Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health. Several cases of persistent infection have been described, but there are few reports that compared the genetic variability among samples collected from the patient during infection. In the current study, we reported a viral genetic analysis of a diabetic male patient with Non-Hodgkin Lymphoma affected by persistent SARS-CoV-2 infection. We sequenced the patient-derived viral isolated both from oro/nasopharyngeal swab and VeroE6 cell line, collected from the same patient at different points of the infection. Due to the insufficient material of the second swab received, in order to obtain a complete coverage of the viral genome, it was convenient to perform a virus isolation after cell culture. Both genomes belonged to Pangolin Lineage B.1, Nextstrain clade 20A and GISAID clade G. The mutation spectrum predicted for the two viral genomes reveal three additionally mutations in the sequence of second sample when compared with mutations set identified in the first sample. Our findings show the evolution of the intra-host variability during the course of a long-lasting infection.
Highlights
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health
The sample oro/nasopharyngeal swab collected on June 30th 2020 (IZSPB_123) was inoculated in VeroE6 cells, and incubation was observed at 24 h intervals
To assess the variational spectrum of the oro/nasopharyngeal swab specimen (IZSPB_141) and viral isolates by VeroE6 cell culture (IZSPB_123), whole genome sequencing of the SARS-CoV-2 samples was performed, generating 887.638 and 881.046 number of reads, respectively, of which more than 99% resulted as mapped reads
Summary
The novel coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic, threatening global public health. SARS-CoV-2 is the seventh member of the Coronaviridae family known to infect humans and it is responsible for respiratory illness of varying severity [1]. The persistence of the virus for more than 30 days has been described [4]. Previous studies have found correlation between infection duration and presence of pre-existing diseases [3] or with severe COVID-19 illness [5]; individuals that can remain positive to virus after symptom resolution were described [6,7,8]. This report describes the case of a diabetic man affected by Non-Hodgkin Lymphoma with persistent SARS-CoV-2 infection.
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