Akademik Veri Yönetim Sistemi
33rd European Congress of Clinical Microbiology and Infectious Diseases, Kobenhavn, Danimarka, 15 - 18 Nisan 2023, ss.1011-1012
Whole Genom Sequencing of SARS CoV 2 Transmission of Health Care Workers
Background
SARS-CoV-2
has caused hospital outbreaks, exposing both healthcare workers and the patients
to infection. Understanding transmission
dynamics is challenging and requirs integration of genomic and epidemiological
data. The aim of this study is to investigate the transmission routes of the SARS-CoV-2
among health care workers (HCW) infected in different time points by whole
genom sequencing (WGS) and contact-tracing data in a university hospital.
Methods
Six clusters of SARS-CoV-2 infection in HCWs which detected
between April 2020 and February 2022 in the Dokuz Eylul University Hospital were
retrospectively analyzed. WGS was done in a total of 32 stored nasopharyngeal
swab samples collected from HCWs and their contacts using the QIAseq DIRECT SARS-CoV-2 protocol (QIAGEN,
Germany) on the NextSeq platform (Illumina). RNA was isolated from 400 μL of sample, using
EZ1 Virus Mini Kit according to the manufacturer's instructions. SARS-CoV-2 RNA
was detected using RealStar®SARS-CoV-2 RT-PCR
Kit (Altona Diagnostics) on the Rotor-Gene-Q system. WGS was performed on samples with Ct <25. Sequence analysis and quality evaluations were performed in the CLC Genomics
Workbench program by using WuhanH1 reference genome (GenBank: NC_045512). Samples covering
at least 96% of the target genome at 10x depth (n=31) were included in the
analysis. A total of 50 WGSs were used
for phylogenetic analysis including 31 samples
of the study group, and 18 external sequences selected from GISAID and GenBank.
MEGA software was used to perform
genomic alignments, and a phylogenetic tree was constructed according to the confidence of 200
bootstrapping values by the maximum likelihood
method. Later, the tree was edited with FigTree.
Results
The median age of the study was 41 (8-76) and 52% were male. Infected
HCWs were asymptomatic or had mild to moderate symptoms. In total, 8 different
lineages and 5 different clades of SARS-CoV-2 were detected (Table 1). Commonly
detected variations (frequency >80%) were identified in the ORF1ab and S
gene regions. In clusters with a strong
epidemiological relationship, samples differed from each other with at most two different variations. In the phylogenetic tree, cluster-1
was consisted of two genomic subgroups indicating
two different entry of the virus into the group, while the other clusters were compatible
with the contact-tracing data (Figure 1). Data of the filiation team collected
by interviewing infected HCWs indicated that improper
use of personal protective equipment, social gatherings
and family contacts played a significant role in the transmission of SARS-CoV-2
to HCWs.
Conclusions
The
findings of the WGS helped to distinguish clusters of infection in HCWs
throughout the pandemic. WGS data has increased the capacity to use the
epidemiological information to understand the complex transmission dynamics of
SARS-CoV2.