Work

Molecular Epidemiological Investigations of Localized SARS-CoV-2 Outbreaks-Utility of Public Algorithms

Year: 2022

Type: article

Abstract: The recent rapid expansion of targeted viral sequencing approaches in conjunction with available bioinformatics have provided an effective platform for studying severe acute respiratory syndrome coronavirus-2 (CoV-2) virions at the molecular level. These means can be adapted to the field of viral molecular epidemiology, wherein localized outbreak clusters can be evaluated and linked. To this end, we have integrated publicly available algorithms in conjunction with targeted RNASeq data in order to qualitatively evaluate similarity or dissimilarity between suspect outbreak strains from hospitals, or assisted living facilities. These tools include phylogenetic clustering and mutational analysis utilizing Nextclade and Ultrafast Sample placement on Existing tRee (UShER). We herein present these outbreak screening tools utilizing three case examples in the context of molecular epidemiology, along with limitations and potential future developments. We anticipate that these methods can be performed in clinical molecular laboratories equipped with CoV-2-sequencing technology.

Source: Epidemiologia

DOI: 10.3390/epidemiologia3030031

Authors: Mahmood Y. Bilal, James S. Klutts

Institutions: University of Iowa Hospitals and Clinics, Iowa City VA Health Care System

Language: English

Topic: SARS-CoV-2 and COVID-19 Research

Subfield: Infectious Diseases

Field: Medicine

Domain: Health Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,047