Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
Identification of SARS-CoV-2 Omicron variant using spike gene target failure and genotyping assays, Gauteng, South Africa, 2021.
复制标题
DOI：
10.1002/jmv.27797
复制
发表时间：
2022-08
影响因子：
12.7
通讯作者：
Treurnicht, Florette K.
中科院分区：
文献类型：
--
作者：
Subramoney, Kathleen;Mtileni, Nkhensani;Bharuthram, Avani;Davis, Ashlyn;Kalenga, Beauty;Rikhotso, Mikateko;Maphahlele, Mpho;Giandhari, Jennifer;Naidoo, Yeshnee;Pillay, Sureshnee;Ramphal, Upasana;Ramphal, Yajna;Tegally, Houriiyah;Wilkinson, Eduan;Mohale, Thabo;Ismail, Arshad;Mashishi, Bonolo;Mbenenge, Nonhlanhla;de Oliveira, Tulio;Makatini, Zinhle;Fielding, Burtram C.;Treurnicht, Florette K.
Omicron BA. 1的传播导致2021年11月南非严重急性呼吸系统综合征冠状病毒2型（SARS-CoV-2）病例迅速增加，因此需要使用更快速的检测方法。因此，我们评估了使用基因分型测定法检测Omicron BA.1的能力，以确定南非豪登省SARS-CoV-2阳性样本中的特定突变。对选择的所有样本进行TaqPath™ COVID-19真实的实时聚合酶链反应测定，以鉴定刺突基因靶失败（SGTF）。使用SARS-CoV-2基因分型检测del 69/70和K417 N突变。对基因分型样本的子集进行全基因组测序，以确认这些结果。在收到的阳性样本中，随机选择11.0%（175/1589），以评估SGTF和检测del 69/70和K417 N突变的基因分型检测是否可以识别Omicron BA.1。我们在98.9%（173/175）的样本中鉴定出SGTF，其中88.0%（154/175）具有del 69/70和K417 N突变。测序的基因型样本（45.7%; 80/175）证实Omicron BA.1（97.5%; 78/80）。我们的数据表明，用于检测del 69/70和K417 N与SGTF偶联的基因分型可有效排除α和β变体并快速检测Omicron BA.1。然而，我们仍然需要检测独特突变的检测方法，以区分其他Omicron亚系。因此，在资源有限的情况下，使用基因分型检测来检测SARS-CoV-2的新优势或新兴谱系将是有益的。
The circulation of Omicron BA.1 led to the rapid increase in severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) cases in South Africa in November 2021, which warranted the use of more rapid detection methods. We, therefore, assessed the ability to detect Omicron BA.1 using genotyping assays to identify specific mutations in SARS‐CoV‐2 positive samples, Gauteng province, South Africa. The TaqPath™ COVID‐19 real‐time polymerase chain reaction assay was performed on all samples selected to identify spike gene target failure (SGTF). SARS‐CoV‐2 genotyping assays were used for the detection of del69/70 and K417N mutation. Whole‐genome sequencing was performed on a subset of genotyped samples to confirm these findings. Of the positive samples received, 11.0% (175/1589) were randomly selected to assess if SGTF and genotyping assays, that detect del69/70 and K417N mutations, could identify Omicron BA.1. We identified SGTF in 98.9% (173/175) of samples, of which 88.0% (154/175) had both the del69/70 and K417N mutation. The genotyped samples (45.7%; 80/175) that were sequenced confirmed Omicron BA.1 (97.5%; 78/80). Our data show that genotyping for the detection of the del69/70 and K417N coupled with SGTF is efficient to exclude Alpha and Beta variants and rapidly detect Omicron BA.1. However, we still require assays for the detection of unique mutations that will allow for the differentiation between other Omicron sublineages. Therefore, the use of genotyping assays to detect new dominant or emerging lineages of SARS‐CoV‐2 will be beneficial in limited‐resource settings.
登录
查看更多内容
DOI：
10.1126/science.abj4336
发表时间：
2021-10-22
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Wilkinson E;Giovanetti M;Tegally H;San JE;Lessells R;Cuadros D;Martin DP;Rasmussen DA;Zekri AN;Sangare AK;Ouedraogo AS;Sesay AK;Priscilla A;Kemi AS;Olubusuyi AM;Oluwapelumi AOO;Hammami A;Amuri AA;Sayed A;Ouma AEO;Elargoubi A;Ajayi NA;Victoria AF;Kazeem A;George A;Trotter AJ;Yahaya AA;Keita AK;Diallo A;Kone A;Souissi A;Chtourou A;Gutierrez AV;Page AJ;Vinze A;Iranzadeh A;Lambisia A;Ismail A;Rosemary A;Sylverken A;Femi A;Ibrahimi A;Marycelin B;Oderinde BS;Bolajoko B;Dhaala B;Herring BL;Njanpop-Lafourcade BM;Kleinhans B;McInnis B;Tegomoh B;Brook C;Pratt CB;Scheepers C;Akoua-Koffi CG;Agoti CN;Peyrefitte C;Daubenberger C;Morang'a CM;Nokes DJ;Amoako DG;Bugembe DL;Park D;Baker D;Doolabh D;Ssemwanga D;Tshiabuila D;Bassirou D;Amuzu DSY;Goedhals D;Omuoyo DO;Maruapula D;Foster-Nyarko E;Lusamaki EK;Simulundu E;Ong'era EM;Ngabana EN;Shumba E;El Fahime E;Lokilo E;Mukantwari E;Philomena E;Belarbi E;Simon-Loriere E;Anoh EA;Leendertz F;Ajili F;Enoch FO;Wasfi F;Abdelmoula F;Mosha FS;Takawira FT;Derrar F;Bouzid F;Onikepe F;Adeola F;Muyembe FM;Tanser F;Dratibi FA;Mbunsu GK;Thilliez G;Kay GL;Githinji G;van Zyl G;Awandare GA;Schubert G;Maphalala GP;Ranaivoson HC;Lemriss H;Anise H;Abe H;Karray HH;Nansumba H;Elgahzaly HA;Gumbo H;Smeti I;Ayed IB;Odia I;Ben Boubaker IB;Gaaloul I;Gazy I;Mudau I;Ssewanyana I;Konstantinus I;Lekana-Douk JB;Makangara JC;Tamfum JM;Heraud JM;Shaffer JG;Giandhari J;Li J;Yasuda J;Mends JQ;Kiconco J;Morobe JM;Gyapong JO;Okolie JC;Kayiwa JT;Edwards JA;Gyamfi J;Farah J;Nakaseegu J;Ngoi JM;Namulondo J;Andeko JC;Lutwama JJ;O'Grady J;Siddle K;Adeyemi KT;Tumedi KA;Said KM;Hae-Young K;Duedu KO;Belyamani L;Fki-Berrajah L;Singh L;Martins LO;Tyers L;Ramuth M;Mastouri M;Aouni M;El Hefnawi M;Matsheka MI;Kebabonye M;Diop M;Turki M;Paye M;Nyaga MM;Mareka M;Damaris MM;Mburu MW;Mpina M;Nwando M;Owusu M;Wiley MR;Youtchou MT;Ayekaba MO;Abouelhoda M;Seadawy MG;Khalifa MK;Sekhele M;Ouadghiri M;Diagne MM;Mwenda M;Allam M;Phan MVT;Abid N;Touil N;Rujeni N;Kharrat N;Ismael N;Dia N;Mabunda N;Hsiao NY;Silochi NB;Nsenga N;Gumede N;Mulder N;Ndodo N;Razanajatovo NH;Iguosadolo N;Judith O;Kingsley OC;Sylvanus O;Peter O;Femi O;Idowu O;Testimony O;Chukwuma OE;Ogah OE;Onwuamah CK;Cyril O;Faye O;Tomori O;Ondoa P;Combe P;Semanda P;Oluniyi PE;Arnaldo P;Quashie PK;Dussart P;Bester PA;Mbala PK;Ayivor-Djanie R;Njouom R;Phillips RO;Gorman R;Kingsley RA;Carr RAA;El Kabbaj S;Gargouri S;Masmoudi S;Sankhe S;Lawal SB;Kassim S;Trabelsi S;Metha S;Kammoun S;Lemriss S;Agwa SHA;Calvignac-Spencer S;Schaffner SF;Doumbia S;Mandanda SM;Aryeetey S;Ahmed SS;Elhamoumi S;Andriamandimby S;Tope S;Lekana-Douki S;Prosolek S;Ouangraoua S;Mundeke SA;Rudder S;Panji S;Pillay S;Engelbrecht S;Nabadda S;Behillil S;Budiaki SL;van der Werf S;Mashe T;Aanniz T;Mohale T;Le-Viet T;Schindler T;Anyaneji UJ;Chinedu U;Ramphal U;Jessica U;George U;Fonseca V;Enouf V;Gorova V;Roshdy WH;Ampofo WK;Preiser W;Choga WT;Bediako Y;Naidoo Y;Butera Y;de Laurent ZR;Sall AA;Rebai A;von Gottberg A;Kouriba B;Williamson C;Bridges DJ;Chikwe I;Bhiman JN;Mine M;Cotten M;Moyo S;Gaseitsiwe S;Saasa N;Sabeti PC;Kaleebu P;Tebeje YK;Tessema SK;Happi C;Nkengasong J;de Oliveira T
通讯作者：
de Oliveira T
DOI：
10.1016/s0140-6736(22)00017-4
发表时间：
2022-01-29
期刊：
Lancet (London, England)
影响因子：
--
作者：
Wolter N;Jassat W;Walaza S;Welch R;Moultrie H;Groome M;Amoako DG;Everatt J;Bhiman JN;Scheepers C;Tebeila N;Chiwandire N;du Plessis M;Govender N;Ismail A;Glass A;Mlisana K;Stevens W;Treurnicht FK;Makatini Z;Hsiao NY;Parboosing R;Wadula J;Hussey H;Davies MA;Boulle A;von Gottberg A;Cohen C
通讯作者：
Cohen C
DOI：
10.1126/science.abn4947
发表时间：
2022-05-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Pulliam JRC;van Schalkwyk C;Govender N;von Gottberg A;Cohen C;Groome MJ;Dushoff J;Mlisana K;Moultrie H
通讯作者：
Moultrie H
影响因子：
64.8
作者：
Viana R;Moyo S;Amoako DG;Tegally H;Scheepers C;Althaus CL;Anyaneji UJ;Bester PA;Boni MF;Chand M;Choga WT;Colquhoun R;Davids M;Deforche K;Doolabh D;du Plessis L;Engelbrecht S;Everatt J;Giandhari J;Giovanetti M;Hardie D;Hill V;Hsiao NY;Iranzadeh A;Ismail A;Joseph C;Joseph R;Koopile L;Kosakovsky Pond SL;Kraemer MUG;Kuate-Lere L;Laguda-Akingba O;Lesetedi-Mafoko O;Lessells RJ;Lockman S;Lucaci AG;Maharaj A;Mahlangu B;Maponga T;Mahlakwane K;Makatini Z;Marais G;Maruapula D;Masupu K;Matshaba M;Mayaphi S;Mbhele N;Mbulawa MB;Mendes A;Mlisana K;Mnguni A;Mohale T;Moir M;Moruisi K;Mosepele M;Motsatsi G;Motswaledi MS;Mphoyakgosi T;Msomi N;Mwangi PN;Naidoo Y;Ntuli N;Nyaga M;Olubayo L;Pillay S;Radibe B;Ramphal Y;Ramphal U;San JE;Scott L;Shapiro R;Singh L;Smith-Lawrence P;Stevens W;Strydom A;Subramoney K;Tebeila N;Tshiabuila D;Tsui J;van Wyk S;Weaver S;Wibmer CK;Wilkinson E;Wolter N;Zarebski AE;Zuze B;Goedhals D;Preiser W;Treurnicht F;Venter M;Williamson C;Pybus OG;Bhiman J;Glass A;Martin DP;Rambaut A;Gaseitsiwe S;von Gottberg A;de Oliveira T
通讯作者：
de Oliveira T
影响因子：
64.8
作者：
Cao Y;Wang J;Jian F;Xiao T;Song W;Yisimayi A;Huang W;Li Q;Wang P;An R;Wang J;Wang Y;Niu X;Yang S;Liang H;Sun H;Li T;Yu Y;Cui Q;Liu S;Yang X;Du S;Zhang Z;Hao X;Shao F;Jin R;Wang X;Xiao J;Wang Y;Xie XS
通讯作者：
Xie XS