Isolation of SARS CoV-2 and evaluation of human-animal cases
Yıl 2022,
, 17 - 25, 15.06.2022
Sabri Hacioglu
,
Ahu Pakdemirli
,
Dilek Dülger
,
Erdem Danyer
,
Ümmü Sena Sarı
,
Özcan Yıldırım
,
Cevdet Yaralı
Öz
Complete genome analyses of SARS CoV-2 isolated from three Turkish patients are compared with other complete genome sequences in the world. In this study, especially the sequence data from animals were also involved in the evaluation. When the genetic data collected from animal and human COVID-19 cases were analyzed, it was evaluated that some recent nucleotide changes in human cases were similar to those of some animal COVID-19 cases. It is recommended that nucleotide or protein changes in human cases in SARS CoV-2 be followed and compared with large-scale studies in animals.
Proje Numarası
TAGEM/HSGYAD/G/20/A5/P6/01
Kaynakça
- Adam DC, Wu P, Wong JY, Lau EHY, Tsang TK, Cauchemez S, Leung GM and Cowling BJ (2020) Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong. Nat. Med. 26, 1714–1719. Available at: http://dx.doi.org/10.1038/s41591-020-1092-0.
- Andersen KG, Rambaut A, Lipkin WI, Holmes EC and Garry RF (2020) The proximal origin of SARS-CoV-2. Nat. Med. 26, 450–452. Available at: https://doi.org/10.1038/s41591-020-0820-9 .
- Cdc (2020) Symptoms of Coronavirus (COVID-19) Know the symptoms of COVID-19, which can include the following. Available at: https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html [Accessed May 4, 2022].
- Cohen J (2020) From mice to monkeys, animals studied for coronavirus answers. Science (80-. ). 368, 221–222. Available at: http://stm.sciencemag.org/content/scitransmed/8/326/326ra21.full.
- Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DGJC, Haagmans BL, Van Der Veer B, Van Den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MPG and Drosten C (2020) Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 25. Available at: /pmc/articles/PMC6988269/.
- Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
- Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, Haagmans BL, Lauber C, Leontovich AM, Neuman BW, Penzar D, Perlman S, Poon LLM, Samborskiy D V., Sidorov IA, Sola I and Ziebuhr J (2020) The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5, 536–544. Available at: https://doi.org/10.1038/s41564-020-0695-z.
- Gunadi, Wibawa H, Marcellus, Hakim MS, Daniwijaya EW, Rizki LP, Supriyati E, Nugrahaningsih DAA, Afiahayati, Siswanto, Iskandar K, Anggorowati N, Kalim AS, Puspitarani DA, Athollah K, Arguni E, Nuryastuti T and Wibawa T (2020) Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. PeerJ 8, 1–15.
- Handrick S, Bestehorn-Willmann M, Eckstein S, Walter MC, Antwerpen MH, Naija H, Stoecker K, Wölfel R and Ben Moussa M (2020) Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis. Virus Genes 56, 767–771. Available at: https://doi.org/10.1007/s11262-020-01795-9.
- Huson DH and Scornavacca C (2012) Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067. Available at: https://pubmed.ncbi.nlm.nih.gov/22780991/.
- Kumar S, Stecher G, Li M, Knyaz C and Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. Available at: https://pubmed.ncbi.nlm.nih.gov/29722887/.
- Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y and Cao WC (2020) Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282–285.
- Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ and Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948. Available at: https://pubmed.ncbi.nlm.nih.gov/17846036/.
- Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Cerrato F, Farhat M, Slater D, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ and MacInnis BL (2020) Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science (80-. ). 371, eabe3261.
- Li H (2018) Minimap2: pairwise alignment for nucleotide sequences I. Birol, ed. Bioinformatics 34, 3094–3100. Available at: https://academic.oup.com/bioinformatics/article/34/18/3094/4994778.
- Li T, Liu D, Yang Y, Guo J, Feng Y, Zhang X, Cheng S and Feng J (2020) Phylogenetic supertree reveals detailed evolution of SARS-CoV-2. Sci. Rep. 10, 1–10.
- El Masry, I., von Dobschuetz, s., plee, L., Larfaoui, F., Yang, Z., song, J., pfeiffer, D., calvin, s., roberts, H., Lorusso, a., Barton-Behravesh, c., Zheng, Z., Kalpravidh, W. & sumption K (2020) Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals, FAO. Available at: http://www.fao.org/documents/card/en/c/cb1739en.
- Nguyen LT, Schmidt HA, Von Haeseler A and Minh BQ (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274. Available at: /pmc/articles/PMC4271533/.
- OIE (2021) Events in animals: OIE - World Organisation for Animal Health. Available at: https://www.oie.int/en/scientific-expertise/specific-information-and-recommendations/questions-and-answers-on-2019novel-coronavirus/events-in-animals/.
OIE (2020) Infection With Sars-Cov-2 in Animals - Oie Last Update in September 2020. 2, 1–6.
- Park SE (2020) Epidemiology, virology, and clinical features of severe acute respiratory syndrome-coronavirus-2 (SARS-COV-2; Coronavirus Disease-19). Clin Exp Pediatr 63, 119–124.
- Rabaan AA, Al-Ahmed SH, Haque S, Sah R, Tiwari R, Singh Malik Y, Dhama K, Iqbal Yatoo M, Katterine Bonilla-Aldana D and Rodriguez-Morales AJ (2020) SARS-CoV-2, SARS-CoV, and MERS-CoV: a comparative overview. Infez Med 2, 174–184.
- Rambaut A (2009) FigTree, version 1.4.3. Comput. Progr. Distrib. by author, website http//tree.bio.ed.ac.uk/software/figtree/.
- Rambaut A, Drummond AJ, Xie D, Baele G and Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904. Available at: https://pubmed.ncbi.nlm.nih.gov/29718447/ .
- Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L and Pybus OG (2020) A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 5, 1403–1407. Available at: https://doi.org/10.1038/s41564-020-0770-5.
- Ronquist F and Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574. Available at: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btg180.
- Schlottau K, Rissmann M, Graaf A, Schön J, Sehl J, Wylezich C, Höper D, Mettenleiter TC, Balkema-Buschmann A, Harder T, Grund C, Hoffmann D, Breithaupt A and Beer M (2020) SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study. The Lancet Microbe 1, e218–e225. Available at: www.thelancet.com/microbe.
- Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. Available at: /pmc/articles/PMC3998144/.
- Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
- WHO (202AD) WHO Coronavirus Disease (COVID-19) Dashboard | WHO Coronavirus Disease (COVID-19) Dashboard. Who.int, 1. Available at: https://covid19.who.int/ [Accessed February 12, 2021].
- 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 and Shi Z-L (2012) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579. Available at: https://doi.org/10.1038/s41586-020-2012-7 .
- Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF and Tan W (2020) A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733. Available at: /pmc/articles/PMC7092803/ .
SARS CoV-2 izolasyonu ve insan-hayvan vakalarının değerlendirilmesi
Yıl 2022,
, 17 - 25, 15.06.2022
Sabri Hacioglu
,
Ahu Pakdemirli
,
Dilek Dülger
,
Erdem Danyer
,
Ümmü Sena Sarı
,
Özcan Yıldırım
,
Cevdet Yaralı
Öz
Üç hastadan izole edilen SARS CoV-2'nin tam genom analizleri dünyadaki diğer tam genom dizileriyle karşılaştırılmıştır. Bu çalışmada özellikle hayvanlardan alınan dizilim verileri de değerlendirmeye dahil edilmiştir. Hayvan ve insan COVID-19 vakalarından toplanan genetik veriler analiz edildiğinde, insan vakalarında yakın zamanda meydana gelen bazı nükleotid değişikliklerinin bazı hayvan COVID-19 vakalarındakine benzer olduğu değerlendirildi. SARS CoV-2'de insan vakalarındaki nükleotid veya protein değişikliklerinin hayvanlarda yapılacak geniş çaplı çalışmalarla takip edilerek karşılaştırılması önerilmektedir.
Proje Numarası
TAGEM/HSGYAD/G/20/A5/P6/01
Kaynakça
- Adam DC, Wu P, Wong JY, Lau EHY, Tsang TK, Cauchemez S, Leung GM and Cowling BJ (2020) Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong. Nat. Med. 26, 1714–1719. Available at: http://dx.doi.org/10.1038/s41591-020-1092-0.
- Andersen KG, Rambaut A, Lipkin WI, Holmes EC and Garry RF (2020) The proximal origin of SARS-CoV-2. Nat. Med. 26, 450–452. Available at: https://doi.org/10.1038/s41591-020-0820-9 .
- Cdc (2020) Symptoms of Coronavirus (COVID-19) Know the symptoms of COVID-19, which can include the following. Available at: https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html [Accessed May 4, 2022].
- Cohen J (2020) From mice to monkeys, animals studied for coronavirus answers. Science (80-. ). 368, 221–222. Available at: http://stm.sciencemag.org/content/scitransmed/8/326/326ra21.full.
- Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW, Bleicker T, Brünink S, Schneider J, Schmidt ML, Mulders DGJC, Haagmans BL, Van Der Veer B, Van Den Brink S, Wijsman L, Goderski G, Romette JL, Ellis J, Zambon M, Peiris M, Goossens H, Reusken C, Koopmans MPG and Drosten C (2020) Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 25. Available at: /pmc/articles/PMC6988269/.
- Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
- Gorbalenya AE, Baker SC, Baric RS, de Groot RJ, Drosten C, Gulyaeva AA, Haagmans BL, Lauber C, Leontovich AM, Neuman BW, Penzar D, Perlman S, Poon LLM, Samborskiy D V., Sidorov IA, Sola I and Ziebuhr J (2020) The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat. Microbiol. 5, 536–544. Available at: https://doi.org/10.1038/s41564-020-0695-z.
- Gunadi, Wibawa H, Marcellus, Hakim MS, Daniwijaya EW, Rizki LP, Supriyati E, Nugrahaningsih DAA, Afiahayati, Siswanto, Iskandar K, Anggorowati N, Kalim AS, Puspitarani DA, Athollah K, Arguni E, Nuryastuti T and Wibawa T (2020) Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia. PeerJ 8, 1–15.
- Handrick S, Bestehorn-Willmann M, Eckstein S, Walter MC, Antwerpen MH, Naija H, Stoecker K, Wölfel R and Ben Moussa M (2020) Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis. Virus Genes 56, 767–771. Available at: https://doi.org/10.1007/s11262-020-01795-9.
- Huson DH and Scornavacca C (2012) Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061–1067. Available at: https://pubmed.ncbi.nlm.nih.gov/22780991/.
- Kumar S, Stecher G, Li M, Knyaz C and Tamura K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549. Available at: https://pubmed.ncbi.nlm.nih.gov/29722887/.
- Lam TTY, Jia N, Zhang YW, Shum MHH, Jiang JF, Zhu HC, Tong YG, Shi YX, Ni XB, Liao YS, Li WJ, Jiang BG, Wei W, Yuan TT, Zheng K, Cui XM, Li J, Pei GQ, Qiang X, Cheung WYM, Li LF, Sun FF, Qin S, Huang JC, Leung GM, Holmes EC, Hu YL, Guan Y and Cao WC (2020) Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583, 282–285.
- Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ and Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948. Available at: https://pubmed.ncbi.nlm.nih.gov/17846036/.
- Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Cerrato F, Farhat M, Slater D, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ and MacInnis BL (2020) Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events. Science (80-. ). 371, eabe3261.
- Li H (2018) Minimap2: pairwise alignment for nucleotide sequences I. Birol, ed. Bioinformatics 34, 3094–3100. Available at: https://academic.oup.com/bioinformatics/article/34/18/3094/4994778.
- Li T, Liu D, Yang Y, Guo J, Feng Y, Zhang X, Cheng S and Feng J (2020) Phylogenetic supertree reveals detailed evolution of SARS-CoV-2. Sci. Rep. 10, 1–10.
- El Masry, I., von Dobschuetz, s., plee, L., Larfaoui, F., Yang, Z., song, J., pfeiffer, D., calvin, s., roberts, H., Lorusso, a., Barton-Behravesh, c., Zheng, Z., Kalpravidh, W. & sumption K (2020) Exposure of humans or animals to SARS-CoV-2 from wild, livestock, companion and aquatic animals, FAO. Available at: http://www.fao.org/documents/card/en/c/cb1739en.
- Nguyen LT, Schmidt HA, Von Haeseler A and Minh BQ (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274. Available at: /pmc/articles/PMC4271533/.
- OIE (2021) Events in animals: OIE - World Organisation for Animal Health. Available at: https://www.oie.int/en/scientific-expertise/specific-information-and-recommendations/questions-and-answers-on-2019novel-coronavirus/events-in-animals/.
OIE (2020) Infection With Sars-Cov-2 in Animals - Oie Last Update in September 2020. 2, 1–6.
- Park SE (2020) Epidemiology, virology, and clinical features of severe acute respiratory syndrome-coronavirus-2 (SARS-COV-2; Coronavirus Disease-19). Clin Exp Pediatr 63, 119–124.
- Rabaan AA, Al-Ahmed SH, Haque S, Sah R, Tiwari R, Singh Malik Y, Dhama K, Iqbal Yatoo M, Katterine Bonilla-Aldana D and Rodriguez-Morales AJ (2020) SARS-CoV-2, SARS-CoV, and MERS-CoV: a comparative overview. Infez Med 2, 174–184.
- Rambaut A (2009) FigTree, version 1.4.3. Comput. Progr. Distrib. by author, website http//tree.bio.ed.ac.uk/software/figtree/.
- Rambaut A, Drummond AJ, Xie D, Baele G and Suchard MA (2018) Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904. Available at: https://pubmed.ncbi.nlm.nih.gov/29718447/ .
- Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, du Plessis L and Pybus OG (2020) A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat. Microbiol. 5, 1403–1407. Available at: https://doi.org/10.1038/s41564-020-0770-5.
- Ronquist F and Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572–1574. Available at: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btg180.
- Schlottau K, Rissmann M, Graaf A, Schön J, Sehl J, Wylezich C, Höper D, Mettenleiter TC, Balkema-Buschmann A, Harder T, Grund C, Hoffmann D, Breithaupt A and Beer M (2020) SARS-CoV-2 in fruit bats, ferrets, pigs, and chickens: an experimental transmission study. The Lancet Microbe 1, e218–e225. Available at: www.thelancet.com/microbe.
- Stamatakis A (2014) RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313. Available at: /pmc/articles/PMC3998144/.
- Swofford DL (2003) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
- WHO (202AD) WHO Coronavirus Disease (COVID-19) Dashboard | WHO Coronavirus Disease (COVID-19) Dashboard. Who.int, 1. Available at: https://covid19.who.int/ [Accessed February 12, 2021].
- 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 and Shi Z-L (2012) A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579. Available at: https://doi.org/10.1038/s41586-020-2012-7 .
- Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, Niu P, Zhan F, Ma X, Wang D, Xu W, Wu G, Gao GF and Tan W (2020) A Novel Coronavirus from Patients with Pneumonia in China, 2019. N. Engl. J. Med. 382, 727–733. Available at: /pmc/articles/PMC7092803/ .