Poster abstracts
Poster number 21 submitted by Dwight Hall
SARS-CoV-2 Diversity and Phylogeny in Indiana COVID-19 Patients
Dwight William Hall (Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University), Quoseena Mir, Rajneesh Srivastava (Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University), Guang-Sheng Lei (Department of Pathology and Laboratory Medicine, IUSM, Indianapolis, Indiana), David James Tauriainen (School of Informatics and Computing, Indiana University Purdue University), Ryan F. Relich, John-Paul Lavik (Department of Pathology and Laboratory Medicine, IUSM, Indianapolis, Indiana), Sarath Chandra Janga (Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University)
Abstract:
The novel coronavirus (COVID-19) outbreak, which initially began in China, has spread to many countries around the globe. The number of confirmed COVID-19 cases increase daily with a death toll exceeding the SARS (Severe Acute Respiratory Syndrome) outbreak in 2002 and 2003. SARS-CoV-2 has led to a pandemic, which put all health organizations on high alert. In this study we aimed to sequence, genotype and map the diversity of the positive COVID-19 Indiana samples onto a global phylogenetic tree of COVID19 strains to understand the evolution and transmission dynamics of Indiana isolates. The phylogenetic analysis for positive COVID-19 samples could lead to insights on which mutations are causing more transmissible and virulent strains of SARS-CoV-2.
Nasal swabs from 40 positive COVID-19 samples were employed for SARS-CoV2 isolation and sequenced using Oxford MinIon Sequencer and processed using Artic Network (https://artic.network/ncov-2019). Consensus sequences of the complete viral genome were assembled using a pipeline proposed by Artic Network. The phylogenetic tree, geographical map, and genotype diversity were built using Nextstrain’s open source software. Resulting phylogenetic trees were analyzed for genomic diversity and geographical origin of the collected samples. Genomic diversity was used to infer mutation sites among the samples. Geographical location was used to determine which countries had the most similar sequences to the samples from Indiana. The phylogenetic tree and transmission map can be viewed at https://covid19-indiana.soic.iupui.edu/.
The global phylogenetic tree indicated that 39 of the Indiana samples belonged to the G (glycine) group, while 1 Indiana sample corresponded to the D (aspartic acid) group classified based on the mutations in the Spike Protein Codon 614. Based on previous studies and our own observations, this modification is attributing to a more transmissible type of SARS-CoV-2 [1-3]. Geographical analysis of the Indiana samples revealed that within the United States, the SARS-CoV-2 sequences were most similar to sequences from Virginia and Michigan while outside the United States, most similar to sequences from Victoria, Australia.
References:
1. Brufsky, A. (2020), Distinct viral clades of SARS‐CoV‐2: Implications for modeling of viral spread. J Med Virol, 92: 1386-1390. doi:10.1002/jmv.25902
2. Bette Korber et al.: Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020, Volume 182(Issue 4):Pages 812-827.e819.
3. Muthukrishnan Eaaswarkhanth, Al Madhoun A, Fahd Al-Mulla: Could the D614G substitution in the SARS-CoV-2 spike (S) protein be associated with higher COVID-19 mortality? International Journal of Infectious Diseases 2020, Volume 96:Pages 459-460.
Keywords: Phylogenetic , SARS-CoV-2 , COVID19