The discovery of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) in Wuhan, Hubei province, China, in December 2019 raised global health warnings. Quickly, in 2020, the virus crossed borders and infected individuals across the world, evolving into the COVID-19 pandemic. Notably, early signs of the virus’s existence were observed in various countries before the initial outbreak in Wuhan. As of 12th of April, the respiratory disease had infected over 762 million people worldwide, with over 6.8 million deaths recorded. This has led scientists to focus their efforts on understanding the virus to develop effective means to diagnose, treat, prevent, and control this pandemic. One of the areas of focus is the isolation of this virus, which plays a crucial role in understanding the viral dynamics in the laboratory. In this study, we report the isolation and detection of locally circulating SARS-CoV-2 in Kenya. The isolates were cultured on Vero Cercopithecus cell line (CCL-81) cells, RNA extraction was conducted from the supernatants, and reverse transcriptase-polymerase chain reaction (RT-PCR). Genome sequencing was done to profile the strains phylogenetically and identify novel and previously reported mutations. Vero CCL-81 cells were able to support the growth of SARS-CoV-2 in vitro, and mutations were detected from the two isolates sequenced (001 and 002). Genome sequencing revealed the circulation of two isolates that share a close relationship with the Benin isolate with the D614G common mutation identified along the S protein. These virus isolates will be expanded and made available to the Kenya Ministry of Health and other research institutions to advance SARS-CoV-2 research in Kenya and the region.
References
[1]
Weiss, S.R. and Navas-Martin, S. (2005) Coronavirus Pathogenesis and the Emerging Pathogen Severe Acute Respiratory Syndrome Coronavirus. Microbiology and Molecular Biology Reviews, 69, 635-664. https://journals.asm.org/doi/10.1128/MMBR.69.4.635-664.2005 https://doi.org/10.1128/MMBR.69.4.635-664.2005
[2]
Dijkman, R. and van der Hoek, L. (2009) Human Coronaviruses 229E and NL63: Close yet still so Far. Journal of the Formosan Medical Association, 108, 270-279. https://doi.org/10.1016/S0929-6646(09)60066-8 https://linkinghub.elsevier.com/retrieve/pii/S0929664609600668
[3]
Su, S., Wong, G., Shi, W., Liu, J., Lai, A.C.K., Zhou, J., et al. (2016) Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends in Microbiology, 24, 490-502. https://doi.org/10.1016/j.tim.2016.03.003 https://linkinghub.elsevier.com/retrieve/pii/S0966842X16000718
[4]
Kin, N., Miszczak, F., Lin, W., Gouilh, M., Vabret, A. and Consortium, E. (2015) Genomic Analysis of 15 Human Coronaviruses oc43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes. Viruses, 7, 2358-2377. https://doi.org/10.3390/v7052358 http://www.mdpi.com/1999-4915/7/5/2358
[5]
Gorbalenya, A.E., Baker, S.C., Baric, R.S., de Groot, R.J., Drosten, C., Gulyaeva, A.A., et al. (2020) The Species Severe Acute Respiratory Syndrome-Related Coronavirus: Classifying 2019-nCoV and Naming It SARS-CoV-2. Nature Microbiology, 5, 536-544. https://doi.org/10.1038/s41564-020-0695-z https://www.nature.com/articles/s41564-020-0695-z
[6]
Li, X., Zai, J., Zhao, Q., Nie, Q., Li, Y., Foley, B.T., et al. (2020) Evolutionary History, Potential Intermediate Animal Host, and Cross-Species Analyses of SARS-CoV-2. Journal of Medical Virology, 92, 602-611. https://doi.org/10.1002/jmv.25731 https://onlinelibrary.wiley.com/doi/10.1002/jmv.25731
[7]
WHO Coronavirus (COVID-19) Dashboard. https://covid19.who.int
[8]
Coronavirus Disease (COVID-19) World Health Organization. https://www.who.int/emergencies/diseases/novel-coronavirus-2019
[9]
Amen, B., Nagarajkumar, Y., Omar, B.D. and Hoda, J. (2020) Epidemiological Trends, Characteristics, and Distribution of COVID-19: Lessons from SARS and MERS Outbreaks and Way Forward. Journal of Infectious Diseases and Epidemiology, 6, 127 p. https://doi.org/10.23937/2474-3658/1510127 https://www.clinmedjournals.org/articles/jide/journal-of-infectious-diseases-and-epidemiology-jide-6-127.php?jid=jide
[10]
Memish, Z.A., Perlman, S., Van Kerkhove, M.D. and Zumla, A. (2020) Middle East Respiratory Syndrome. The Lancet, 395, 1063-1077. https://doi.org/10.1016/S0140-6736(19)33221-0 https://linkinghub.elsevier.com/retrieve/pii/S0140673619332210
The Global Asthma Report 2022. http://globalasthmareport.org/
[13]
Saeedi, P., Petersohn, I., Salpea, P., Malanda, B., Karuranga, S., Unwin, N., et al. (2019) Global and Regional Diabetes Prevalence Estimates for 2019 and Projections for 2030 and 2045: Results from the International Diabetes Federation Diabetes Atlas. 9th Edition. Diabetes Research and Clinical Practice, 157, Article 107843. https://doi.org/10.1016/j.diabres.2019.107843 https://linkinghub.elsevier.com/retrieve/pii/S0168822719312306
[14]
Yang, J., Zheng, Y., Gou, X., Pu, K., Chen, Z., Guo, Q., et al. (2020) Prevalence of Comorbidities and Its Effects in Patients Infected with SARS-CoV-2: A Systematic Review and Meta-Analysis. International Journal of Infectious Diseases, 94, 91-95. https://doi.org/10.1016/j.ijid.2020.03.017 https://linkinghub.elsevier.com/retrieve/pii/S1201971220301363
[15]
Bertagnolio, S., Thwin, S.S., Silva, R., Nagarajan, S., Jassat, W., Fowler, R., et al. (2022) Clinical Features of, and Risk Factors for, Severe or Fatal COVID-19 among People Living with HIV Admitted to Hospital: Analysis of Data from the WHO Global Clinical Platform of COVID-19. The Lancet HIV, 9, e486-e495. https://doi.org/10.1016/S2352-3018(22)00097-2 https://linkinghub.elsevier.com/retrieve/pii/S2352301822000972
[16]
Hussein, R., Guedes, M., Ibraheim, N., Ali, M.M., El-Tahir, A., Allam, N., et al. (2022) Impact of COVID-19 and Malaria Coinfection on Clinical Outcomes: A Retrospective Cohort Study. Clinical Microbiology and Infection, 28, 1152.E1-1152.E6. https://linkinghub.elsevier.com/retrieve/pii/S1198743X22001677
[17]
Kim, J.M., Chung, Y.S., Jo, H.J., Lee, N.J., Kim, M.S., Woo, S.H., et al. (2020) Identification of Coronavirus Isolated from a Patient in Korea with COVID-19. Osong Public Health and Research Perspectives, 11, 3-7. https://doi.org/10.24171/j.phrp.2020.11.1.02 http://ophrp.org/journal/view.php?doi=10.24171/j.phrp.2020.11.1.02
[18]
Kim, J.M., Kim, H.M., Lee, E.J., Jo, H.J., Yoon, Y., Lee, N.J., et al. (2020) Detection and Isolation of SARS-COV-2 in Serum, Urine, and Stool Specimens of COVID-19 Patients from the Republic of Korea. Osong Public Health and Research Perspectives, 11, 112-117. https://doi.org/10.24171/j.phrp.2020.11.3.02 http://ophrp.org/journal/view.php?doi=10.24171/j.phrp.2020.11.3.02
[19]
Sichamba, P., Wamunyokoli, F., Borus, P., Nzunza, R., Silvanos, O., Symekher, S., et al. (2022) A Retrospective Analysis of Wastewater Confirms Dominant Circulation of SARS-CoV-2 Delta Variant in Nairobi, Kenya, between April 2021 and August 2021. American Journal of Molecular Biology, 12, 109-121. https://doi.org/10.4236/ajmb.2022.123010 http://www.scirp.org/Journal/Paperabs.aspx?paperid=118170
[20]
(2020) First Case of COVID-19 in the United States. The New England Journal of Medicine, 382, e53. https://doi.org/10.1056/NEJMc2004794 http://www.nejm.org/doi/10.1056/NEJMc2004794
[21]
CDC (2020) Coronavirus Disease 2019 (COVID-19). Centers for Disease Control and Prevention. https://www.cdc.gov/coronavirus/2019-ncov/index.html
[22]
Taştan, C., Yurtsever, B., Karakuş, G., Dilek Kançaği, D., Demir, S., Abanuz, S., et al. (2020) SARS-CoV-2 Isolation and Propagation from Turkish COVID-19 Patients. Turkish Journal of Biology, 44, 192-202. https://doi.org/10.3906/biy-2004-113 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314506/
[23]
Sims, A.C., Tilton, S.C., Menachery, V.D., Gralinski, L.E., Schäfer, A., Matzke, M.M., et al. (2013) Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells. Journal of Virology, 87, 3885-3902. https://doi.org/10.1128/JVI.02520-12 https://journals.asm.org/doi/10.1128/JVI.02520-12
[24]
Tabibzadeh, A., Zamani, F., Laali, A., Esghaei, M., Safarnezhad Tameshkel, F., Keyvani, H., et al. (2020) SARS-CoV-2 Molecular and Phylogenetic Analysis in COVID-19 Patients: A Preliminary Report from Iran. Infection, Genetics and Evolution, 84, Article 104387. https://doi.org/10.1016/j.meegid.2020.104387 https://linkinghub.elsevier.com/retrieve/pii/S1567134820302185
[25]
Bolger, A.M., Lohse, M. and Usadel, B. (2014) Trimmomatic: A Flexible Trimmer for Illumina Sequence Data. Bioinformatics, 30, 2114-2120. https://doi.org/10.1093/bioinformatics/btu170 https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu170
[26]
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A.A., Dvorkin, M., Kulikov, A.S., et al. (2012) Spades: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 19, 455-477. https://doi.org/10.1089/cmb.2012.0021 http://www.liebertpub.com/doi/10.1089/cmb.2012.0021
[27]
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic Local Alignment Search Tool. Journal of Molecular Biology, 215, 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2 https://linkinghub.elsevier.com/retrieve/pii/S0022283605803602
Edgar, R.C. (2004) MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic Acids Research, 32, 1792-1797. https://doi.org/10.1093/nar/gkh340 https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkh340
[30]
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011) Mega5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28, 2731-2739. https://doi.org/10.1093/molbev/msr121 https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msr121
[31]
Genomic Epidemiology of SARS-CoV-2 with Subsampling Focused Globally over the Past 6 Months. https://nextstrain.org/ncov/gisaid/global/6m
[32]
Harcourt, J., Tamin, A., Lu, X., Kamili, S., Sakthivel, S.K., Murray, J., et al. (2020) Severe Acute Respiratory Syndrome Coronavirus-2 from Patient with Coronavirus Disease, United States. Emerging Infectious Diseases, 26, 1266-1273. http://wwwnc.cdc.gov/eid/article/26/6/20-0516_article.htm
[33]
Park, Y.J., Choe, Y.J., Park, O., Park, S.Y., Kim, Y.M., Kim, J., et al. (2020) Contact Tracing during Coronavirus Disease Outbreak, South Korea, 2020. Emerging Infectious Diseases, 26, 2465-2468. https://doi.org/10.3201/eid2610.201315
[34]
Chan, J.F.W., Chan, K.H., Choi, G.K.Y., To, K.K.W., Tse, H., Cai, J.P., et al. (2013) Differential Cell Line Susceptibility to the Emerging Novel Human Betacoronavirus 2c EMC/2012: Implications for Disease Pathogenesis and Clinical Manifestation. The Journal of Infectious Diseases, 207, 1743-1752. https://academic.oup.com/jid/article-lookup/doi/10.1093/infdis/jit123 https://doi.org/10.1093/infdis/jit123
[35]
Harcourt, J., Tamin, A., Lu, X., Kamili, S., Sakthivel Kumar, S., Murray, J., et al. (2020) Isolation and Characterization of SARS-CoV-2 from the First US COVID-19 Patient. Microbiology. https://doi.org/10.1101/2020.03.02.972935 http://biorxiv.org/lookup/doi/10.1101/2020.03.02.972935
[36]
Park, W.B., Kwon, N.J., Choi, S.J., Kang, C.K., Choe, P.G., Kim, J.Y., et al. (2020) Virus Isolation from the First Patient with SARS-COV-2 in Korea. The Korean Academy of Medical Sciences, 35, e84. https://doi.org/10.3346/jkms.2020.35.e84 https://jkms.org/DOIx.php?id=10.3346/jkms.2020.35.e84
[37]
Munne, K., Bhanothu, V., Bhor, V., Patel, V., Mahale, S.D. and Pande, S. (2021) Detection of SARS-CoV-2 Infection by RT-PCR Test: Factors Influencing Interpretation of Results. VirusDisease, 32, 187-189. https://doi.org/10.1007/s13337-021-00692-5 https://link.springer.com/10.1007/s13337-021-00692-5
[38]
Goudouris, E.S. (2021) Laboratory Diagnosis of COVID-19.Jornal de Pediatria, 97, 7-12. https://doi.org/10.1016/j.jped.2020.08.001 https://linkinghub.elsevier.com/retrieve/pii/S0021755720301996
[39]
Watson, J., Whiting, P.F. and Brush, J.E. (2020) Interpreting a COVID-19 Test Result. BMJ, 369, m1808. https://doi.org/10.1136/bmj.m1808 https://www.bmj.com/lookup/doi/10.1136/bmj.m1808
[40]
Binny, R.N., Priest, P., French, N.P., Parry, M., Lustig, A., Hendy, S.C., et al. (2022) Sensitivity of Reverse Transcription Polymerase Chain Reaction Tests for Severe Acute Respiratory Syndrome Coronavirus 2 through Time. The Journal of Infectious Diseases, 227, 9-17. https://doi.org/10.1093/infdis/jiac317 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9384503/
[41]
Phan, T. (2020) Genetic Diversity and Evolution of SARS-CoV-2. Infection, Genetics and Evolution, 81, Article 104260. https://doi.org/10.1016/j.meegid.2020.104260 https://linkinghub.elsevier.com/retrieve/pii/S1567134820300915
[42]
Zhao, N., Zhou, N., Fan, H., Ding, J., Xu, X., Dong, X., et al. (2022) Mutations and Phylogenetic Analyses of SARS-COV-2 among Imported COVID-19 from Abroad in Nanjing, China. Frontiers in Microbiology, 13, Article 851323. https://doi.org/10.3389/fmicb.2022.851323 https://www.frontiersin.org/articles/10.3389/fmicb.2022.851323/full
[43]
Isabel, S., Graña-Miraglia, L., Gutierrez, J.M., Bundalovic-Torma, C., Groves, H.E., Isabel, M.R., et al. (2020) Evolutionary and Structural Analyses of SARS-CoV-2 D614G Spike Protein Mutation Now Documented Worldwide. Scientific Reports, 10, Article 14031. https://doi.org/10.1038/s41598-020-70827-z https://www.nature.com/articles/s41598-020-70827-z
[44]
Zhang, L., Jackson, C.B., Mou, H., Ojha, A., Rangarajan, E.S., Izard, T., et al. (2020) The D614G Mutation in the SARS-CoV-2 Spike Protein Reduces S1 Shedding and Increases Infectivity. Microbiology. https://doi.org/10.1101/2020.06.12.148726 http://biorxiv.org/lookup/doi/10.1101/2020.06.12.148726
[45]
Zhou, B., Thao, T.T.N., Hoffmann, D., Taddeo, A., Ebert, N., Labroussaa, F., et al. (2021) SARS-CoV-2 Spike D614G Change Enhances Replication and Transmission. Nature, 592, 122-127. https://doi.org/10.1038/s41586-021-03361-1 http://www.nature.com/articles/s41586-021-03361-1
[46]
Korber, B., Fischer, W.M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., et al. (2020) Tracking Changes in SARS-COV-2 Spike: Evidence That D614G Increases Infectivity of the COVID-19 Virus. Cell, 182, 812-827, e19. https://doi.org/10.1016/j.cell.2020.06.043 https://linkinghub.elsevier.com/retrieve/pii/S0092867420308205
[47]
Kozlovskaya, L., Piniaeva, A., Ignatyev, G., Selivanov, A., Shishova, A., Kovpak, A., et al. (2020) Isolation and Phylogenetic Analysis of SARS-CoV-2 Variants Collected in Russia during the COVID-19 Outbreak. International Journal of Infectious Diseases, 99, 40-46. https://doi.org/10.1016/j.ijid.2020.07.024 https://linkinghub.elsevier.com/retrieve/pii/S120197122030566X
[48]
Tang, X., Wu, C., Li, X., Song, Y., Yao, X., Wu, X., et al. (2020) On the Origin and Continuing Evolution of SARS-CoV-2. National Science Review, 7, 1012-1023. https://doi.org/10.1093/nsr/nwaa036 https://academic.oup.com/nsr/article/7/6/1012/5775463
