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BackgroundEpigenetic alterations upon microbial challenge have been described as both a defence strategy and a result of pathogenic manipulation. While most COVID-19 studies focus on inflammatory and immune-mediated responses, little is known about epigenetic modifications in response to SARS-CoV-2 infection. MethodsEpigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation and module identification analyses. ResultsDifferential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1 and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome. ConclusionsAltered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. As in vitro SARS-CoV-2 infection corroborated in vivo exposure results, this indicates DNA methylation is involved in immune cell responses to challenge with this virus. Future studies should determine whether this reflects host-induced protective antiviral defence or targeted viral hijacking to evade host defence.
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BackgroundThe COVID-19 pandemic has highlighted the need for rapid, cost effective and easy-to-use diagnostic tools for SARS-CoV-2 rapid antigen detection (RAD) for use in point of care settings or as self-tests, to limit disease transmission. Using saliva samples would further greatly facilitate sample collection, diagnostic feasibility, and mass screening. ObjectiveWe tested two rapid antigen immunochromatographic tests designed for detection of SARS-CoV-2 in saliva: Rapid Response COVID-19 Antigen Rapid Test Cassette for oral fluids (Rapid Response) and DIAGNOS COVID-19 Antigen Saliva Test (DIAGNOS). Evaluation of detection limit was performed with purified SARS-CoV-2 nucleocapsid protein and titrated live SARS-CoV-2 virus and compared to Abbott Panbio COVID-19 Ag Rapid Test (Panbio) designed for nasopharyngeal samples. Sensitivity and specificity were further evaluated on RT-qPCR positive and negative saliva samples from individuals hospitalized with COVID-19 (n=34); and asymptomatic health care personnel (n=20). ResultsThe limit of detection of the saliva test from DIAGNOS was comparable with the Panbio test and showed higher sensitivity than Rapid Response for both nucleocapsid protein and diluted live viruses. DIAGNOS and Rapid Response further detected seven (47%) and five (33%), respectively, of the 15 RT-qPCR positive saliva samples in individuals hospitalized with COVID-19. Of the 39 RT-qPCR negative samples, all were negative with both tests (specificity 100%; 95% c.i. 0.91-1.00). Only one of the RT-qPCR positive saliva samples (Ct 21.6) contained infectious virus as determined by cell culture and was also positive using the saliva RADs. ConclusionThe results show that the DIAGNOS test exhibit a similar limit of detection as the Panbio RAD and may be an important and easy-to-use saliva RAD complement to detect infectious individuals.
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The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.
