Objective: To describe the alterations of the composition of vaginal microbiota in pregnant women with COVID-19. Design: Prospective observational single-centre study Setting: Tertiary referral hospital Participants: Pregnant women with COVID-19 Methods: The vaginal swabs were collected during the active phase of infection and consecutively, within a month after recovering from infection. In three patients, longitudinal samples before, in the course, and after infection were also obtained. The microbiome alterations were examined by 16S rRNA gene sequencing. Main outcome measures: Vaginal microbiota profiles in pregnant women with COVID-19 Results: Nineteen pregnant women with COVID-19 and 28 healthy controls who were matched according to the maternal age and gestational week were recruited. Shannon index and inverse Simpson index for cross-sectional cohort indicate that alpha diversity is significantly higher in women with COVID-19 (P=0.007 and P=0.006, respectively). There was a significantly decrease in Firmicutes (P=0.007) and Lactobacillus (P=0.019) with an increase in Bacteroidetes (P=0.024) in women with COVID-19 when compared to those of healthy controls. The higher amounts of Ureaplasma were found in women with the moderate/severe disease, compared to those of the asymptomatic/mild disease (P=0.001). Lactobacillus gasseri disappeared in women with the moderate/severe disease. Prevotella timonensis was identified only in the COVID-19 group. In longitudinal analysis, Actinobacteria was elevated, Firmicutes and Bacteroides depleted during the active phase. Conclusion: The study revealed that vaginal dysbiosis with a low abundance of Lactobacillus and an increase in Bacteroidetes is associated with COVID-19.

The application of metabolomics for studying modifications in host metabolism due to viral infections has proven to be a game-changing approach. Prior to our study, only one other ‘omics’ study has been carried out that investigates the interplay between the host and CCHFV and its subsequent pathogenesis. We employed NMR spectroscopy, given its advantages in terms of reproducibility, minimal sample preparation, and capability to analyze complex biofluids. Our methodology builds upon the proven success of metabolomics in the research of other viral hemorrhagic fevers such as Ebola, Marburg, and Dengue. Our research underlines the critical role of SAH, a metabolite involved in numerous biochemical reactions. We provide new insights into the metabolic alterations occurring in CCHF patients. These alterations not only shed light on the disease’s pathogenesis but also pave the way for potential biomarkers and therapeutic targets. Among all the metabolites detected, S-Adenosyl-L-homocysteine and Carnosine stood out as the most prevalent, warranting further exploration of their roles in CCHFV pathogenesis and their potential as therapeutic targets.

Convalescent plasma samples that can be collected from individuals after the resolution of infection and vaccination are an invaluable source of neutralization antibodies against the virus. Although plaque reduction assay with replicative virus is the gold standard of analyzing neutralization potency of convalescent plasma, it is a technically demanding procedure requiring high biosafety level (BSL-3/4) laboratory and equipment. The abundance of neutralizing antibodies varies among individuals, therefore fast and reliable methods to identify neutralization potency of plasma samples are needed. In this paper, G-protein deficient vesicular stomatitis virus (VSV-ΔG) carrying a C-terminal 21 amino acid truncated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein was generated for pseudovirus neutralization assay. We analyzed SARS-CoV-2 neutralizing potency of vaccinated human convalescent plasma samples (n=13) and plasma samples of healthy people (n=2). Human convalescent plasma samples were examined against the ancestral Wuhan strain and two SARS-CoV-2 variants (B.1.1.7, and B.1.351) using a VSV-ΔG-Sdel21 pseudovirus and Vero E6 cell line. Neutralization values against pseudotyped virus were compared to those of plaque reduction assay against authentic virus. The serum neutralizing titer of convalescent plasma measured by pseudovirus assay has a good correlation with that measured by plaque reduction assay (R 2= 0.7). The pseudovirus assay is safer and timesaving than the replicative virus-based plaque reduction assay, and has several advantages in evaluating a new vaccine, newly emergent variants, and approved vaccine efficacy against variants of concern as well as in viral fusion-focused treatment analysis that can be performed under BSL-2 conditions.

Objective: There is a need for the immunogenicity of different boosters after widely used inactivated vaccine regimens. We aimed to determine the effects of BNT162b2 and CoronaVac boosters on the humoral and cellular immunity of individuals who had two doses of CoronaVac vaccination. Methods: The study was conducted in three centers (Koc University Hospital, Istanbul University Cerrahpasa Hospital, and Istanbul University, Istanbul Medical School Hospital) in Istanbul. Individuals who had two doses of CoronaVac and no history of COVID-19 were included. The baseline blood samples were collected three to five months after two doses of CoronaVac. Follow-up samples were taken one and three months after third doses of CoronaVac or one dose of mRNA BNT162b2 boosters. Neutralizing antibody titers were detected by plaque reduction assay. T cell responses were evaluated by Elispot assay and flow cytometry. Results: We found a 3.38-fold increase in neutralizing antibody titers (Geometric Mean Titer [GMT], 78.69) one month after BNT162b2 booster and maintained at the three months (GMT, 80). However, in the CoronaVac group, significantly lower GMTs than BNT162b2 after 1 month and 3 months (21.44 and 28.44, respectively) indicated the weak immunogenicity of the CoronaVac booster (p<0.001). In the ELISpot assay, IL-2 levels after BNT162b2 were higher than baseline and CoronaVac booster (p<0.001) and IFN-γ levels were significantly higher than baseline (P<0.001). The CD8+CD38+CD69+ and CD4+CD38+CD69+ T cells were stimulated significantly at the 3 rd month of the BNT162b2 boosters. Conclusion: The neutralizing antibody levels after three months of the BNT162b2 booster were higher than the antibody levels after CoronaVac. On the other hand, specific T cells might contribute to immune protection. By considering the waning immunity, we suggest a new booster dose with BNT162b2 for the countries that already have two doses of primary CoronaVac regimens.