RNA Copy Number Research Articles

Initial analysis of viral dynamics and circulating viral variants during the mRNA-1273 Phase 3 COVE trial

The mRNA-1273 vaccine for coronavirus disease 2019 (COVID-19) demonstrated 93.2% efficacy in reduction of symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in the blinded portion of the Phase 3 Coronavirus Efficacy (COVE) trial. While mRNA-1273 demonstrated high efficacy in prevention of COVID-19, including severe disease, its effect on the viral dynamics of SARS-CoV-2 infections is not understood. Here, in exploratory analyses, we assessed the impact of mRNA-1273 vaccination in the ongoing COVE trial (number NCT04470427) on SARS-CoV-2 copy number and shedding, burden of disease and infection, and viral variants. Viral variants were sequenced in all COVID-19 and adjudicated COVID-19 cases (n = 832), from July 2020 in the blinded part A of the study to May 2021 of the open-label part B of the study, in which participants in the placebo arm started to receive the mRNA-1273 vaccine after US Food and Drug Administration emergency use authorization of mRNA-1273 in December 2020. mRNA-1273 vaccination significantly reduced SARS-CoV-2 viral copy number (95% confidence interval) by 100-fold on the day of diagnosis compared with placebo (4.1 (3.4–4.8) versus 6.2 (6.0–6.4) log10 copies per ml). Median times to undetectable viral copies were 4 days for mRNA-1273 and 7 days for placebo. Vaccination also substantially reduced the burden of disease and infection scores. Vaccine efficacies (95% confidence interval) against SARS-CoV-2 variants circulating in the United States during the trial assessed in this post hoc analysis were 82.4% (40.4–94.8%) for variants Epsilon and Gamma and 81.2% (36.1–94.5%) for Epsilon. The detection of other, non-SARS-CoV-2, respiratory viruses during the trial was similar between groups. While additional study is needed, these data show that in SARS-CoV-2-infected individuals, vaccination reduced both the viral copy number and duration of detectable viral RNA, which may be markers for the risk of virus transmission.

A high-dose inoculum size results in persistent viral infection and arthritis in mice infected with chikungunya virus.

Chikungunya virus (CHIKV) is an emerging mosquito-transmitted alphavirus that leads to acute fever and chronic debilitating polyarthralgia. To date, the mechanism underlying chronic recurrent arthralgia is unknown. In the present study, newborn wild-type C57BL/6 mice were infected with CHIKV, and the virological and pathological features of CHIKV infection were analyzed over a period of 50 days. Acute viral infection was readily established by footpad inoculation of CHIKV at doses ranging from 10 plaque forming unit (PFU) to 106 PFU, during which inoculation dose-dependent viral RNA and skeletal muscle damage were detected in the foot tissues. However, persistent CHIKV was observed only when the mice were infected with a high dose of 106 PFU of CHIKV, in which low copy numbers (103−104) of viral positive strand RNA were continuously detectable in the feet from 29 to 50 dpi, along with a low level and progressive reduction in virus-specific CD8+ T cell responses. In contrast, viral negative strand RNA was detected at 50 dpi but not at 29 dpi and was accompanied by significant local skeletal muscle damage at 50 dpi when mild synovial hyperplasia appeared in the foot joints, although the damage was briefly repaired at 29 dpi. These results demonstrated that a high viral inoculation dose leads to viral persistence and progression to chronic tissue damage after recovery from acute infection. Taken together, these results provide a useful tool for elucidating the pathogenesis of persistent CHIKV infection and viral relapse-associated chronic arthritis.

Knockdown of <i>FLT4</i>, <i>Nup98</i>, and <i>Nup205</i> cellular genes as a suppressor for the viral activity of Influenza A/WSN/33 (H1N1) in A549 cell culture

Objectives. To evaluate the effect of cellular genes FLT4, Nup98, and Nup205 on the reproduction of the influenza A virus in A549 human lung cancer cell line.Methods. The work was carried out using the equipment of the center for collective use of the I.I. Mechnikov Research Institute of Vaccines and Sera (Russia). The virus-containing fluid was collected within three days from the moment of transfection and infection and the intensity of viral reproduction was assessed by viral titration and hemagglutination reaction. The viral RNA concentration was determined by real-time reverse-transcription polymerase chain reaction (RT-PCR). To calculate statistically significant differences between groups, the nonparametric Mann–Whitney test was used.Results. In cells treated with small interfering RNAs (siRNAs) targeted at FLT4, Nup98, and Nup205 genes, a significant decrease in their expression and indicators of viral reproduction (virus titer, hemagglutinating activity, viral RNA concentration) was observed at a multiplicity of infection (MOI) = 0.1. Additionally, it was found that a decrease in the expression of target genes using siRNA does not lead to a significant decrease in cell survival. The viral titer in cells treated with siRNA FLT4.2, Nup98.1, and Nup205 on the first day was lower by an average of 1.0 lg, and on the second and third days, by 2.2–2.3 lg, compared to cells treated with nonspecific siRNA. During real-time RT-PCR, a significant decrease in the concentration of viral RNA was observed with siRNA Nup98.1 (up to 190 times) and Nup205 (up to 30 times) on the first day, 26 and 29 times on the second day, and 6 and 30 times on the third day, respectively. For FLT4.2 siRNA, the number of viral RNA copies decreased by 23, 18, and 16 times on the first, second, and third days. Similar results were obtained when determining the hemagglutinating activity of the virus. The hemagglutinating activity on the third day most strongly decreased in cells treated with siRNA Nup205 and FLT4.2 (16 times). In cells treated with siRNA FLT4.1, Nup98.1, and Nup98.2, hemagglutinating activity decreased by 8 times.Conclusions. In the present study, three cellular genes (FLT4, Nup98, and Nup205) were identified—the decrease in the expression of which effectively suppresses viral reproduction— and the original siRNA sequences were obtained. The results obtained are important for creating therapeutic and prophylactic medication, whose action is based on the RNA interference mechanism.

Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.

Understanding the flavivirus infection process in mosquito hosts is important and fundamental in the search for novel control strategies that target the mosquitoes’ ability to carry and transmit pathogenic arboviruses. A group of viruses known as insect-specific viruses (ISVs) has been shown to interfere with the infection and replication of a secondary arbovirus infection in mosquitoes and mosquito-derived cell lines. However, the molecular mechanisms behind this interference are unknown. Therefore, in the present study, we infected the Aedes albopictus cell line U4.4 with either the West Nile virus (WNV), the insect-specific Lammi virus (LamV) or an infection scheme whereby cells were pre-infected with LamV 24 h prior to WNV challenge. The qPCR analysis showed that the dual-infected U4.4 cells had a reduced number of WNV RNA copies compared to WNV-only infected cells. The transcriptome profiles of the different infection groups showed a variety of genes with altered expression. WNV-infected cells had an up-regulation of a broad range of immune-related genes, while in LamV-infected cells, many genes related to stress, such as different heat-shock proteins, were up-regulated. The transcriptome profile of the dual-infected cells was a mix of up- and down-regulated genes triggered by both viruses. Furthermore, we observed an up-regulation of signal peptidase complex (SPC) proteins in all infection groups. These SPC proteins have shown importance for flavivirus assembly and secretion and could be potential targets for gene modification in strategies for the interruption of flavivirus transmission by mosquitoes.

Estimation of the reference lead (Pb) concentration levels affecting immune cells in the blood of Black-headed Gulls (Chroicocephalus ridibundus, Laridae)

The biological effects of lead (Pb) contamination have been reported in various species. There are no restrictions on the use of Pb products, including bullets, in the areas south of Hokkaido, Japan. Local governments have announced the presence of Pb in the soil sediments of water bodies. Previous studies have confirmed the relationship between blood Pb level (BLL) and immune cells. This study was performed with the aim of clarifying the effect of Pb contamination on immune cells. In total, 170 Black-headed Gulls (<em>Chroicocephalus ridibundus</em>) were captured, including a population in Tokyo Bay between November 2018 and April 2021 and a population in Mikawa Bay between January 2019 and April 2021. Linear regression analysis was performed with the white blood cell count (WBC), proportion of heterophils (Het), proportion of lymphocytes (Lym), ratio of heterophils and lymphocytes (H/L ratio), copy number of CD4 messenger RNA, and copy number of CD8α messenger RNA as the objective variables, and the BLL as the explanatory variable. The group with BLL < 1.0 µg/dL had a significantly lower Het and higher Lym than that with BLL > 3.5 µg/dL (<em>P</em> < 0.05). In addition, the group with BLL < 1.0 µg/dL had a significantly lower H/L ratio than that with BLL > 3.5 µg/dL. CD8α and WBC were higher in the group with BLL ranging from 1.0 to 3.5 µg/dL than in the group with BLL < 1.0 µg/dL. This study suggests that the effect of Pb pollution on the immune cells of Black-headed Gulls is lower than some previous criteria values. It is possible that gulls affected by Pb contamination suffer indirect negative effects on immune function, possibly making them more susceptible to infectious diseases. Pb is a major environmental pollutant, against which measures must be taken.

Heat Treatment Promotes Ubiquitin-Mediated Proteolysis of SARS-CoV-2 RNA Polymerase and Decreases Viral Load

Despite extensive efforts, COVID-19 pandemic caused by the SARS-CoV-2 virus is still at large. Vaccination is an effective approach to curb virus spread, but several variants (e.g., delta, delta plus, omicron, and IHU) appear to weaken or possibly escape immune protection. Thus, novel and quickly scalable approaches to restrain SARS-CoV-2 are urgently needed. Multiple evidences showed thermal sensitivity of SARS-CoV-2 and negative correlation between environmental temperature and COVID-19 transmission with unknown mechanism. Here, we reveal a potential mechanism by which mild heat treatment destabilizes the wild-type RNA-dependent RNA polymerase (also known as nonstructural protein 12 (NSP12)) of SARS-CoV-2 as well as the P323L mutant commonly found in SARS-CoV-2 variants, including omicron and IHU. Mechanistically, heat treatment promotes E3 ubiquitin ligase ZNF598-dependent NSP12 ubiquitination leading to proteasomal degradation and significantly decreases SARS-CoV-2 RNA copy number and viral titer. A mild daily heat treatment maintains low levels of both wild-type and P323L mutant of NSP12, suggesting clinical potential. Collectively, this novel mechanism, heat-induced NSP12 degradation, suggests a prospective heat-based intervention against SARS-CoV-2.

Molecular detection and quantification of bluetongue virus in small ruminant and Culicoides vectors in Gujarat, India

The present study was carried out to detect bluetongue virus (BTV) in Culicoides vectors and the biological samples of small ruminants with the use of PCR based molecular methods. The vectors were collected using the UV LED CDC traps, placed near animal sheds and then identified by morphological and PCR based methods. Primers specific to genus Culicoides and species Culicoides oxystoma were used in PCR reaction. The end point RT-PCR protocols were used for tentative and confirmatory diagnosis of BTV and its two serotypes viz. BTV-1 and BTV-16, whereas, the real time RT-PCR was used for confirmation of BTV and quantization of viral RNA load. Out of a total of 132 blood samples and 55 tissue samples viz., spleen, liver, kidney, thymus and heart blood of aborted fetuses and 09 pooled samples of Culicoides, total 21 (6.93%) samples i.e., 11 blood samples, 08 spleens and 02 pooled Culicoides samples were detected positive for BTV by NS1 gene specific RT-PCR. In nested PCR, 8 additional samples were found positive for BTV. Among these 29 positive samples, 6 were collected from spleens of aborted fetuses which was indicative of transplacental transmission of BTV among small ruminants. All the positive samples were of either of BTV-1 and BTV-16 serotypes as confirmed by serotype specific PCR. In real time PCR, plasmid vector based positive control was prepared, which confirmed the 21 samples to be BTV positive, whereas, quantization of viral RNA, showed that out of all clinical samples tested, highest and lowest RNA copy numbers i.e. 3566.41 and 81.79 were found in blood sample and spleen of sheep, respectively.

"Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates.

Antisense sequence-specific knockdown of pathogenic RNA offers opportunities to find new solutions for therapeutic treatments. However, to gain a desired therapeutic effect, the multiple turnover catalysis is critical to inactivate many copies of emerging RNA sequences, which is difficult to achieve without sacrificing the sequence-specificity of cleavage. Here, engineering two or three catalytic peptides into the bulge–loop inducing molecular framework of antisense oligonucleotides achieved catalytic turnover of targeted RNA. Different supramolecular configurations revealed that cleavage of the RNA backbone upon sequence-specific hybridization with the catalyst accelerated with increase in the number of catalytic guanidinium groups, with almost complete demolition of target RNA in 24 h. Multiple sequence-specific cuts at different locations within and around the bulge–loop facilitated release of the catalyst for subsequent attacks of at least 10 further RNA substrate copies, such that delivery of only a few catalytic molecules could be sufficient to maintain knockdown of typical RNA copy numbers. We have developed fluorescent assay and kinetic simulation tools to characterise how the limited availability of different targets and catalysts had restrained catalytic reaction progress considerably, and to inform how to accelerate the catalytic destruction of shorter linear and larger RNAs even further.

On the relation between input and output distributions of scRNA-seq experiments.

Single-cell RNA sequencing determines RNA copy numbers per cell for a given gene. However, technical noise poses the question how observed distributions (output) are connected to their cellular distributions (input). We model a single-cell RNA sequencing setup consisting of PCR amplification and sequencing, and derive probability distribution functions for the output distribution given an input distribution. We provide copy number distributions arising from single transcripts during PCR amplification with exact expressions for mean and variance. We prove that the coefficient of variation of the output of sequencing is always larger than that of the input distribution. Experimental data reveals the variance and mean of the input distribution to obey characteristic relations, which we specifically determine for a HeLa dataset. We can calculate as many moments of the input distribution as are known of the output distribution (up to all). This, in principle, completely determines the input from the output distribution. Source code freely available at https://github.com/danielschw188/InputOutputSCRNASeq. Supplementary data are available at Bioinformatics online.

SARS-CoV-2 RT-qPCR Test Detection Rates Are Associated with Patient Age, Sex, and Time since Diagnosis

Quantifying the detection rate of the widely used quantitative RT-PCR (RT-qPCR) test for severe acute respiratory syndrome coronavirus 2 and its dependence on patient demographic characteristics and disease progression is key in designing epidemiologic strategies. Analyzing 843,917 test results of 521,696 patients, a “positive period” was defined for each patient between diagnosis of coronavirus disease 2019 and the last positive test result. The fraction of positive test results within this period was then used to estimate detection rate. Regression analyses were used to determine associations of detection with time of sampling after diagnosis, patient demographic characteristics, and viral RNA copy number based on RT-qPCR cycle threshold values of the next positive test result. The overall detection rate in tests performed within 14 days after diagnosis was 83.1%. This rate was higher at days 0 to 5 after diagnosis (89.3%). Furthermore, detection rate was strongly associated with age and sex. Finally, the detection rate with the Allplex 2019-nCoV RT-qPCR kit was associated, at the single-patient level, with viral RNA copy number (P < 10−9). These results show that the reliability of the test result is reduced in later days as well as for women and younger patients, in whom the viral loads are typically lower.

Tomatidine reduces Chikungunya virus progeny release by controlling viral protein expression.

Tomatidine, a natural steroidal alkaloid from unripe green tomatoes has been shown to exhibit many health benefits. We recently provided in vitro evidence that tomatidine reduces the infectivity of Dengue virus (DENV) and Chikungunya virus (CHIKV), two medically important arthropod-borne human infections for which no treatment options are available. We observed a potent antiviral effect with EC50 values of 0.82 μM for DENV-2 and 1.3 μM for CHIKV-LR. In this study, we investigated how tomatidine controls CHIKV infectivity. Using mass spectrometry, we identified that tomatidine induces the expression of p62, CD98, metallothionein and thioredoxin-related transmembrane protein 2 in Huh7 cells. The hits p62 and CD98 were validated, yet subsequent analysis revealed that they are not responsible for the observed antiviral effect. In parallel, we sought to identify at which step of the virus replication cycle tomatidine controls virus infectivity. A strong antiviral effect was seen when in vitro transcribed CHIKV RNA was transfected into Huh7 cells treated with tomatidine, thereby excluding a role for tomatidine during CHIKV cell entry. Subsequent determination of the number of intracellular viral RNA copies and viral protein expression levels during natural infection revealed that tomatidine reduces the RNA copy number and viral protein expression levels in infected cells. Once cells are infected, tomatidine is not able to interfere with active RNA replication yet it can reduce viral protein expression. Collectively, the results delineate that tomatidine controls viral protein expression to exert its antiviral activity. Lastly, sequential passaging of CHIKV in presence of tomatidine did not lead to viral resistance. Collectively, these results further emphasize the potential of tomatidine as an antiviral treatment towards CHIKV infection.

Correlation of Respiratory Aerosols and Metabolic Carbon Dioxide

Respiratory aerosols from breathing and talking are an important transmission route for viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Previous studies have found that particles with diameters ranging from 10 nm to 145 μm are produced from different regions in the respiratory system and especially smaller particles can remain airborne for long periods while carrying viral RNA. We present the first study in which respiratory aerosols have been simultaneously measured with carbon dioxide (CO2) to establish the correlation between the two concentrations. CO2 concentrations are easily available through low-cost sensors and could be used to estimate viral exposure through this correlation, whereas source-specific aerosol measurements are complicated and not possible with low-cost sensors. The increase in both respiratory aerosols and CO2 was linear over ten minutes in a 2 m3 chamber for all participants, suggesting a strong correlation. On average, talking released more particles than breathing, with 14,600 ± 16,800 min−1 (one-σ standard deviation) and 6210 ± 5630 min−1 on average, respectively, while CO2 increased with 139 ± 33 ppm min−1 during talking and 143 ± 29 ppm min−1 during breathing. Assuming a typical viral load of 7×106 RNA copies per mL of oral fluid, ten minutes of talking and breathing are estimated to produce 1 and 16 suspended RNA copies, respectively, correlating to a CO2 concentration of around 1800 ppm in a 2 m3 chamber. However, viral loads can vary by several orders of magnitude depending on the stage of the disease and the individual. It was therefore concluded that, by measuring CO2 concentrations, only the number and volume concentrations of released particles can be estimated with reasonable certainty, while the number of suspended RNA copies cannot.

Inactivation of human norovirus by chlorous acid water, a novel chlorine-based disinfectant

IntroductionHuman norovirus (HuNoV) is a leading cause of infectious gastroenteritis. Since HuNoV shows resistance to alcohol, chlorine-based sanitizers are applied to decontaminate the virus on environmental surfaces. Chlorous acid water (CA) has been recently approved as a novel chlorine-based disinfectant categorized as a Type 2 OTC medicine in Japan. In this study, we aimed to evaluate the capability of CA to inactivate HuNoV. MethodsHuNoV (genogroups GII.2 and GII.4) was exposed to the test disinfectants including CA and sodium hypochlorite (NaClO), and the residual RNA copy was measured by reverse transcription quantitative PCR (RT-qPCR) after pretreatment with RNase. In addition, the log10 reduction of HuNoV RNA copy number by CA and NaClO was compared in the presence of bovine serum albumin (BSA), sheep red blood cells (SRBC), polypeptone, meat extract or amino acids to evaluate the stability of these disinfectants under organic-matter-rich conditions. ResultsIn the absence of organic substances, CA with 200 ppm free available chlorine provided >3.0 log10 reduction in the HuNoV RNA copy number within 5 min. Even under high organic matter load (0.3% each of BSA and SRBC or 0.5% polypeptone), 200 ppm CA achieved >3.0 log10 reduction in HuNoV RNA copy number while less than 1.0 log10 reduction was observed with 1,000 ppm sodium hypochlorite (NaClO) in the presence of 0.5% polypeptone. CA reacted with only cysteine, histidine and glutathione while NaClO reacted with all of the amino acids tested. ConclusionsCA is an effective disinfectant to inactivate HuNoV under organic-matter-rich conditions.

Impact of animal saliva on the performance of rapid antigen tests for detection of SARS-CoV-2 (wildtype and variants B.1.1.7 and B.1.351)

SARS-CoV-2 infects several animal species and SARS-CoV-2 variants of concern (VOCs) may even show (as in humans) enhanced inter- and intra-species transmission rates. We correlated sensitivity data of SARS-CoV-2 rapid antigen tests (RATs) to viral RNA genome equivalents analyzed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR). Further, we checked their suitability for testing animals by assessing saliva and VOC effects. Viral loads up to 2 logs (RNA copy number) under the hypothetical SARS-CoV-2 infectivity threshold were detected by most analyzed RATs. However, while saliva from various animal species showed generally no adverse effects on the RATs’ analytical sensitivities, the detection of VOCs B.1.1.7 and B.1.351 was in some RATs inferior to non-VOC viruses.

In Vitro Evaluation of Anti-Lung Cancer and Anti-COVID-19 Effects using Fermented Black Color Ginseng Extract

Ginseng is known as the “king” of herbal plants and has been used widely in Asia for centuries. Ginseng contains active saponins, including protopanaxadiols, protopanaxatriols, and other compounds. There are many methods for processing ginseng, such as steaming, fermentation, expansion, and conversion of active compounds, which can improve its biological activity. In this study, we investigated the cytotoxic and oxidative effects of fermented black color ginseng (FBCG), black ginseng (BG), and white ginseng (WG) on a human lung carcinoma cell line (A549). Moreover, we found that treatment with FBCG induced oxidative stress in the A549 cell line and increases the apoptosis percentage; these effects were linked to the stimulation of the caspase 3/mitogen-activated protein kinase (caspase 3/MAPK) pathway. We also evaluated the anti-coronavirus disease-2019 (COVID-19) effect of FBCG on a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected Vero E6 cell line. Our results suggest that FBCG not only inhibits the replication of this strain of virus in the cell but also reduces the number of viral RNA (vRNA) copies in the extracellular environment. Taken together, these data show that FBCG has both potential anti-lung cancer and anti-COVID-19 effects.

Sequential determination of viral load, humoral responses and phylogenetic analysis in fatal and non-fatal cases of Crimean-Congo hemorrhagic fever patients from Gujarat, India, 2019.

BackgroundThirty-four CCHF cases (17 fatal; 17 survived) were confirmed from Gujarat state, India during the year 2019. We aimed to find out the viral load, antibody kinetics, cytokine profile and phylogenetic analysis between fatal and non- fatal cases.MethodsThirty four cases were included in this study. Blood and urine samples were collected from all the cases on the day of admission to hospital. Non-fatal cases were followed weekly for understanding the profile of viral kinetics, anti-CCHFV IgM and IgG antibodies. We also quantified the cytokines in both fatal and non-fatal cases. For epidemiological correlation, livestock were screened for anti-CCHF IgG antibodies and the tick pool specimens were tested by real time RT-PCR. Virus isolation was attempted on tick pools and human specimens and phylogenetic analysis performed on human and ticks complete genome sequences.ResultsCCHF cases were detected throughout year in 2019 with the peak in August. Out of 34 cases, eight secondary CCHF cases were reported. Cases were predominantly detected in males and in 19–45 years age group (55.88%). The persistence of viremia was observed till 76th POD (post onset date) in one case whereas anti-CCHFV IgM and IgG was detected amongst these cases from the 2nd and 20th POD respectively. Positivity observed amongst livestock and tick pools were was 21.57% and 7.4% respectively. The cytokine analysis revealed a significant increase in the level of serum IL-6, IL-10 and IFN-γ during the acute phase of the infection, but interestingly IL-10 lowered to normal upon clearance of the virus in the clinically recovered case. Fatal cases had high viral RNA copy numbers. Bleeding from one or two mucosal sites was significantly associated with fatality (OR-16.47;p-0.0034 at 95% CI). We could do CCHF virus isolation from two cases. Phylogenetic analysis revealed circulation of re-assortment of Asian-West African genotypes in humans and ticks.ConclusionsThe persistence of CCHF viral RNA was detected till 76th POD in one of the survivors. The circulation of a re-assortment Asian-West African genotype in a CCHF case is also reported first time from India.

Ozone Gas Inhibits SARS-CoV-2 Transmission and Provides Possible Control Measures

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths currently. Mounting effective responses to the pandemic have become top priorities for governments around the world. Laboratory experiments have confirmed for the first time that fumigation with ozone (O3) at low O3 doses (7500–15,000 μg m−3·min) can inhibit the SARS-CoV-2 and inactivate the virus at high O3 doses (129,000 μg m−3·min). The RNA copy number of SARS-CoV-2 significantly decreased (95.9–97.7% reduction) when exposed to O3 at a low concentration of 250 μg m−3 for 30 and 60 min. A significant negative relationship between the numbers of confirmed SARS-CoV-2 cases and ambient O3 in Chinese cities indicated that the spread of SARS-CoV-2 may have been inhibited by high O3. An analysis of data from Chongqing showed that the transmission of COVID-19 increased when the O3 mixing ratios in the air were relatively low, and transmission decreased when O3 increased. Based on these findings, we also propose a new Safety O3 Emission (SOE) method to increase indoor O3 to levels (< 160 μg m−3) that inhibit the transmission of the SARS-CoV-2 but are not harmful for humans. This could serve as timely and low-cost solution for suppressing COVID-19 outbreaks throughout the world.

Combining IL-6 and SARS-CoV-2 RNAaemia-based risk stratification for fatal outcomes of COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic rapidly increases the use of mechanical ventilation (MV). Such cases further require extracorporeal membrane oxygenation (ECMO) and have a high mortality. We aimed to identify prognostic biomarkers pathophysiologically reflecting future deterioration of COVID-19. Clinical, laboratory, and outcome data were collected from 102 patients with moderate to severe COVID-19. Interleukin (IL)-6 level and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copy number in plasma were assessed with ELISA kit and quantitative PCR. Twelve patients died or required ECMO owing to acute respiratory distress syndrome despite the use of MV. Among various variables, a ratio of oxygen saturation to fraction of inspired oxygen (SpO2/FiO2), IL-6, and SARS-CoV-2 RNA on admission before intubation were strongly predictive of fatal outcomes after the MV use. Moreover, among these variables, combining SpO2/FiO2, IL-6, and SARS-CoV-2 RNA showed the highest accuracy (area under the curve: 0.934). In patients with low SpO2/FiO2 (< 261), fatal event-rate after the MV use at the 30-day was significantly higher in patients with high IL-6 (> 49 pg/mL) and SARS-CoV-2 RNAaemia (> 1.5 copies/μL) compared to those with high IL-6 or RNAaemia or without high IL-6 and RNAaemia (88% vs. 22% or 8%, log-rank test P = 0.0097 or P < 0.0001, respectively). Combining SpO2/FiO2 with high IL-6 and SARS-CoV-2 RNAaemia which reflect hyperinflammation and viral overload allows accurately and before intubation identifying COVID-19 patients at high risk for ECMO use or in-hospital death despite the use of MV.

In vitro Inhibition of Border Disease Virus Replication With Lentivirus-Mediated shRNAs.

Background: Border disease is believed to be one of the most important diseases in the animal husbandry industry, which has not yet been eradicated in Iran. The development of approaches based on the application of interfering RNA (RNAi) for antiviral therapy has attracted a great deal of attention over the recent years. The present research was conducted to design, construct, and apply shRNA against the NS3 gene of BDV to evaluate the prevention of BDV proliferation in the cell culture system. For this purpose, the suitable oligonucleotide sequence of NS3 gene coding was selected utilizing BDV- X818 strain. Afterwards, using shRNA design software, shRNA molecules were designed and synthesized. These shRNAs were cloned into the desired vectors and were finally transfected in HEK293T cells employing the third generation of lentiviral packaging system. Subsequently, these shRNA expressing lentiviruses were transduced to the MDBK cell line to challenge to border virus. In order to evaluate the efficacy of shRNAs, the viral infectious titer and RNA copy number were calculated with TCID50 and Real-time RT-PCR tests, respectively.Results: The results revealed that shRNAs 1, 2, and 3 decreased viral RNA by more than 90% compared to the control groups. BDV titer noticeably decreased after the challenge with shRNAs 1, 2, and 3 from ~88% up to 99% in comparison with the control groups.Conclusions: Overall, it could be concluded that RNAi may be considered as a strong treatment proposal against viruses, such as BDV.

Gamma-irradiated SARS-CoV-2 vaccine candidate, OZG-38.61.3, confers protection from SARS-CoV-2 challenge in human ACEII-transgenic mice

The SARS-CoV-2 virus caused the most severe pandemic around the world, and vaccine development for urgent use became a crucial issue. Inactivated virus formulated vaccines such as Hepatitis A and smallpox proved to be reliable approaches for immunization for prolonged periods. In this study, a gamma-irradiated inactivated virus vaccine does not require an extra purification process, unlike the chemically inactivated vaccines. Hence, the novelty of our vaccine candidate (OZG-38.61.3) is that it is a non-adjuvant added, gamma-irradiated, and intradermally applied inactive viral vaccine. Efficiency and safety dose (either 1013 or 1014 viral RNA copy per dose) of OZG-38.61.3 was initially determined in BALB/c mice. This was followed by testing the immunogenicity and protective efficacy of the vaccine. Human ACE2-encoding transgenic mice were immunized and then infected with the SARS-CoV-2 virus for the challenge test. This study shows that vaccinated mice have lowered SARS-CoV-2 viral RNA copy numbers both in oropharyngeal specimens and in the histological analysis of the lung tissues along with humoral and cellular immune responses, including the neutralizing antibodies similar to those shown in BALB/c mice without substantial toxicity. Subsequently, plans are being made for the commencement of Phase 1 clinical trial of the OZG-38.61.3 vaccine for the COVID-19 pandemic.