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Objectives Coronavirus Disease-19 (COVID-19) is a respiratory infection characterized by the main symptoms of pneumonia and fever. It is caused by the novel coronavirus severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2), which is known to spread via respiratory droplets. We aimed to determine the rate and likelihood of SARS-CoV-2 transmission from COVID-19 patients through non-respiratory routes. Methods Serum, urine, and stool samples were collected from 74 hospitalized patients diagnosed with COVID-19 based on the detection of SARS-CoV-2 in respiratory samples. The SARS-CoV-2 RNA genome was extracted from each specimen and real-time reverse transcription polymerase chain reaction performed. CaCo-2 cells were inoculated with the specimens containing the SARS-COV-2 genome, and subcultured for virus isolation. After culturing, viral replication in the cell supernatant was assessed. Results Of the samples collected from 74 COVID-19 patients, SARS-CoV-2 was detected in 15 serum, urine, or stool samples. The virus detection rate in the serum, urine, and stool samples were 2.8% (9/323), 0.8% (2/247), and 10.1% (13/129), and the mean viral load was 1,210 ± 1,861, 79 ± 30, and 3,176 ± 7,208 copy/μL, respectively. However, the SARS-CoV-2 was not isolated by the culture method from the samples that tested positive for the SARS-CoV-2 gene. Conclusion While the virus remained detectable in the respiratory samples of COVID-19 patients for several days after hospitalization, its detection in the serum, urine, and stool samples was intermittent. Since the virus could not be isolated from the SARS-COV-2-positive samples, the risk of viral transmission via stool and urine is expected to be low.

Background A reservoir of HIV-1 is a major obstacle in eliminating HIV-1 in patients because it can reactivate in stopping antiretroviral therapy (ART). Histone modifications, such as acetylation and methylation, play a critical role in the organization of chromatin domains and the up- or downregulation of gene expression. Although many studies have reported that an epigenetic mechanism is strongly involved in the maintenance of HIV-1 transcriptional latency, neither the epigenetic control of viral replication nor how HIV-1 latency is maintained is not fully understood. Results We re-analyzed a high throughput parallel DNA sequencing (ChIP-seq) data from previous work to investigate the effect of histone modifications, H3K4me3 and H3K9ac, on HIV-1 latency in terms of chromosome distribution. The outputs of ChIP-seq from uninfected CD4+ T cell lines and HIV-1 latently infected cells were aligned to hg18 using bowtie and then analyzed using various software packages. Certain chromosomes (16, 17, 19, and 22) were significantly enriched for histone modifications in both decreased and increased islands. In the same chromosomes in HIV-1 latently infected cells, 38 decreased and 41 increased islands from common islands of H3K4me3 and H3K9ac were selected for functional annotation. In Gene Ontology analysis, the 38 genes associated with decreased islands were involved in the regulation of biological process, regulation of cellular process, biological regulation, and purinergic receptor signaling pathway, while the 41 genes associated with increased islands were involved in nucleic acid binding, calcium-activated cation channel activity, DNA binding, and zinc ion binding. In Pathway Commons analysis, the 38 genes were strongly involved in the p63 transcription factor network, while the 41 genes were involved in the RNA polymerase III transcription termination pathway. Several genes such as Nuclear factor I X (NFIX) and TNF receptor association factor 4 (TRAF4) were selected as candidate genes for HIV latency. Especially, NFIX was highly expressed in HIV-1 latently infected cell lines and showed a dramatic reduction in expression after phorbol-13-myristate-12-acetate (PMA) treatment. Conclusions These results show that the unique enrichment of histone modifications and its linked genes in specific chromosomes might play a critical role in the establishment and maintenance of HIV-1 latency. Electronic supplementary material The online version of this article (doi:10.1186/s40246-017-0105-7) contains supplementary material, which is available to authorized users.

The ratio of percentage of total H3K4me3 or H3K9ac islands to percentage expected by random chance for each chromosome in three different HIV-1 latently infected cell lines.

Chromosomal distribution of H3K9ac binding sites in HIV-1 latently infected cells. Enrichment pattern of increased islands of H3K9ac among individual chromosomes is shown as bar chart. Percent of total H3K9ac islands (red bar) and what would be expected by random chance (blue bars) for each chromosome is shown. The value in parenthesis means p value.

Functional annotation of 38 decreased (A) and 41 increased (B) genes in chromosomes 16, 17, 19, and 22 of HIV-1 latently infected cells using WebGestalt. The x-axis values are â log10 of raw p values.

Lists of 38 decreased genes and 41 increased genes identified in the co-occurrence of two histone modifications, H3K4me3 and H3K9ac.

Chromosomal distribution of H3K9ac binding sites in HIV-1 latently infected cells. Enrichment pattern of decreased islands of H3K9ac among individual chromosomes is shown as bar chart. Percent of total H3K9ac islands (red bar) and what would be expected by random chance (blue bars) for each chromosome is shown. The value in parenthesis means p value.

Chromosomal distribution of H3K4me3 binding sites in HIV-1 latently infected cells. Enrichment pattern of increased islands of H3K4me3 among individual chromosomes is shown as bar chart. Percent of total H3K4me3 islands (red bar) and what would be expected by random chance (blue bars) for each chromosome is shown. The value in parenthesis means p value.

HIV-1 reservoirs remain a major barrier to HIV-1 eradication. Although combination antiretroviral therapy (cART) can successfully reduce viral replication, it cannot reactivate HIV-1 provirus in this reservoir. Therefore, HIV-1 provirus reactivation strategies by cell activation or epigenetic modification are proposed for the eradication of HIV-1 reservoirs. Although treatment with the protein kinase A (PKA) activator cyclic AMP (cAMP) or epigenetic modifying agents such as histone deacetylase inhibitors (HDACi) alone can induce HIV-1 reactivation in latently infected cells, the synergism of these agents has not been fully evaluated. In the present study, we observed that treatment with 500μM of dibutyryl-cAMP, 1μM of vorinostat, or 1μM of trichostatin A alone effectively reactivated HIV-1 in both ACH2 and NCHA1 cells latently infected with HIV-1 without cytotoxicity. In addition, treatment with the PKA inhibitor KT5720 reduced the increased HIV-1 p24 level in the supernatant of these cells. After dibutyryl-cAMP treatment, we found an increased level of the PKA substrate phosphorylated cyclic AMP response element-binding protein. When we treated cells with a combination of dibutyryl-cAMP and vorinostat or trichostatin A, the levels of HIV-1 p24 in the supernatant and levels of intracellular HIV-1 p24 were dramatically increased in both ACH2 and NCHA1 cells compared with those treated with a single agent. These results suggest that combined treatment with a PKA activator and an HDACi is effective for reactivating HIV-1 in latently infected cells, and may be an important approach to eradicate HIV-1 reservoirs.