater than 90%.

与ACE2、中和抗体结合活性高

Immobilized SARS-CoV-2 S1 protein (D614G), His Tag (Cat. No. S1N-C5256) at 2 μg/mL (100 μL/well) can bind Human ACE2, Fc Tag (Cat. No. AC2-H5257) with a linear range of 0.2-3 ng/mL.

Protocol

Immobilized SARS-CoV-2 S1 protein (D614G), His Tag (Cat. No. S1N-C5256) at 2 μg/mL (100 μL/well) can bind Anti-SARS-CoV-2 Neutralizing Antibody, Human IgG1 (Cat. No. SAD-S35) ) with a linear range of 0.2-3 ng/mL.

Protocol

前沿进展
  • Antibody Resistance of SARS-CoV-2 Variants B.1.351 and B.1.1.7

    Pengfei Wang, Manoj S. Nair, Lihong Liu et al

    doi: https://doi.org/10.1101/2021.01.25.428137

    Abstract: The COVID-19 pandemic has ravaged the globe, and its causative agent, SARS-CoV-2, continues to rage. Prospects of ending this pandemic rest on the development of effective interventions. Single and combination monoclonal antibody(mAb) therapeutics have received emergency use authorization, with more in the pipeline. Furthermore, multiple vaccine constructs have shown promise8, including two with ~95% protective efficacy against COVID-19. However, these interventions were directed toward the initial SARS-CoV-2 that emerged in 2019. The recent emergence of new SARS-CoV-2 variants B.1.1.7 in the UK and B.1.351 in South Africa is of concern because of their purported ease of transmission and extensive mutations in the spike protein. We now report that B.1.1.7 is refractory to neutralization by most mAbs to the N-terminal domain (NTD) of spike and relatively resistant to a few mAbs to the receptor-binding domain (RBD). It is not more resistant to convalescent plasma or vaccinee sera. Findings on B.1.351 are more worrisome in that this variant is not only refractory to neutralization by most NTD mAbs but also by multiple individual mAbs to the receptor-binding motif on RBD, largely due to an E484K mutation. Moreover, B.1.351 is markedly more resistant to neutralization by convalescent plasma (9.4 fold) and vaccinee sera (10.3-12.4 fold). B.1.351 and emergent variants with similar spike mutations present new challenges for mAb therapy and threaten the protective efficacy of current vaccines.

  • SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma

    Constantinos Kurt Wibmer, Frances Ayres, Tandile Hermanus et al

    doi: https://doi.org/10.1101/2021.01.18.427166

    Abstract: SARS-CoV-2 501Y.V2, a novel lineage of the coronavirus causing COVID-19, contains multiple mutations within two immunodominant domains of the spike protein. Here we show that this lineage exhibits complete escape from three classes of therapeutically relevant monoclonal antibodies. Furthermore 501Y.V2 shows substantial or complete escape from neutralizing antibodies in COVID-19 convalescent plasma. These data highlight the prospect of reinfection with antigenically distinct variants and may foreshadow reduced efficacy of current spike-based vaccines.

  • Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

    Allison J. Greaney, Andrea N. Loes, Katharine H.D. Crawford et al

    doi: https://doi.org/10.1101/2020.12.31.425021

    Abstract: The evolution of SARS-CoV-2 could impair recognition of the virus by human antibody-mediated immunity. To facilitate prospective surveillance for such evolution, we map how convalescent serum antibodies are impacted by all mutations to the spike’s receptor-binding domain (RBD), the main target of serum neutralizing activity. Binding by polyclonal serum antibodies is affected by mutations in three main epitopes in the RBD, but there is substantial variation in the impact of mutations both among individuals and within the same individual over time. Despite this inter- and intra-person heterogeneity, the mutations that most reduce antibody binding usually occur at just a few sites in the RBD’s receptor binding motif. The most important site is E484, where neutralization by some sera is reduced >10-fold by several mutations, including one in emerging viral lineages in South Africa and Brazil. Going forward, these serum escape maps can inform surveillance of SARS-CoV-2 evolution.

  • Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

    Volz, Mishra*, Chand et al

    doi: https://doi.org/10.1101/2020.12.30.20249034

    Abstract: 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. Fourth, we assess the association of VOC frequency with independent estimates of the overall SARS-CoV-2 reproduction number through time. Finally, we fit a semi-mechanistic model directly to local VOC and non-VOC case incidence to estimate the reproduction numbers over time for each. There is a consensus among all analyses that the VOC has a substantial transmission advantage, with the estimated difference in reproduction numbers between VOC and non-VOC ranging between 0.4 and 0.7, and the ratio of reproduction numbers varying between 1.4 and 1.8. We note that these estimates of transmission advantage apply to a period where high levels of social distancing were in place in England; extrapolation to other transmission contexts therefore requires caution.

  • Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England

    Davies, Barnard, Jarvis et al

    doi: https://doi.org/10.1101/2020.12.24.20248822

    Abstract: A novel SARS-CoV-2 variant, VOC 202012/01, emerged in southeast England in November 2020 and appears to be rapidly spreading towards fixation. We fitted a two-strain mathematical model of SARS-CoV-2 transmission to observed COVID-19 hospital admissions, hospital and ICU bed occupancy, and deaths; SARS-CoV-2 PCR prevalence and seroprevalence; and the relative frequency of VOC 202012/01 in the three most heavily affected NHS England regions (South East, East of England, and London). We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2. We were unable to find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants. Nevertheless, the increase in transmissibility is likely to lead to a large increase in incidence, with COVID-19 hospitalisations and deaths projected to reach higher levels in 2021 than were observed in 2020, even if regional tiered restrictions implemented before 19 December are maintained. Our estimates suggest that control measures of a similar stringency to the national lockdown implemented in England in November 2020 are unlikely to reduce the effective reproduction number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed. We project that large resurgences of the virus are likely to occur following easing of control measures. It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden.

  • Early empirical assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020

    Leung, Shum, Leung et al

    doi: https://doi.org/10.1101/2020.12.20.20248581

    Abstract: Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor binding domain of the spike protein have rapidly become prevalent in the UK. We estimated that the earlier 501Y lineage without amino acid deletion Δ69/Δ70 circulating mainly between early September to mid-November was 10% (6-13%) more transmissible than the 501N lineage, and the currently dominant 501Y lineage with amino acid deletion Δ69/Δ70 circulating since late September was 75% (70-80%) more transmissible than the 501N lineage.

  • Mutation Landscape of SARS-CoV-2 in Africa

    Nassir, Musanabaganwa, Mwikarago

    doi: https://doi.org/10.1101/2020.12.20.423630

    Abstract: COVID-19 disease has had a relatively less severe impact in Africa. To understand the role of SARS CoV2 mutations on COVID-19 disease in Africa, we analysed 282 complete nucleotide sequences from African isolates deposited in the NCBI Virus Database. Sequences were aligned against the prototype Wuhan sequence (GenBank accession: NC_045512.2) in BWA v. 0.7.17. SAM and BAM files were created, sorted and indexed in SAMtools v. 1.10 and marked for duplicates using Picard v. 2.23.4. Variants were called with mpileup in BCFtools v. 1.11. Phylograms were created using Mr. Bayes v 3.2.6. A total of 2,349 single nucleotide polymorphism (SNP) profiles across 294 sites were identified. Clades associated with severe disease in the United States, France, Italy, and Brazil had low frequencies in Africa (L84S=2.5%, L3606F=1.4%, L3606F/V378I/=0.35, G251V=2%). Sub Saharan Africa (SSA) accounted for only 3% of P323L and 4% of Q57H mutations in Africa. Comparatively low infections in SSA were attributed to the low frequency of the D614G clade in earlier samples (25% vs 67% global). Higher disease burden occurred in countries with higher D614G frequencies (Egypt=98%, Morocco=90%, Tunisia=52%, South Africa) with D614G as the first confirmed case. V367F, D364Y, V483A and G476S mutations associated with efficient ACE2 receptor binding and severe disease were not observed in Africa. 95% of all RdRp mutations were deaminations leading to CpG depletion and possible attenuation of virulence. More genomic and experimental studies are needed to increase our understanding of the temporal evolution of the virus in Africa, clarify our findings, and reveal hot spots that may undermine successful therapeutic and vaccine interventions.

  • Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown

    Tegally, Wilkinson, Lessells et al

    doi: https://www.medrxiv.org/content/10.1101/2020.10.28.20221143v1

    Abstract: In March 2020, the first cases of COVID-19 were reported in South Africa. The epidemic spread very fast despite an early and extreme lockdown and infected over 600,000 people, by far the highest number of infections in an African country. To rapidly understand the spread of SARS-CoV-2 in South Africa, we formed the Network for Genomics Surveillance in South Africa (NGS-SA). Here, we analyze 1,365 high quality whole genomes and identify 16 new lineages of SARS-CoV-2. Most of these unique lineages have mutations that are found hardly anywhere else in the world. We also show that three lineages spread widely in South Africa and contributed to ∼42% of all of the infections in the country. This included the first identified C lineage of SARS-CoV-2, C.1, which has 16 mutations as compared with the original Wuhan sequence. C.1 was the most geographically widespread lineage in South Africa, causing infections in multiple provinces and in all of the eleven districts in KwaZulu-Natal (KZN), the most sampled province. Interestingly, the first South-African specific lineage, B.1.106, which was identified in April 2020, became extinct after nosocomial outbreaks were controlled. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify and control the spread of SARS-CoV-2.

  • Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa

    Tegally, Wilkinson, Giovanetti et al

    doi: https://doi.org/10.1101/2020.12.21.20248640

    Summary: Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.

  • Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report

    Giandharia, Pillaya, Wilkinson et al

    Int J Infect Dis(2020)11, 128

    doi: https://doi.org/10.1016/j.ijid.2020.11.128

    Abstract: Objectives: The Network for Genomic Surveillance in South Africa (NGS-SA) was formed to investigate the introduction and understand the early transmission dynamics of the SARS-CoV-2 epidemic in South-Africa.
    Design: This paper presents the first results from this group, which is a molecular epidemiological study of the first 21 SARS-CoV-2 whole genomes sampled in the first port of entry – KwaZulu-Natal (KZN) –during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), it aimed to shed light on the patterns of infections in South Africa.
    Results: Two of the largest provinces – Gauteng and KZN – had a slow growth rate for the number of detected cases, while the epidemic spread faster in the Western Cape and Eastern Cape. The estimates of transmission potential suggested a decrease towards R = 1 since the first cases and deaths, but a subsequent estimated R average of 1.39 between 6–18 May 2020. It was also demonstrated that early transmission in KZN was associated with multiple international introductions and dominated by lineages B1 and B. Evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic was also provided.
    Conclusion: The COVID-19 pandemic in South Africa was very heterogeneous in its spatial dimension, with many distinct introductions of SARS-CoV2 in KZN and evidence of nosocomial transmission, which inflated early mortality in KZN. The epidemic at the local level was still developing and NGS-SA aimed to clarify the dynamics in South Africa and devise the most effective measures as the outbreak evolved.

  • Brief report: New Variant Strain of SARS-CoV-2 Identified in Travelers from Brazil

    January 12, 2021

    National Institute of Infectious Diseases, JAPAN

    Technical detail: The variant isolate (GISAID ID: EPI_ISL_792680 to 792683) belongs to B.1.1.248 lineage and has 12 mutations in the spike protein, including N501Y and E484K. - N501Y is a mutation found in variant strains including VOC-202012/01 and 501Y.V2, implicated to increase transmissibility. - The E484K was reported to be an escape mutation from a monoclonal antibody which neutralize SARSCoV-2 (1,2). The E484K has been observed in variant isolates escaping from convalescent plasma (3) and with a 10-fold decrease in neutralization capability by convalescent plasma (4)(both in preprint articles), suggesting possible change in antigenicity. - In Brazil, a variant isolate with E484K belonging to B.1.1.248 was reported on January 6, 2021 (5), but it is not identical to the new variant isolate identified in Japan.

  • Researchers Discover New Variant of COVID-19 Virus in Columbus, Ohio

    January 13, 2021

    The Ohio State University Wexner Medical Center

    Scientists at The Ohio State University Wexner Medical Center and College of Medicine have discovered a new variant of SARS-Cov-2, the virus that causes COVID-19. The new variant carries a mutation identical to the U.K. strain, but it likely arose in a virus strain already present in the United States. The researchers also report the evolution of another U.S. strain that acquired three other gene mutations not previously seen together in SARS-CoV2.

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