MOLECULAR AND EPIDEMIOLOGICAL ASPECTS OF SARS-COV-2
DOI:
https://doi.org/10.11603/1681-2727.2021.1.11949Keywords:
pandemic, COVID-19, SARS-CoV-2, mutations, molecular epidemiological studiesAbstract
An unprecedented epidemic of emerging COVID-19 infection continues for the second year in the world. Initial data on the rate of evolution of its pathogen SARS-CoV-2 gave reason to believe that the virus has low mutation rates, but its genome is prone to recombinations, insertions and deletions, as is typical for other coronaviruses.
Recently, more and more reports have appeared about the formation of new variants of the virus due to adaptive mutations in the region of protein S. This increases the risks of the intensity of transmission of the pathogen, the effect on the clinical course of the disease and a decrease in the effectiveness of modern innovative vaccines. The British, Brazilian, North African and others variants of SARS-CoV-2 (VОС 202012/01, P.1 and 501Y.V2, respectively) appeared, susceptibility to the new virus of some animal species, infection of minks from humans and the subsequent return of the virus to human population were revealed. This indicates both the further rooting of the virus in the human population and the inconstancy and continuation of the formation of a new parasitic system at the present stage.
Given the continuation of the COVID-19 pandemic in the world and the difficult epidemic situation of this infection in Ukraine, constant molecular-epidemiological monitoring of the circulation of the new SARS-CoV-2 virus among both humans and animals is necessary. It must become an integral part of the overall infrastructure that is aimed at countering this infection.
The unpredictable evolutionary changes of the virus in the process of its adaptation to new species hosts during the formation of a new parasitic system do not allow making clear predictions about the pronounced seasonality of this infection in the near future and the ability to properly control the epidemic process by means of specific prophylaxis.
References
COVID-19 coronavirus pandemic: Last updated: February 18, 2021 : Wordometer. Retrieved from: https://www.worldometers.info/coronavirus/.
Komisarenko, S. V. (2020) World coronavirus crisis. Kyiv: LAT& [In Ukrainian].
Severe acute respiratory syndrome coronavirus 2: From Wikipedia, the free encyclopedia. Retrieved from: https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2#/media/File:SARS-CoV-2_genome.svg.
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Chen, J., Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet (London, England), 395 (10224), 565-574. Retrieved from: https://doi.org/10.1016/S0140-6736(20)30251-8.
van Dorp, L., Richard, D., Tan, C., Shaw, L. P., Acman, M., & Balloux, F. (2020). No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nature Communications, 11 (1), 5986. Retrieved from: https://doi.org/10.1038/s41467-020-19818-2.
Genomic epidemiology data infrastructure needs for SARS-CoV-2 : modernizing pandemic response strategies / Committee on Data Needs to Monitor the Evolution of SARS-CoV-2 ; Board on Health Sciences Policy, Health and Medicine Division ; Board on Life Sciences, Division on Earth and Life Studies ; The National Academies of Sciences, Engineering, Medicine. (2020). The National Academies Press.
Zhou, P., Yang, X. L.., Wang, X.G., Hu, B., Zhang, L., Zhang, W., Si H. R., Zhu Y., Li B., Huang C.L., Chen H. D., Chen J., Luo Y., Guo H., Jiang R. D., Liu M. Q., Chen Y., Shen X. R., Wang X., Zheng X. S., Zhao K., Chen Q. J., Deng F., Liu L. L., Yan B., Zhan F. X., Wang Y. Y., Xiao G.F., Shi Z. L. (2020). Addendum: A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature, 579, 270-273. Retrieved from: https://doi.org/10.1038/s41586-020-2012-7.
Chen, Z., Boon, S. S., Wang, M. H., Chan, R., & Chan, P. (2021). Genomic and evolutionary comparison between SARS-CoV-2 and other human coronaviruses. Journal of Virological Methods, 289, 114032. Retrieved from: Retrieved from: https://doi.org/10.1016/j.jviromet.2020.114032.
Paraskevis, D., Kostaki, E. G., Magiorkinis, G., Panayiotakopoulos, G., Sourvinos, G., & Tsiodras, S. (2020). Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 79, 104212. Retrieved from: https://doi.org/10.1016/j.meegid.2020.104212.
Zhou, H., Chen, X., Hu, T., Li, J., Song, H., Liu, Y., Wang, P., Liu, D., Yang, J., Holmes, E. C., Hughes, A. C., Bi, Y., & Shi, W. (2020). A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein. Current biology: CB, 30 (11), 2196-2203.e3. Retrieved from: https://doi.org/10.1016/j.cub.2020.05.023.
Sironi, M., Hasnain, S. E., Rosenthal, B., Phan, T., Luciani, F., Shaw, M. A., Sallum, M. A., Mirhashemi, M. E., Morand, S., González-Candelas, F. (2020) SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective. Infection Genetics and Evolution 84,104384. Retrieved from: https://doi.org/10.1016/j.meegid.2020.104384.
Lam, T.T., Jia, N., Zhang, Y.W., Shum, M.H., Jiang, J.F., Zhu, H.C., Tong, Y.G. et al. (2020). Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature, 583 (7815), 282-285. Retrieved from: https://doi.org/10.1038/s41586-020-2169-0.
Frutos, R., Serra-Cobo, J., Chen, T., & Devaux, C. A. (2020). COVID-19: Time to exonerate the pangolin from the transmission of SARS-CoV-2 to humans. Infection, Genetics and Evolution, 84. Retrieved from: https://doi.org/10.1016/j.meegid.2020.104493.
Li, X., Zai, J., Zhao, Q., Nie, Q., Li, Y., Foley, B. T., & Chaillon, A. (2020). Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2. Journal of Medical Virology, 92 (6), 602-611. Retrieved from: https://doi.org/10.1002/jmv.25731.
Ghosh, S., & Malik, Y. S. (2020). Drawing Comparisons between SARS-CoV-2 and the Animal Coronaviruses. Microorganisms, 8 (11), 1840. Retrieved from: https://doi.org/10.3390/microorganisms8111840.
Andrés, C., Garcia-Cehic, D., Gregori, J., Piñana, M., Rodriguez-Frias, F., Guerrero-Murillo, M., Esperalba, J., et al. (2020) Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients. Emerging Microbes & Infections, 9 (1), 1900-1911. https://doi.org/10.1080/22221751.2020.1806735.
Ling, J., Hickman, R. A., Li, J., Lu, X., Lindahl, J. F., Lundkvist, Å., & Järhult, J. D. (2020). Spatio-temporal mutational profile appearances of Swedish SARS-CoV-2 during the early pandemic. Viruses, 12 (9), 1026. Retrieved from: https://doi.org/10.3390/v12091026.
Gupta, A. M., Chakrabarti, J., & Mandal, S. (2020). Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants. Microbes and Infection, 22 (10), 598-607. Retrieved from: https://doi.org/10.1016/j.micinf.2020.10.004.
Martin, J., Klapsa, D., Wilton, T., Zambon, M., Bentley, E., Bujaki, E., Fritzsche, M., Mate, R., & Majumdar, M. (2020). Tracking SARS-CoV-2 in Sewage: Evidence of Changes in Virus Variant Predominance during COVID-19 Pandemic. Viruses, 12 (10), 1144. Retrieved from: https://doi.org/10.3390/v12101144.
Gunadi, Wibawa, H., Marcellus, Hakim, M.S., Daniwijaya, E.W., Rizki, L. P., Supriyati, E., Nugrahaningsih, D., et al. (2020). Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. PeerJ, 8, e10575. Retrieved from: https://doi.org/10.7717/peerj.10575.
Daniloski, Z., Jordan, T.X., Ilmain, J.K., Guo, X., Bhabha, G., tenOever, B.R., & Sanjana, N.E. (2021). The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. eLife, 10, e65365. Retrieved from: https://doi.org/10.7554/eLife.65365.
Garvin, M.R., Prates, E., Pavicic, M., Jones, P., Amos, B.K., Geiger, A., Shah, M.B., et al. (2020). Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol, 21 (1), 304. Retrieved from: https://doi.org/10.1186/s13059-020-02191-0.
Sasaki, M., Uemura, K., Sato, A., Toba, S., Sanaki, T., Maenaka, K., Hall, W.W., Orba, Y., & Sawa, H. (2021). SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells. PLoS Pathogens, 17 (1), e1009233. Retrieved from: https://doi.org/10.1371/journal.ppat.1009233.
Rehman, S., Mahmood, T., Aziz, E., & Batool, R. (2020). Identification of novel mutations in SARS-COV-2 isolates from Turkey. Archives of Virology, 165 (12), 2937-2944. Retrieved from: https://doi.org/10.1007/s00705-020-04830-0.
Borges, V., Isidro, J., Cortes-Martins, H., Duarte, S., Vieira, L., Leite, R., Gordo, I., Caetano, C.P., et al. Portuguese network for SARS-CoV-2 genomics, & Gomes, J. P. (2020). Massive dissemination of a SARS-CoV-2 Spike Y839 variant in Portugal. Emerging Microbes & Infections, 9 (1), 2488-2496. Retrieved from: https://doi.org/10.1080/22221751.2020.1844552.
Sun, Y.S., Xu, F., An, Q., Chen, C., Yang, Z.N., Lu, H.J., Chen, J.C. et al. (2020). A SARS-CoV-2 variant with the 12-bp deletion at E gene. Emerging Microbes & Infections, 9 (1), 2361-2367. Retrieved from: https://doi.org/10.1080/22221751.2020.1837017.
Khrustalev, V.V., Giri, R., Khrustaleva, T.A., Kapuganti, S.K., Stojarov, A.N., & Poboinev, V.V. (2020). Translation-Associated Mutational U-Pressure in the First ORF of SARS-CoV-2 and Other Coronaviruses. Frontiers in Microbiology, 11, 559165. Retrieved from: https://doi.org/10.3389/fmicb.2020.559165.
Simmonds P. (2020). Rampant C→U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses: causes and consequences for their short- and long-term evolutionary trajectories. mSphere, 5 (3), e00408-20. Retrieved from: https://doi.org/10.1128/mSphere.00408-20.
Zehender, G., Lai, A., Bergna, A., Meroni, L., Riva, A., Balotta, C., Tarkowski, M., Gabrieli, A., Bernacchia, D., Rusconi, S., Rizzardini, G., Antinori, S., & Galli, M. (2020). Genomic characterization and phylogenetic analysis of SARS-COV-2 in Italy. Journal of medical virology, 92 (9), 1637-1640. Retrieved from: https://doi.org/10.1002/jmv.25794.
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020). A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiology, 5 (11), 1403-1407. Retrieved from: https://doi.org/10.1038/s41564-020-0770-5.
Surleac, M., Banica, L., Casangiu, C., Cotic, M., Florea, D., Sandulescu, O., Milu, P., Streinu-Cercel, A., Vlaicu, O., Paraskevis, D., Paraschiv, S., & Otelea, D. (2020). Molecular epidemiology analysis of SARS-CoV-2 strains circulating in Romania during the first months of the pandemic. Life (Basel, Switzerland), 10 (8), 152. https://doi.org/10.3390/life10080152.
Variant SARS-CoV-2 – United Kingdom. WHO. Disease Outbreak News (2020). 21 December 2020. Retrieved from: https://www.who.int/csr/don/21-december-2020-sars-cov2-variant-united-kingdom/en/.
SARS-CoV-2 Variants. WHO. Disease Outbreak News (2020). 31 December 2020. Retrieved from: https://www.who.int/csr/don/31-december-2020-sars-cov2-variants/en/.
Golubchik, T., Lythgoe, K.A., Hall, M., Ferretti, L., Fryer, H.R., MacIntyre-Cockett, G., de Cesare, M., Trebes, A. (2021). Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein. medRxiv, 2021.01.12.20249080. Retrieved from: https://www.medrxiv.org/content/10.1101/2021.01.12.20249080v1.
Fratev, F. (2020). The SARS-CoV-2 S1 spike protein mutation N501Y alters the protein interactions with both hACE2 and human derived antibody: A Free energy of perturbation study. bioRxiv,12.23.424283. Retrieved from: https://doi.org/10.1101/2020.12.23.424283.
Castro, A., Carter, H., Zanetti, M. (2021). Potential global impact of the N501Y mutation on MHC-II presentation and immune escape. bioRxiv, 2021.02.02.429431. Retrieved from: https://doi.org/10.1101/2021.02.02.429431.
(2020). European Centre for Disease Prevention and Control. Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom (2020). 20 December. ECDC: Stockholm. Retrieved from: https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf.
Fiorentini, S., Messali, S., Zani, A., Caccuri, F., Giovanetti, M., Ciccozzi, M., & Caruso, A. (2021). First detection of SARS-CoV-2 spike protein N501 mutation in Italy in August, 2020. The Lancet. Infectious diseases, S1473-3099(21)00007-4. Advance online publication. Retrieved from: https://doi.org/10.1016/S1473-3099(21)00007-4.
Faria, N.R., Claro, I.M., Candido, D., Franco, L.A.M., Andrade, P.S., Coletti, T.M., Silva, C.A.M., et al. on behalf of CADDE Genomic Network (2021). Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings. Retrieved from: https://virological.org/t/genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-manaus-preliminary-findings/586.
Infographic: Mutation of SARS-CoV2 – current variants of concern (2021). ECDC. 8 February 2021. Retrieved from: https://www.ecdc.europa.eu/en/publications-data/covid-19-infographic-mutations-current-variants-concern.
European Centre for Disease Prevention and Control. Risk related to spread of new SARS-CoV-2 variants of concern in the EU/EEA, first update (2021). 21 January 2021. ECDC: Stockholm; 2021. Retrieved from: https://www.ecdc.europa.eu/en/publications-data/covid-19-risk-assessment-spread-new-variants-concern-eueea-first-update.
(2021). A completely new coronavirus variant found in Finland - possibly difficult to detect by tests. Vita Laboratoriot. 18.02.2021. Retrieved from: https://vita.fi/uutiset/suomesta-loytynyt-taysin-uusi-koronavirusvariantti-mahdollisesti-vaikea-havaita-testeilla/ [in Russian]
Hodcroft, E.B., Domman, D.B., Snyder, D.J., Oguntuyo, K., Van Diest, M., Densmore, K.H., Schwalm, K.C., Femling (2021). Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677. medRxiv: the preprint server for health sciences, 2021.02.12.21251658. Retrieved from: https://doi.org/10.1101/2021.02.12.21251658.
Cases of SARS-CoV-2 in Animals in the United States (2021). Animal and Plant Health Inspection Service. U.S. department of agriculture. Last Modified: Feb 22, 2021. Retrieved from: https://www.aphis.usda.gov/aphis/ourfocus/animalhealth/sa_one_health/sars-cov-2-animals-us.
Evaluation for SARS-CoV-2 Testing in Animals (2020). CDC. Updated Aug. 12, 2020. Retrieved from: https://www.cdc.gov/coronavirus/2019-ncov/animals/animal-testing.html.
Elaswad, A., Fawzy, M., Basiouni, S., & Shehata, A.A. (2020). Mutational spectra of SARS-CoV-2 isolated from animals. PeerJ, 8, e10609. Retrieved from: https://doi.org/10.7717/peerj.10609.
Hoffmann, M., Zhang, L., Krüger, N., Graichen, L., Kleine-Weber, H., Hofmann-Winkler, H., Kempf, A., Nessler, S., Riggert, J., Winkler, M. S., Schulz, S., Jäck, H.-M., Pöhlmann, S. (2021) SARS-CoV-2 mutations acquired in mink reduce antibody-mediated neutralization. bioRxiv 2021.02.12.430998. Retrieved from: https://doi.org/10.1101/2021.02.12.430998.
Oude Munnink, B.B., Sikkema, R.S., Nieuwenhuijse, D.F., Molenaar, R.J., Munger, E., Molenkamp, R., van der Spek, A., et al. (2021). Transmission of SARS-CoV-2 on mink farms between humans and mink and back to humans. Science (New York, N.Y.), 371 (6525), 172-177. Retrieved from: https://doi.org/10.1126/science.abe5901.
European Centre for Disease Prevention and Control. Detection of new SARS-CoV-2 variants related to mink (2020). 12 November 2020. ECDC: Stockholm; 2020. Retrieved from: https://www.ecdc.europa.eu/en/publications-data/detection-new-sars-cov-2-variants-mink.
Zadorozhnа, V.I., & Vynnyk, N.P. (2020) Coronavirus 2019-nCOV: new challenges for health and humanity. Infektsiini khvoroby, (1), 5-15. Retrieved from: https://doi.org/10.11603/1681-2727.2020.1.11091 [in Ukrainian].
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