Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico

被引：16

作者：

Taboada, Blanca ^{[1
]}

Zarate, Selene ^{[2
]}

Garcia-Lopez, Rodrigo ^{[1
]}

Munoz-Medina, Jose Esteban ^{[3
]}

Sanchez-Flores, Alejandro ^{[4
]}

Herrera-Estrella, Alfredo ^{[5
]}

Boukadida, Celia ^{[6
]}

Gomez-Gil, Bruno ^{[7
]}

Selem Mojica, Nelly ^{[8
]}

Rosales-Rivera, Mauricio ^{[1
,9
]}

Salas-Lais, Angel Gustavo ^{[10
]}

Gutierrez-Rios, Rosa Maria ^{[11
]}

Loza, Antonio ^{[1
]}

Rivera-Gutierrez, Xaira ^{[1
]}

Vazquez-Perez, Joel Armando ^{[12
]}

Matias-Florentino, Margarita ^{[6
]}

Perez-Garcia, Marissa ^{[6
]}

Avila-Rios, Santiago ^{[6
]}

Hurtado, Juan Manuel ^{[13
]}

Herrera-Najera, Carla Ivon ^{[14
]}

Nunez-Contreras, Jose de Jesus ^{[15
]}

Sarquiz-Martinez, Brenda ^{[10
]}

Garcia-Arias, Victor Eduardo ^{[16
]}

Santiago-Mauricio, Maria Guadalupe ^{[17
]}

Martinez-Miguel, Bernardo ^{[18
]}

Enciso-Ibarra, Julissa ^{[7
]}

Chaidez-Quiroz, Cristobal ^{[19
]}

Isa, Pavel ^{[1
]}

Wong-Chew, Rosa Maria ^{[20
]}

Jimenez-Corona, Maria-Eugenia ^{[21
]}

Lopez, Susana ^{[1
]}

Arias, Carlos F. ^{[1
]}

机构：

[1] Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Genet Desarrollo & Fisiol Mol, Cuernavaca 62210, Morelos, Mexico

[2] Univ Autonoma Ciudad Mexico, Posgrad Ciencias Genom, Mexico City 03100, DF, Mexico

[3] Inst Mexicano Seguro Social, Coordinac Calidad Insumos & Labs Especializ, Mexico City 07760, DF, Mexico

[4] Univ Nacl Autonoma Mexico, Inst Biotecnol, Unidad Univ Secuenciac Masiva & Bioinformat, Cuernavaca 62210, Morelos, Mexico

[5] Ctr Invest & Estudios Avanzados IPN, Lab Nacl Genom Biodiversidad, Unidad Genom Avanzada, Guanajuato 36824, Mexico

[6] Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Ctr Invest Enfermedades Infecciosas, Mexico City 14080, DF, Mexico

[7] Ctr Invest Alimentac & Desarrollo AC, Mazatlan 82000, Sinaloa, Mexico

[8] Univ Nacl Autonoma Mexico, Ctr Ciencias Matemat, Morelia 58089, Michoacan, Mexico

[9] Univ Autonoma Estado Morelos, Ctr Invest Ciencias, Cuernavaca 62209, Morelos, Mexico

[10] Inst Mexicano Seguro Social, Lab Cent Epidemiol, Mexico City 02990, DF, Mexico

[11] Univ Nacl Autonoma Mexico, Inst Biotecnol, Dept Microbiol Mol, Cuernavaca 62210, Morelos, Mexico

[12] Inst Nacl Enfermedades Resp Ismael Cosio Villegas, Mexico City 14080, DF, Mexico

[13] Univ Nacl Autonoma Mexico, Inst Biotecnol, Unidad Computo, Cuernavaca 62210, Morelos, Mexico

[14] Inst Mexicano Seguro Social, Unidad Invest Med Yucatan, Merida 97150, Yucatan, Mexico

[15] Inst Mexicano Seguro Social, Unidad Invest Biomed Zacatecas, Zacatecas 98000, Zacatecas, Mexico

[16] Inst Mexicano Seguro Social, Ctr Invest Biomed Occidente, Guadalajara 44340, Jalisco, Mexico

[17] Inst Mexicano Seguro Social, Ctr Invest Biomed Noreste, Monterrey 64720, Nuevo Leon, Mexico

[18] Inst Mexicano Seguro Social, Div Labs Especializados, Mexico City 07760, DF, Mexico

[19] Ctr Invest Alimentac & Desarrollo AC, Lab Nacl Invest Inocuidad Alimentaria, Culiacan 80129, Sinaloa, Mexico

[20] Univ Nacl Autonoma Mexico, Fac Med, Div Invest, Lab Invest Enfermedades Infecciosas, Mexico City 04510, DF, Mexico

[21] Inst Nacl Cardiol Ignacio Chavez, Dept Epidemiol, Mexico City 14080, DF, Mexico

来源：

VIRUSES-BASEL | 2022年 / 14卷 / 06期

关键词：

SARS-CoV-2; variants of concern; delta variant; genomic surveillance; ALIGNMENT;

D O I：

10.3390/v14061165

中图分类号：

Q93 [微生物学];

学科分类号：

071005 ; 100705 ;

摘要：

In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described herein, and phylogenetic analyses and haplotype networks are used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the main sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variant associated with the third wave of the COVID-19 pandemic in Mexico and highlights the importance of SARS-CoV-2 genomic surveillance for the timely identification of emerging variants that may impact public health.

引用

页数：14

共 41 条

[11] Complex heatmaps reveal patterns and correlations in multidimensional genomic data [J].

Gu, Zuguang ;

Eils, Roland ;

Schlesner, Matthias .

BIOINFORMATICS, 2016, 32 (18) :2847-2849

[12]

Hodcroft EmmaB., 2021, NATURE, P1, DOI DOI 10.1038/s41586-021-03677-y

[13]

Kalyaanamoorthy S, 2017, NAT METHODS, V14, P587, DOI [10.1038/NMETH.4285, 10.1038/nmeth.4285]

[14] MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability [J].

Katoh, Kazutaka ;

Standley, Daron M. .

MOLECULAR BIOLOGY AND EVOLUTION, 2013, 30 (04) :772-780

[15]

Langmead B, 2012, NAT METHODS, V9, P357, DOI [10.1038/NMETH.1923, 10.1038/nmeth.1923]

[16] Neutralisation of the SARS-CoV-2 Delta variant sub-lineages AY.4.2 and B.1.617.2 with the mutation E484K by Comirnaty (BNT162b2 mRNA) vaccine-elicited sera, Denmark, 1 to 26 November 2021 [J].

Lassauniere, Ria ;

Polacek, Charlotta ;

Fonager, Jannik ;

Bennedbaek, Marc ;

Boding, Lasse ;

Rasmussen, Morten ;

Fomsgaard, Anders .

EUROSURVEILLANCE, 2021, 26 (49)

[17] POPART: full-feature software for haplotype network construction [J].

Leigh, Jessica W. ;

Bryant, David .

METHODS IN ECOLOGY AND EVOLUTION, 2015, 6 (09) :1110-1116

[18] Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum [J].

Liu, Chang ;

Ginn, Helen M. ;

Dejnirattisai, Wanwisa ;

Supasa, Piyada ;

Wang, Beibei ;

Tuekprakhon, Aekkachai ;

Nutalai, Rungtiwa ;

Zhou, Daming ;

Mentzer, Alexander J. ;

Zhao, Yuguang ;

Duyvesteyn, Helen M. E. ;

Lopez-Camacho, Cesar ;

Slon-Campos, Jose ;

Walter, Thomas S. ;

Skelly, Donal ;

Johnson, Sile Ann ;

Ritter, Thomas G. ;

Mason, Chris ;

Costa Clemens, Sue Ann ;

Naveca, Felipe Gomes ;

Nascimento, Valdinete ;

Nascimento, Fernanda ;

da Costa, Cristiano Fernandes ;

Resende, Paola Cristina ;

Pauvolid-Correa, Alex ;

Siqueira, Marilda M. ;

Dold, Christina ;

Temperton, Nigel ;

Dong, Tao ;

Pollard, Andrew J. ;

Knight, Julian C. ;

Crook, Derrick ;

Lambe, Teresa ;

Clutterbuck, Elizabeth ;

Bibi, Sagida ;

Flaxman, Amy ;

Bittaye, Mustapha ;

Belij-Rammerstorfer, Sandra ;

Gilbert, Sarah C. ;

Malik, Tariq ;

Carroll, Miles W. ;

Klenerman, Paul ;

Barnes, Eleanor ;

Dunachie, Susanna J. ;

Baillie, Vicky ;

Serafin, Natali ;

Ditse, Zanele ;

Da Silva, Kelly ;

Paterson, Neil G. ;

Williams, Mark A. .

CELL, 2021, 184 (16) :4220-+

[19] IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era [J].

Minh, Bui Quang ;

Schmidt, Heiko A. ;

Chernomor, Olga ;

Schrempf, Dominik ;

Woodhams, Michael D. ;

von Haeseler, Arndt ;

Lanfear, Robert .

MOLECULAR BIOLOGY AND EVOLUTION, 2020, 37 (05) :1530-1534

[20] SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion [J].

Mlcochova, Petra ;

Kemp, Steven A. ;

Dhar, Mahesh Shanker ;

Papa, Guido ;

Meng, Bo ;

Ferreira, Isabella A. T. M. ;

Datir, Rawlings ;

Collier, Dami A. ;

Albecka, Anna ;

Singh, Sujeet ;

Pandey, Rajesh ;

Brown, Jonathan ;

Zhou, Jie ;

Goonawardane, Niluka ;

Mishra, Swapnil ;

Whittaker, Charles ;

Mellan, Thomas ;

Marwal, Robin ;

Datta, Meena ;

Sengupta, Shantanu ;

Ponnusamy, Kalaiarasan ;

Radhakrishnan, Venkatraman Srinivasan ;

Abdullahi, Adam ;

Charles, Oscar ;

Chattopadhyay, Partha ;

Devi, Priti ;

Caputo, Daniela ;

Peacock, Tom ;

Wattal, Chand ;

Goel, Neeraj ;

Satwik, Ambrish ;

Vaishya, Raju ;

Agarwal, Meenakshi ;

Chauhan, Himanshu ;

Dikid, Tanzin ;

Gogia, Hema ;

Lall, Hemlata ;

Verma, Kaptan ;

Dhar, Mahesh Shanker ;

Singh, Manoj K. ;

Soni, Namita ;

Meena, Namonarayan ;

Madan, Preeti ;

Singh, Priyanka ;

Sharma, Ramesh ;

Sharma, Rajeev ;

Kabra, Sandhya ;

Kumar, Sattender ;

Kumari, Swati .

NATURE, 2021, 599 (7883) :114-+

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