코로나 바이러스-19의 진화 (ML, NJ 계통수, 변이의 종류 등)

소개

"코로나 바이러스-19의 진화 (ML, NJ 계통수, 변이의 종류 등)"에 대한 내용입니다.

목차

1. Introduction
2. Phylogenetic tree and explanation
3. Major various variants of human SARS-CoV-2
4. Reference

본문내용

Introduction
SARS-CoV-2(Severe acute respiratory syndrome coronavirus 2)는 coronavirus disease 19 (COVID-19)를 유발하는 바이러스로, COVID-19는 중국 허베이성 우한시에서 처음 발견되어 WHO에 의해 2020년 3월 11일 pandemic이 선언되어 지금까지 유지되는 중이다[1]. SARS-CoV-2는 coronavirus 중에서도 betacoronavirus에 속한다[[2]. SARS-CoV-2는 처음 발견된 이래 많은 변이들을 만들어 왔다.

Phylogenetic tree and explanation
NCBI에서 SARS-CoV-2 reference genome, Pangolin(천산갑) SARS-CoV-2, Bat SARS-CoV-2, 7 종의 변이와 외군(outgroup)으로 Bat betacoronavirus, Porcine gammacoronavirus를 총 12개의 full genome(약 27000 bp – 30000 bp)을 얻었다. 서열들의 NCBI Accession Code는 다음과 같다.

참고자료

· “Severe Acute Respiratory Syndrome Coronavirus 2.” Wikipedia, Wikimedia Foundation, 11 Apr. 2022, https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2.
· Wong, Antonio, et al. “Global Epidemiology of Bat Coronaviruses.” Viruses, vol. 11, no. 2, 2019, p. 174., https://doi.org/10.3390/v11020174.
· Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41:95-98.
· Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., Calcott, B. (2016) PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular biology and evolution. DOI: dx.doi.org/10.1093/molbev/msw260
· L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32:268-274. https://doi.org/10.1093/molbev/msu300
· D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, and L.S. Vinh (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35:518–522. https://doi.org/10.1093/molbev/msx281
· Rambaut. “Rambaut/Figtree: Automatically Exported from Code.google.com/p/Figtree.” GitHub, https://github.com/rambaut/figtree.
· Phylogenetic and molecular evolutionary analyses were conducted using MEGA version X (Kumar, Stecher, Li, Knyaz, and Tamura 2018).
· Mann, Christian, et al. “Detection of SARS Cov-2 Coronavirus Omicron Variant with Mass Spectrometry.” The Analyst, vol. 147, no. 6, 2022, pp. 1181–1190., https://doi.org/10.1039/d2an00028h.
· Planas, Delphine, et al. “Considerable Escape of SARS-COV-2 Variant Omicron to Antibody Neutralization.” 2021, https://doi.org/10.1101/2021.12.14.472630.
· “Variants of SARS-COV-2.” Wikipedia, Wikimedia Foundation, 12 Apr. 2022, https://en.wikipedia.org/wiki/Variants_of_SARS-CoV-2.