Competing endogenous RNA network mediated by circ_3205 in SARS-CoV-2 infected cells

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a new member of the Betacoronaviridae family, responsible for the recent pandemic outbreak of COVID-19. To start exploring the molecular events that follow host cell infection, we queried VirusCircBase and identified a circular RNA (circRNA) predicted to be synthesized by SARS-CoV-2, circ_3205, which we used to probe: (i) a training cohort comprised of two pools of cells from three nasopharyngeal swabs of SARS-CoV-2 infected (positive) or uninfected (negative, UCs) individuals; (ii) a validation cohort made up of 12 positive and 3 negative samples. The expression of circRNAs, miRNAs and miRNA targets was assayed through real-time PCR. CircRNA-miRNA interactions were predicted by TarpMiR, Analysis of Common Targets for circular RNAs (ACT), and STarMir tools. Enrichment of the biological processes and the list of predicted miRNA targets were retrieved from DIANA miRPath v3.0. Our results showed that the predicted SARS-CoV-2 circ_3205 was expressed only in positive samples and its amount positively correlated with that of SARS-CoV-2 Spike (S) mRNA and the viral load (r values = 0.80952 and 0.84867, Spearman's correlation test, respectively). Human (hsa) miR-298 was predicted to interact with circ_3205 by all three predictive tools. KCNMB4 and PRKCE were predicted as hsa-miR-298 targets. Interestingly, the function of both is correlated with blood coagulation and immune response. KCNMB4 and PRKCE mRNAs were upregulated in positive samples as compared to UCs (6 and 8.1-fold, p values = 0.049 and 0.02, Student's t test, respectively) and their expression positively correlated with that of circ_3205 (r values = 0.6 and 0.25, Spearman's correlation test, respectively). We propose that our results convincingly suggest that circ_3205 is a circRNA synthesized by SARS-CoV-2 upon host cell infection and that it may behave as a competitive endogenous RNA (ceRNA), sponging hsa-miR-298 and contributing to the upregulation of KCNMB4 and PRKCE mRNAs.

Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach

BACKGROUND

The SARS-CoV-2 virus has assumed considerable importance during the COVID-19 pandemic. Its mutation rate is high, involving the spike (S) gene and thus there has been a rapid spread of new variants. Herein, we describe a rapid, easy, adaptable, and affordable workflow to uniquely identify all currently known variants through as few analyses. Our method only requires two conventional PCRs of the S gene and two Sanger sequencing reactions, and possibly another PCR/sequencing assay on a N gene portion to identify the B.1.160 lineage.

METHODS

We selected an S gene 1312 bp portion containing a set of SNPs useful for discriminating all variants. Mathematical, statistical, and bioinformatic analyses demonstrated that our choice allowed us to identify all variants even without looking for all related mutations, as some of them are shared by different variants (e.g., N501Y is found in the Alpha, Beta, and Gamma variants) whereas others, that are more informative, are unique (e.g., A57 distinctive to the Alpha variant).

RESULTS

A "weight" could be assigned to each mutation that may be present in the selected portion of the S gene. The method's robustness was confirmed by analyzing 80 SARS-CoV-2-positive samples.

CONCLUSIONS

Our workflow identified the variants without the need for whole-genome sequencing and with greater reliability than with commercial kits.

Sensitivity assessment of droplet digital PCR for SARS-CoV-2 detection

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the gold standard method for the diagnosis of COVID-19 infection. Due to pre-analytical and technical limitations, samples with low viral load are often misdiagnosed as false-negative samples. Therefore, it is important to evaluate other strategies able to overcome the limits of RT-qPCR. Blinded swab samples from two individuals diagnosed positive and negative for COVID-19 were analyzed by droplet digital PCR (ddPCR) and RT-qPCR in order to assess the sensitivity of both methods. Intercalation chemistries and a World Health Organization (WHO)/Center for Disease Control and Prevention (CDC)-approved probe for the SARS-CoV-2 N gene were used. SYBR-Green RT-qPCR is not able to diagnose as positive samples with low viral load, while, TaqMan Probe RT-qPCR gave positive signals at very late Ct values. On the contrary, ddPCR showed higher sensitivity rate compared to RT-qPCR and both EvaGreen and probe ddPCR were able to recognize the sample with low viral load as positive even at 10-fold diluted concentration. In conclusion, ddPCR shows higher sensitivity and specificity compared to RT-qPCR for the diagnosis of COVID-19 infection in false-negative samples with low viral load. Therefore, ddPCR is strongly recommended in clinical practice for the diagnosis of COVID-19 and the follow-up of positive patients until complete remission.

Evaluation of isavuconazole MIC strips for susceptibility testing of Aspergillus and Scedosporium species

Isavuconazole is a new triazole with an expanded-spectrum and potent activity against moulds and yeasts. It has been authorized for use in adults for the treatment of invasive aspergillosis and for mucormycosis. The only commercially available isavuconazole susceptibility test is the minimum inhibitory concentration (MIC) strip isavuconazole test. The objective of this study was to assess the in vitro activity of isavuconazole using gradient concentration MIC strips, compared with the EUCAST broth microdilution reference method. A total of 147 clinically relevant fungal isolates comprising 120 Aspergillus sp. and 27 Scedosporium apiospermum complex were tested for susceptibility to isavuconazole using the EUCAST broth microdilution method and by the MIC strip isavuconazole test. The percent essential agreement between the two methods was calculated within a 1-fold dilution. The geometric means for the MICs using the EUCAST reference methods and the strip test were respectively: 0.60 mg/l and 0.65 mg/l for A. fumigatus, 0.70 mg/l and 0.77 mg/l for A. flavus, 1.50 mg/l and 1.25 mg/l for A. niger, 0.41 mg/l and 0.38 mg/l for A. terreus, 1.22 mg/l and 1.08 mg/l for S. apiospermum complex. The isavuconazole MIC strips showed good agreement with the EUCAST reference method. Isavuconazole MIC strips could be useful for susceptibility testing of Aspergillus sp. and S. apiospermum complex.

Oxytocin plasma levels in orgasmic and anorgasmic women

The study aimed to evaluate oxytocin (Oxt) serum levels before and after sexual intercourse in women affected by anorgasmia. The sample was constituted of 15 anorgasmic women and 16 orgasmic women. The Female Sexual Function Index (FSFI, cutoff ≤26.55) and the Female Sexual Distress Scale (FSDS, cutoff ≥15) questionnaires were used to assess sexual function and sexual distress, respectively. Serum Oxt levels were measured before sexual intercourse (T0) and 5 min after coital sexual activity (T1). Anorgasmic women had an unpleasant sexual experience (FSFI total score, 20.1 ± 1.2;) and were stressed (FSDS score, 19.4 ± 1.3), whereas orgasmic women were fully satisfied with their sexual activity (FSFI total score 28.7 ± 1.3; FSDS score 11.5 ± 1.8). At T0, anorgasmic women had lower levels of Oxt than orgasmic women, 1.8 ± 0.2 pg/mL versus 2.1 ± 0.5 pg/mL, respectively, [95% CI: (-0.58, -0.01); p < .04]. At T1, Oxt levels did not change in anorgasmic women (1.8 ± 0.2 pg/mL versus 2 ± 0.4 pg/mL, p = .09). Finally, orgasmic women had higher levels of Oxt than anorgasmic women, 4.6 ± 0.7 pg/mL versus 2 ± 0.4 pg/mL, respectively [95% CI: (-3.02, -2.17); p < .001]. The repetitive processes to experience the sexual body sensations could represent a survival behavior of species by attachment to a partner.

Focal epilepsy as a long term sequela of Parvovirus B19 encephalitis

Human Parvovirus B19 (PVB19), the etiological agent of the fifth disease, is associated with a large spectrum of pathologies, among which is encephalitis. Since it has been detected from the central nervous system in children or in immunocompromised patients, its causative role in serious neurological manifestations is still unclear. Here we report the case of an 18-year-old healthy boy who developed encephalitis complicated by prolonged status epilepticus. The detection of PVB19 DNA in his serum and, subsequently, in his cerebrospinal fluid supports the hypothesis that this virus could potentially play a role in the pathogenesis of neurological complications. In addition, the detection of viral DNA and the presence of specific IgM and IgG antibodies in serum, together with clinical findings such as skin rash, support the presence of a disseminated viral infection. In the presence of neurological disorders, especially when there are no specific signs, but seizures and rash are present, it is important to search for PVB19 both in immunocompromised and immunocompetent patients. Moreover, the introduction of the PVB19 DNA test into diagnostic protocols of neuropathies, especially those undiagnosed, could clarify the etiological agent that otherwise could remain unrecognized.

Detection of serum IgA to HSV1 and its diagnostic role in sudden hearing loss

A viral etiology of sudden hearing loss has been hypothesized by many authors. HSV1 neurotropism and its involvement in sudden hearing loss has implicated HSV1 as one of the most accredited etiological agents. A non-invasive method such as the titration of HSV1-specific IgA was evaluated to determine the role of HSV1 as a possible cause sudden hearing loss. A prospective study was carried out by titration of serum IgA to HSV1 in 93 patients and in a control group of 50 healthy subjects and 35 subjects suffering from recent herpes labialis reactivation. Statistical analysis of the results disclosed that IgA titers to HSV1 higher than 1:80 are suggestive for the association of HSV1 infection and sudden hearing loss. Moreover, acyclovir therapy was effective in 81% of patients who showed high specific IgA titers. Overall, the titration of specific serum IgA to HSV1 can be a useful tool to determine the viral etiology of certain cases of sudden hearing loss. This method is simple to perform and minimally invasive. It can lead to a rapid presumptive diagnosis and to prompt specific therapy, reducing the need for corticosteroids.