Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

Abstract

A B S T R A C TBackground: While respiratory viral infections are recognized as a frequent cause of illness in hematopoietic stem cell transplantation (HSCT) recipients, HCoV−OC43 infections have rarely been investigated as healthcareassociated infections in this population. Objectives: In this report, HCoV−OC43 isolates collected from HSCT patients were retrospectively characterized to identify potential clusters of infection that may stand for a hospital transmission. Study design: Whole-genome and S gene sequences were obtained from nasal swabs using next-generation sequencing and phylogenetic trees were constructed. Similar identity matrix and determination of the most common ancestor were used to compare clusters of patient's sequences. Amino acids substitutions were analysed. Results: Genotypes B, E, F and G were identified. Two clusters of patients were defined from chronological data and phylogenetic trees. Analyses of amino acids substitutions of the S protein sequences identified substitutions specific for genotype F strains circulating among European people. Conclusions: HCoV−OC43 may be implicated in healthcare-associated infections.

Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses

“…When circulating OC43 isolates were analyzed for comparative genomics in Belgium, that study showed evidence of diversity. 21 This diversity has also been seen in several other geographic regions, [22][23][24][25][26] and several genotype clusters have since been defined. 22,23 In Japan, investigators found genotypes switching from 1 year to the next in outbreaks among children.…”

Phylogenetic characteristics of Non-SARS human coronavirus in southern Taiwan, 2012–2013

“…However, for HCoV-OC43 in sample YC101/TWN/2013, the S and RdRp genes were clustered with genotype F, whereas the N gene was clustered with genotype G, implying a recombination event between genotypes F and G.

Fig. 1 Phylogenetic analysis based on the nucleocapsid, S1 domain of spike, and RNA-dependent RNA polymerase (RdRp) genes of human coronavirus OC43 in this study (marked with symbols) and representative sequences retrieved from GenBank (accession number) and literatures [ 2 , [9] , [10] , [11] , [12] ].

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“…The phylogenetic trees based on the N, S, and RdRp genes of HCoVs from this study and representative sequences retrieved from GenBank and literatures were constructed using neighbor-joining method and Kimura’s two-parameter model in MEGA X ( http://www.megasoftware.net/ ) and evaluated with 1000 bootstrap pseudoreplicates [ 2 , 7 , [9] , [10] , [11] , [12] , [13] ]. The assignment of genotypes or genogroups followed those described in earlier studies [ 2 , 7 , [9] , [10] , [11] , [12] , [13] ]. Profiles of amino acid substitutions in the S1 domain of the S protein of HCoV-OC43 were also analyzed.…”

Coronavirus Detection in the Clinical Microbiology Laboratory

“…On the research side, mNGS was used to propose an evolutionary pathway of the SARS-CoV-2 virus from its origin in bats, 37 for the detection of a cluster of severe lower respiratory tract infections associated with a novel subgenotype of HCoV-NL63, 38 and in identifying an outbreak of health care–associated infections with HCoV-OC43 in hematopoietic stem cell transplant patients, 39 in addition to illuminating a global understanding of the epidemiology of coronaviruses in bats. 40 The applications of mNGS for identification and diagnosis of novel strains of coronaviruses are vast and, when used, initially will provide a quicker and better understanding of the biology and epidemiology of coronaviruses.…”