medigraphic.com
Centro de Investigaciones Regionales Dr. Hideyo Noguchi, Universidad Autónoma de Yucatán

2024, Number 2

Next >>

Rev Biomed 2024; 35 (2)

SARS-CoV-2 Genomic Surveillance in Nayarit, Mexico (Summer- Winter 2021-2022)

Covantes-Rosales CE, Barajas-Carrillo VW, Toledo-Ibarra GA, Díaz-Resendiz KJG, Benitez-Trinidad AB, Ventura-Ramón GH, Girón-Pérez DA, Gómez-Gil B, Girón-Pérez MI

Language: English
References: 36
Page: 51-58
PDF size: 487.40 Kb.


ABSTRACT

Background. COVID-19, whose etiologic agent is SARS-CoV-2, an RNA virus, is characterized by a high mutation rate. Therefore, while more subjects are infected, greater probability that the virus will potentially undergo changes that confer evolutionary advantages (immune response evasion, increased virulence, and reduced vaccination efficacy). Efforts to acquire herd immunity through vaccination may be compromised in low- and middle-income countries, where the vaccination process is slow and inequitable. This may lead to new variant outbreaks with greater transmission capacity. Therefore, it is important to surveillance the circulating variants in the populations.
Methods. In this sense, in Tepic, Nayarit, Mexico, 100 viral genomes of positive patients were sequenced during the beginning and end of the third (August 4th to September 3rd, 2021) and fourth (January 3rd, to February 2nd, 2022) COVID-19 waves.
Results. Sequence analysis revealed the presence of several variants; alpha (B.1.1.7), gamma (P.1), local variant (B.1.1.519), mu (B.1.621), delta (B.1.617.2), and its subtypes (AY.3, AY.4, AY.10, AY.11, AY.20, and AY.23.1) during the third wave. Later, during the fourth wave, delta subtypes were still detected (AY.26 and AY.113), as well as omicron (B.1.1.529) and omicron subtypes (B.A.1 and BA.1.1).
Conclusion. Obtained data revealed a progressive shift of the dominant variants, delta, and subtypes in the third wave and omicron and subtypes in the fourth wave.


REFERENCES

  1. Johns Hopkins, COVID-19 Map - Johns HopkinsCoronavirus Resource Center. [Online] 2023. [Accessedon 05/09/23]. Available data at https://coronavirus.jhu.edu/map.html.

  2. Dumache R, Enache A, Macasoi I, Dehelean CA,Dumitrascu V, Mihailescu A, et al. SARS-CoV-2: AnOverview of the Genetic Profile and Vaccine Effectivenessof the Five Variants of Concern. Pathogens. 2022; 11(5),516. https://doi:10.3390/pathogens11050516.

  3. Qureshi MF. SARS-Cov-2: Interaction BetweenMutations and Variants and Their Influence on Treatmentand Preventive Strategies. J Gstro Hepato. 2022; 8: 1-6.

  4. Liu Y, Yan LM, Wan L, Xiang TX, Le A, Liu JM, et al.Viral dynamics in mild and severe cases of COVID-19.The Lancet Infectious Diseases. 2020; 20(6), 656-657.https://doi.org/10.1016/S1473-3099(20)30232-2.

  5. Cella E, Benedetti F, Fabris S, Borsetti A, PezzutoA, Ciotti M, et al. SARS-CoV-2 lineages andsub-lineages circulating worldwide: A DynamicOverview. Chemotherapy. 2021;66(1-2):3-7. doi:10.1159/000515340.

  6. World Health Organization (WHO). Tracking SARSCoV-2 variants. Geneva: WHO. [Online] 2023a.(Accessed on 05 September 2023]. Available from:https://www.who.int/en/activities/tracking-SARS-CoV-2-variants.

  7. World Health Organization (WHO). Formerly monitoredvariants. Geneva: WHO. [Online] 2023b. (Accessed on02 September 2023). Available from: https://www.who.int/activities/tracking-SARS-CoV-2-variants/formerlymonitored-variants

  8. Mastrovito B, Naimi C, Kouam L, Naudot X, FournierL, Spaccaferri G, et al. Investigation of outbreak casesinfected with the SARS-CoV-2 B. 1.640 variant in afully vaccinated elderly population, Normandy, France,November to December 2021. Euro Surveill. 2022;27(6), 2200078. https://doi.org/10.2807/1560-7917.ES.2022.27.6.2200078.

  9. Park AK, Kim IH, Kim HM, Lee H, Lee NJ., Kim, etal. SARS-CoV-2 B. 1.619 and B. 1.620 Lineages, SouthKorea, 2021. Emerg Infect Dis. 2022; 28(2), 415. https://doi.org/10.3201/eid2802.211653.

  10. Dudas G, Hong SL, Potter BI, Calvignac-Spencer S,Niatou-Singa FS, Tombolomako TB, et al. Emergenceand spread of SARS-CoV-2 lineage B. 1.620 with variantof concern-like mutations and deletions. Nat Commun.2021; 12(1), 5769. https://doi.org/10.1038/s41467-021-26055-8.

  11. Tegally H, Ramuth M, Amoaka D, Scheepers C,Wilkinson E, Giovanetti M, et al. Genomic epidemiologyof SARS-CoV-2 in Mauritius reveals a new wave ofinfections dominated by the B.1.1.318, a variant underinvestigation. medRxiv. 2021; 06. https://doi.org/10.1101/2021.06.16.21259017.

  12. Zemaitis, L., Alzbutas, G., Gecys, D., Pautienius,A., Ugenskiene, R., Sukys, et al. Determining theInternational Spread of B.1.1.523 SARS-CoV-2 Lineagewith a Set of Mutations Highly Associated with ReducedImmune Neutralization. Microorganisms. 2022; 10(7),

  13. 1356. https://doi.org/10.3390/microorganisms10071356.13. Cosar B, Karagulleoglu ZY, Unal S, Ince AT, UncuogluDB, Tuncer G, et al. SARS-CoV-2 mutations and theirviral variants. Cytokine Growth Factor Rev. 2022; Feb;63:10-22. doi: 10.1016/j.cytogfr.2021.06.001.

  14. Barajas-Carrillo, V. W., Covantes-Rosales, C. E.,Zambrano-Soria, M., Castillo-Pacheco, L. A., Girón-Pérez, D. A., Mercado-Salgado, et al. SARS-CoV-2Transmission Risk Model in an Urban Area of Mexico,Based on GIS Analysis and Viral Load. Int J Environ ResPublic Health. 2022 Mar 24;19(7):3840. doi: 10.3390/ijerph19073840.

  15. Consorcio Mexicano de Vigilancia Genómica (CoViGen-Mex). [Online] [Accessed in 12 December 2022].Available data at http://mexcov2.ibt.unam.mx:8080/COVID-TRACKER/somos.

  16. Girón-Pérez DA, Benitez-Trinidad AB, Ruiz-ManzanoRA, Toledo-Ibarra GA, Ventura-Ramón GH, Covantes-Rosales CE, et al. Correlation of hematologicalparameters and cycle threshold in ambulatory patientswith SARS‐CoV‐2 infection. Int J Lab Hematol. 2021Aug;43(4):873-880. doi: 10.1111/ijlh.13606.

  17. Corman VM, Landt O, Kaiser M, Molenkamp R, MeijerA, Chu DK, et al. Detection of 2019 novel coronavirus(2019-nCoV) by real-time RT-PCR. Euro Surveill. 2020;25(3), 2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045.

  18. Parra-Lucares A, Segura P, Rojas V, Pumarino C, Saint-Pierre G, Toro L. Emergence of SARS-CoV-2 Variants inthe World: How Could This Happen?. Life. 2022; 12(2),

  19. https://doi.org/10.3390/life12020194.19. Machingaidze S, Wiysonge CS. UnderstandingCOVID-19 vaccine hesitancy. Nat Med. 2021Aug;27(8):1338-1339. doi: 10.1038/s41591-021-01459-7.

  20. Fan G, Song H, Yip S, Zhang T, He D. Impact of lowvaccine coverage on the resurgence of COVID-19in Central and Eastern Europe. One Health. 2022May 19;14:100402. doi: https://doi.org/10.1016/j.onehlt.2022.100402.

  21. Petersen E, Ntoumi F, Hui DS, Abubakar A, Kramer LD,Obiero C. et al. Emergence of new SARS-CoV-2 Variantof Concern Omicron (B. 1.1. 529)-highlights Africa’sresearch capabilities, but exposes major knowledge gaps,inequities of vaccine distribution, inadequacies in globalCOVID-19 response and control efforts. Int J InfectDis. 2022 Jan;114:268-272. https://doi.org/10.1016/j.ijid.2021.11.040.

  22. Tsheten T, Lowe C, Wangdi K, Kelly M, Mationg ML,Williams GM, et al. COVID-19 continues its rampagein children and in unvaccinated communities due to theDelta and Omicron variants. Infect Dis Trop Med. 2022;8: e810. https://doi.org/10.32113/idtm_20223_810.

  23. Taboada B, Zárate S, Iša P, Boukadida C, Vazquez-PerezJA, Muñoz-Medina JE, et al. Genetic Analysis of SARSCoV-2 Variants in Mexico during the First Year of theCOVID-19 Pandemic. Viruses. 2021; 13, 2161. https://doi.org/10.3390/v13112161.

  24. Hasan MR, Kalikiri MK, Mirza F, Sundararaju S,Sharma A, Xaba T, et al. Real-time SARS-CoV-2genotyping by high-throughput multiplex PCR revealsthe epidemiology of the variants of concern in Qatar.Int J Infect Dis. 2021 Nov;112:52-54. https://doi.org/10.1016/j.ijid.2021.09.006.

  25. Rahman M, Shirin T, Rahman S, Rahman MM, HossainME, Khan MH, et al. The emergence of SARS‐CoV‐2variants in Dhaka city, Bangladesh. Transbound EmergDis. 2021 Nov;68(6):3000-3001. https://doi.org/10.1111/tbed.14203.

  26. Paul P, France AM, Aoki Y, Batra D, Biggerstaff M,Dugan V, et al. Genomic surveillance for SARS-CoV-2variants circulating in the United States, December2020–May 2021. MMWR Morb Mortal Wkly Rep. 2021Jun 11;70(23):846-850. http://doi.org/10.15585/mmwr.mm7023a3.

  27. Ito K, Piantham C, Nishiura H. Predicted dominanceof variant Delta of SARS-CoV-2 before Tokyoolympic games, Japan, July 2021. Euro Surveill. 2021;26(27), 2100570. https://doi.org/10.2807/1560-7917.ES.2021.26.27.2100570.

  28. Ntoumi F, Mapanguy CCM, Tomazatos A, Pallerla SR,Casadei N, Angelov A, et al. Genomic surveillance ofSARS-CoV-2 in the Republic of Congo. Int J InfectDis. 2021 Apr;105:735-738. https://doi.org/10.1016/j.ijid.2021.03.036.

  29. Rimoldi SG, Stefani F, Gigantiello A, Polesello S,Comandatore F, Mileto D, et al. Presence and infectivityof SARS-CoV-2 virus in wastewaters and rivers. SciTotal Environ. 2020 Nov 20;744:140911. https://doi.org/10.1016/j.scitotenv.2020.140911.

  30. Márquez S, Prado-Vivar B, Guadalupe JJ, Becerra-Wong M, Gutierrez B, Fernández-Cadena JC, et al.SARS-CoV-2 genome sequencing from COVID-19 inEcuadorian patients: a whole country analysis. medRxiv.2021; 03.19.21253620. https://doi.org/10.1101/2021.03.19.21253620.

  31. Mora EL, Espinoza J, Dabanch J, Cruz R. Emergenciade variante Delta-B. 1.617. 2. Su impacto potencial enla evolución de la pandemia por SARS-CoV-2. BoletínMicológico. 2021; 36(1). https://doi.org/10.22370/bolmicol.2021.36.1.2883.

  32. Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B,Ferreira IA, et al. SARS-CoV-2 B. 1.617. 2 Delta variantreplication and immune evasion. Nature. 2021; (599):114–119 https://doi.org/10.1038/s41586-021-03944-y.

  33. Luo CH, Morris CP, Sachithanandham J, Amadi A,Gaston D, Li M, et al. Infection with the SARS-CoV-2delta variant is associated with higher infectious virusloads compared to the alpha variant in both unvaccinatedand vaccinated individuals. medRxiv. 2021; 21262077.https://doi.org/10.1101/2021.08.15.21262077.

  34. Wang C, & Han J. Will the COVID-19 pandemic endwith the Delta and Omicron variants?. Environ ChemLett. 2022; 20(4): 2215–2225. https://doi.org/10.1007/s10311-021-01369-7.

  35. Riediker M, Briceno-Ayala L, Ichihara G, Albani D,Poffet D, Tsai DH, et al. Higher viral load and infectivityincrease risk of aerosol transmission for Delta andOmicron variants of SARS-CoV-2. Swiss Med Wkly.2022 Jan 6;152:w30133. https://doi.org/10.4414/smw.2022.w30133.

  36. Young M, Crook H, Scott J, Edison P. Covid-19:virology, variants, and vaccines. BMJ Med. 2022Apr 1;1(1):e000040. https://doi.org/10.1136/bmjmed-2021-00004.




2020     |     www.medigraphic.com