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10 pages, 1497 KiB

Open AccessArticle

Anti-Influenza Activity of Medicinal Material Extracts from Qinghai–Tibet Plateau

by Olga Kurskaya, Elena Prokopyeva, Hongtao Bi, Ivan Sobolev, Tatyana Murashkina, Alexander Shestopalov, Lixin Wei and Kirill Sharshov

Viruses 2022, 14(2), 360; https://doi.org/10.3390/v14020360 - 10 Feb 2022

Cited by 5 | Viewed by 2201

Abstract

To discover sources for novel anti-influenza drugs, we evaluated the antiviral potential of nine extracts from eight medicinal plants and one mushroom (Avena sativa L., Hordeum vulgare Linn. var. nudum Hook. f., Hippophae rhamnoides Linn., Lycium ruthenicum Murr., Nitraria tangutorum Bobr., Nitraria [...] Read more.

To discover sources for novel anti-influenza drugs, we evaluated the antiviral potential of nine extracts from eight medicinal plants and one mushroom (Avena sativa L., Hordeum vulgare Linn. var. nudum Hook. f., Hippophae rhamnoides Linn., Lycium ruthenicum Murr., Nitraria tangutorum Bobr., Nitraria tangutorum Bobr. by-products, Potentilla anserina L., Cladina rangiferina (L.) Nyl., and Armillaria luteo-virens) from the Qinghai–Tibetan plateau against the influenza A/H3N2 virus. Concentrations lower than 125 μg/mL of all extracts demonstrated no significant toxicity in MDCK cells. During screening, seven extracts (A. sativa, H. vulgare, H. rhamnoides, L. ruthenicum, N. tangutorum, C. rangiferina, and A. luteo-virens) exhibited antiviral activity, especially the water-soluble polysaccharide from the fruit body of the mushroom A. luteo-virens. These extracts significantly reduced the infectivity of the human influenza A/H3N2 virus in vitro when used at concentrations of 15.6–125 μg/mL. Two extracts (N. tangutorum by-products and P. anserina) had no A/H3N2 virus inhibitory activity. Notably, the extract obtained from the fruits of N. tangutorum and N. tangutorum by-products exhibited different anti-influenza effects. The results suggest that extracts of A. sativa, H. vulgare, H. rhamnoides, L. ruthenicum, N. tangutorum, C. rangiferina, and A. luteo-virens contain substances with antiviral activity, and may be promising sources of new antiviral drugs. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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18 pages, 4333 KiB

Open AccessArticle

Computational Analysis of Mutations in the Receptor-Binding Domain of SARS-CoV-2 Spike and Their Effects on Antibody Binding

by Marine E. Bozdaganyan, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova and Philipp S. Orekhov

Viruses 2022, 14(2), 295; https://doi.org/10.3390/v14020295 - 30 Jan 2022

Cited by 10 | Viewed by 2974

Abstract

Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding [...] Read more.

Currently, SARS-CoV-2 causing coronavirus disease 2019 (COVID-19) is responsible for one of the most deleterious pandemics of our time. The interaction between the ACE2 receptors at the surface of human cells and the viral Spike (S) protein triggers the infection, making the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein a focal target for the neutralizing antibodies (Abs). Despite the recent progress in the development and deployment of vaccines, the emergence of novel variants of SARS-CoV-2 insensitive to Abs produced in response to the vaccine administration and/or monoclonal ones represent a potential danger. Here, we analyzed the diversity of neutralizing Ab epitopes and assessed the possible effects of single and multiple mutations in the RBD of SARS-CoV-2 S-protein on its binding affinity to various antibodies and the human ACE2 receptor using bioinformatics approaches. The RBD-Ab complexes with experimentally resolved structures were grouped into four clusters with distinct features at sequence and structure level. The performed computational analysis indicates that while single amino acid replacements in RBD may only cause partial impairment of the Abs binding, moreover, limited to specific epitopes, the variants of SARS-CoV-2 with multiple mutations, including some which were already detected in the population, may potentially result in a much broader antigenic escape. Further analysis of the existing RBD variants pointed to the trade-off between ACE2 binding and antigenic escape as a key limiting factor for the emergence of novel SAR-CoV-2 strains, as the naturally occurring mutations in RBD tend to reduce its binding affinity to Abs but not to ACE2. The results provide guidelines for further experimental studies aiming to identify high-risk RBD mutations that allow for an antigenic escape. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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18 pages, 5223 KiB

Open AccessArticle

Microarray-Based Detection of Antibodies against SARS-CoV-2 Proteins, Common Respiratory Viruses and Type I Interferons

by Elena Savvateeva, Marina Filippova, Vladimir Valuev-Elliston, Nurana Nuralieva, Marina Yukina, Ekaterina Troshina, Vladimir Baklaushev, Alexander Ivanov and Dmitry Gryadunov

Viruses 2021, 13(12), 2553; https://doi.org/10.3390/v13122553 - 20 Dec 2021

Cited by 17 | Viewed by 3441

Abstract

A microarray-based assay to detect IgG and IgM antibodies against betacoronaviruses (SARS-CoV-2, SARS, MERS, OC43, and HKU1), other respiratory viruses and type I interferons (IFN-Is) was developed. This multiplex assay was applied to track antibody cross-reactivity due to previous contact with similar viruses [...] Read more.

A microarray-based assay to detect IgG and IgM antibodies against betacoronaviruses (SARS-CoV-2, SARS, MERS, OC43, and HKU1), other respiratory viruses and type I interferons (IFN-Is) was developed. This multiplex assay was applied to track antibody cross-reactivity due to previous contact with similar viruses and to identify antibodies against IFN-Is as the markers for severe COVID-19. In total, 278 serum samples from convalescent plasma donors, COVID-19 patients in the intensive care unit (ICU) and patients who recovered from mild/moderate COVID-19, vaccine recipients, prepandemic and pandemic patients with autoimmune endocrine disorders, and a heterogeneous prepandemic cohort including healthy individuals and chronically ill patients were analyzed. The anti-SARS-CoV-2 microarray results agreed well with the ELISA results. Regarding ICU patients, autoantibodies against IFN-Is were detected in 10.5% of samples, and 10.5% of samples were found to simultaneously contain IgM antibodies against more than two different viruses. Cross-reactivity between IgG against the SARS-CoV-2 nucleocapsid and IgG against the OC43 and HKU1 spike proteins was observed, resulting in positive signals for the SARS-CoV-2 nucleocapsid in prepandemic samples from patients with autoimmune endocrine disorders. The presence of IgG against the SARS-CoV-2 nucleocapsid in the absence of IgG against the SARS-CoV-2 spike RBD should be interpreted with caution. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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10 pages, 1885 KiB

Open AccessArticle

IgG Antibodies Develop to Spike but Not to the Nucleocapsid Viral Protein in Many Asymptomatic and Light COVID-19 Cases

by Maria Tutukina, Anna Kaznadzey, Maria Kireeva and Ilya Mazo

Viruses 2021, 13(10), 1945; https://doi.org/10.3390/v13101945 - 28 Sep 2021

Cited by 15 | Viewed by 12367

Abstract

Since SARS-CoV-2 appeared in late 2019, many studies on the immune response to COVID-19 have been conducted, but the asymptomatic or light symptom cases were somewhat understudied as respective individuals often did not seek medical help. Here, we analyze the production of the [...] Read more.

Since SARS-CoV-2 appeared in late 2019, many studies on the immune response to COVID-19 have been conducted, but the asymptomatic or light symptom cases were somewhat understudied as respective individuals often did not seek medical help. Here, we analyze the production of the IgG antibodies to viral nucleocapsid (N) protein and receptor-binding domain (RBD) of the spike protein and assess the serum neutralization capabilities in a cohort of patients with different levels of disease severity. In half of light or asymptomatic cases the antibodies to the nucleocapsid protein, which serve as the main target in many modern test systems, were not detected. They were detected in all cases of moderate or severe symptoms, and severe lung lesions correlated with respective higher signals. Antibodies to RBD were present in the absolute majority of samples, with levels being sometimes higher in light symptom cases. We thus suggest that the anti-RBD/anti-N antibody ratio may serve as an indicator of the disease severity. Anti-RBD IgG remained detectable after a year or more since the infection, even with a slight tendency to raise over time, and the respective signal correlated with the serum capacity to inhibit the RBD interaction with the ACE-2 receptor. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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14 pages, 3012 KiB

Open AccessArticle

Antiviral Activity of Umifenovir In Vitro against a Broad Spectrum of Coronaviruses, Including the Novel SARS-CoV-2 Virus

by Irina Leneva, Nadezhda Kartashova, Artem Poromov, Anastasiia Gracheva, Ekaterina Korchevaya, Ekaterina Glubokova, Olga Borisova, Anna Shtro, Svetlana Loginova, Veronika Shchukina, Ravil Khamitov and Evgeny Faizuloev

Viruses 2021, 13(8), 1665; https://doi.org/10.3390/v13081665 - 23 Aug 2021

Cited by 17 | Viewed by 5446

Abstract

An escalating pandemic of the novel SARS-CoV-2 virus is impacting global health, and effective antivirals are needed. Umifenovir (Arbidol) is an indole-derivative molecule, licensed in Russia and China for prophylaxis and treatment of influenza and other respiratory viral infections. It has been shown [...] Read more.

An escalating pandemic of the novel SARS-CoV-2 virus is impacting global health, and effective antivirals are needed. Umifenovir (Arbidol) is an indole-derivative molecule, licensed in Russia and China for prophylaxis and treatment of influenza and other respiratory viral infections. It has been shown that umifenovir has broad spectrum activity against different viruses. We evaluated the sensitivity of different coronaviruses, including the novel SARS-CoV-2 virus, to umifenovir using in vitro assays. Using a plaque assay, we revealed an antiviral effect of umifenovir against seasonal HCoV-229E and HCoV-OC43 coronaviruses in Vero E6 cells, with estimated 50% effective concentrations (EC50) of 10.0 ± 0.5 µM and 9.0 ± 0.4 µM, respectively. Umifenovir at 90 µM significantly suppressed plaque formation in CMK-AH-1 cells infected with SARS-CoV. Umifenovir also inhibited the replication of SARS-CoV-2 virus, with EC50 values ranging from 15.37 ± 3.6 to 28.0 ± 1.0 µM. In addition, 21–36 µM of umifenovir significantly suppressed SARS-CoV-2 virus titers (≥2 log TCID50/mL) in the first 24 h after infection. Repurposing of antiviral drugs is very helpful in fighting COVID-19. A safe, pan-antiviral drug such as umifenovir could be extremely beneficial in combating the early stages of a viral pandemic. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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24 pages, 5568 KiB

Open AccessArticle

SARS-CoV-2 Seroprevalence Structure of the Russian Population during the COVID-19 Pandemic

by Anna Y. Popova, Viacheslav S. Smirnov, Elena E. Andreeva, Elena A. Babura, Sergey V. Balakhonov, Natalia S. Bashketova, Svetlana A. Bugorkova, Maxim V. Bulanov, Natalia. N. Valeullina, Viacheslav. V. Vetrov, Dmitriy. V. Goryaev, Tatyana N. Detkovskaya, Elena B. Ezhlova, Natalia N. Zaitseva, Olga A. Istorik, Irina. V. Kovalchuk, Dmitriy N. Kozlovskikh, Svetlana Y. Kombarova, Olga. P. Kurganova, Alexander. E. Lomovtsev, Lena A. Lukicheva, Ludmila V. Lyalina, Albina. A. Melnikova, Olga M. Mikailova, Alexei K. Noskov, Ludmila N. Noskova, Elena E. Oglezneva, Tatyana P. Osmolovskaya, Marina A. Patyashina, Natalia A. Penkovskaya, Lada V. Samoilova, Tatyana F. Stepanova, Olga E. Trotsenko and Areg A. Totolian Show full author list Hide full author list

Viruses 2021, 13(8), 1648; https://doi.org/10.3390/v13081648 - 19 Aug 2021

Cited by 20 | Viewed by 3034

Abstract

The SARS-CoV-2 pandemic, which came to Russia in March 2020, is accompanied by morbidity level changes and can be tracked using serological monitoring of a representative population sample from Federal Districts (FDs) and individual regions. In a longitudinal cohort study conducted in 26 [...] Read more.

The SARS-CoV-2 pandemic, which came to Russia in March 2020, is accompanied by morbidity level changes and can be tracked using serological monitoring of a representative population sample from Federal Districts (FDs) and individual regions. In a longitudinal cohort study conducted in 26 model regions of Russia, distributed across all FDs, we investigated the distribution and cumulative proportions of individuals with antibodies (Abs) to the SARS-CoV-2 nucleocapsid antigen (Ag), in the period from June to December 2020, using a three-phase monitoring process. In addition, during the formation of the cohort of volunteers, the number of seropositive convalescents, persons who had contact with patients or COVID-19 convalescents, and the prevalence of asymptomatic forms of infection among seropositive volunteers were determined. According to a uniform methodology, 3 mL of blood was taken from the examined individuals, and plasma was separated, from which the presence of Abs to nucleocapsid Ag was determined on a Thermo Scientific Multiascan FC device using the “ELISA anti-SARS-CoV-2 IgG” reagent set (prod. Scientific Center for Applied Microbiology and Biotechnology), in accordance with the developer’s instructions. Volunteers (74,158) were surveyed and divided into seven age groups (1–17, 18–29, 30–39, 40–49, 59–59, 60–69, and 70+ years old), among whom 14,275 were identified as having antibodies to SARS-CoV-2. The average percent seropositive in Russia was 17.8% (IQR: 8.8–23.2). The largest proportion was found among children under 17 years old (21.6% (IQR: 13.1–31.7). In the remaining groups, seroprevalence ranged from 15.6% (IQR: 8–21.1) to 18.0% (IQR: 13.4–22.6). During monitoring, three (immune) response groups were found: (A) groups with a continuous increase in the proportion of seropositive; (B) those with a slow rate of increase in seroprevalence; and (C) those with a two-phase curve, wherein the initial increase was replaced by a decrease in the percentage of seropositive individuals. A significant correlation was revealed between the number of COVID-19 convalescents and contact persons, and between the number of contacts and healthy seropositive volunteers. Among the seropositive volunteers, more than 93.6% (IQR: 87.1–94.9) were asymptomatic. The results show that the COVID-19 pandemic is accompanied by an increase in seroprevalence, which may be important for the formation of herd immunity. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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13 pages, 3223 KiB

Open AccessArticle

What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2

by Vladimir Fedorov, Ekaterina Kholina, Sergei Khruschev, Ilya Kovalenko, Andrew Rubin and Marina Strakhovskaya

Viruses 2021, 13(8), 1615; https://doi.org/10.3390/v13081615 - 15 Aug 2021

Cited by 9 | Viewed by 3035

Abstract

We compared the electrostatic properties of the spike proteins (S-proteins) of three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, and their interactions with photosensitizers (PSs), octacationic octakis(cholinyl)zinc phthalocyanine (Zn-PcChol₈₊) and monocationic methylene blue (MB). We found a major common PS binding site at [...] Read more.

We compared the electrostatic properties of the spike proteins (S-proteins) of three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, and their interactions with photosensitizers (PSs), octacationic octakis(cholinyl)zinc phthalocyanine (Zn-PcChol₈₊) and monocationic methylene blue (MB). We found a major common PS binding site at the connection of the S-protein stalk and head. The molecules of Zn-PcChol₈₊ and MB also form electrostatic encounter complexes with large area of negative electrostatic potential at the head of the S-protein of SARS-CoV-2, between fusion protein and heptad repeat 1 domain. The top of the SARS-CoV spike head demonstrates a notable area of electrostatic contacts with Zn-PcChol₈₊ and MB that corresponds to the N-terminal domain. The S-protein protomers of SARS-CoV-2 in “open” and “closed” conformations demonstrate different ability to attract PS molecules. In contrast with Zn-PcChol₈₊, MB possesses the ability to penetrate inside the pocket formed as a result of SARS-CoV-2 receptor binding domain transition into the “open” state. The existence of binding site for cationic PSs common to the S-proteins of SARS-CoV, SARS-CoV-2, and MERS-CoV creates prospects for the wide use of this type of PSs to combat the spread of coronaviruses. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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15 pages, 2218 KiB

Open AccessArticle

IFN-λ1 Displays Various Levels of Antiviral Activity In Vitro in a Select Panel of RNA Viruses

by Marina Plotnikova, Alexey Lozhkov, Ekaterina Romanovskaya-Romanko, Irina Baranovskaya, Mariia Sergeeva, Konstantin Kаа, Sergey Klotchenko and Andrey Vasin

Viruses 2021, 13(8), 1602; https://doi.org/10.3390/v13081602 - 12 Aug 2021

Cited by 16 | Viewed by 3343

Abstract

Type III interferons (lambda IFNs) are a quite new, small family of three closely related cytokines with interferon-like activity. Attention to IFN-λ is mainly focused on direct antiviral activity in which, as with IFN-α, viral genome replication is inhibited without the participation of [...] Read more.

Type III interferons (lambda IFNs) are a quite new, small family of three closely related cytokines with interferon-like activity. Attention to IFN-λ is mainly focused on direct antiviral activity in which, as with IFN-α, viral genome replication is inhibited without the participation of immune system cells. The heterodimeric receptor for lambda interferons is exposed mainly on epithelial cells, which limits its possible action on other cells, thus reducing the likelihood of developing undesirable side effects compared to type I IFN. In this study, we examined the antiviral potential of exogenous human IFN-λ1 in cellular models of viral infection. To study the protective effects of IFN-λ1, three administration schemes were used: ‘preventive’ (pretreatment); ‘preventive/therapeutic’ (pre/post); and ‘therapeutic’ (post). Three IFN-λ1 concentrations (from 10 to 500 ng/mL) were used. We have shown that human IFN-λ1 restricts SARS-CoV-2 replication in Vero cells with all three treatment schemes. In addition, we have shown a decrease in the viral loads of CHIKV and IVA with the ‘preventive’ and ‘preventive/therapeutic’ regimes. No significant antiviral effect of IFN-λ1 against AdV was detected. Our study highlights the potential for using IFN-λ as a broad-spectrum therapeutic agent against respiratory RNA viruses. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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15 pages, 2076 KiB

Open AccessArticle

Substitution Arg140Gly in Hemagglutinin Reduced the Virulence of Highly Pathogenic Avian Influenza Virus H7N1

by Anastasia Treshchalina, Yulia Postnikova, Elizaveta Boravleva, Alexandra Gambaryan, Alla Belyakova, Aydar Ishmukhametov, Galina Sadykova, Alexey Prilipov and Natalia Lomakina

Viruses 2021, 13(8), 1584; https://doi.org/10.3390/v13081584 - 11 Aug 2021

Cited by 4 | Viewed by 2105

Abstract

The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. The H7 viruses circulate in ducks, poultry and equines and have repeatedly caused outbreaks of disease in humans. The laboratory strain A/chicken/Rostock/R0p/1934 (H7N1) (R0p), which was previously derived from the [...] Read more.

The H7 subtype of avian influenza viruses (AIV) stands out among other AIV. The H7 viruses circulate in ducks, poultry and equines and have repeatedly caused outbreaks of disease in humans. The laboratory strain A/chicken/Rostock/R0p/1934 (H7N1) (R0p), which was previously derived from the highly pathogenic strain A/FPV/Rostock/1934 (H7N1), was studied in this work to ascertain its biological property, genome stability and virulent changing mechanism. Several virus variants were obtained by serial passages in the chicken lungs. After 10 passages of this virus through the chicken lungs we obtained a much more pathogenic variant than the starting R0p. The study of intermediate passages showed a sharp increase in pathogenicity between the fifth and sixth passage. By cloning these variants, a pair of strains (R5p and R6p) was obtained, and the complete genomes of these strains were sequenced. Single amino acid substitution was revealed, namely reversion Gly140Arg in HA1. This amino acid is located at the head part of the hemagglutinin, adjacent to the receptor-binding site. In addition to the increased pathogenicity in chicken and mice, R6p differs from R5p in the shape of foci in cell culture and an increased affinity for a negatively charged receptor analogue, while maintaining a pattern of receptor-binding specificity and the pH of conformational change of HA. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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25 pages, 2705 KiB

Open AccessArticle

Universal Live-Attenuated Influenza Vaccine Candidates Expressing Multiple M2e Epitopes Protect Ferrets against a High-Dose Heterologous Virus Challenge

by Daria Mezhenskaya, Irina Isakova-Sivak, Victoria Matyushenko, Svetlana Donina, Andrey Rekstin, Konstantin Sivak, Kirill Yakovlev, Anastasia Katelnikova, Kirill Kryshen, Valery Makarov and Larisa Rudenko

Viruses 2021, 13(7), 1280; https://doi.org/10.3390/v13071280 - 30 Jun 2021

Cited by 10 | Viewed by 2863

Abstract

The development of an influenza vaccine with broad protection and durability remains an attractive idea due to the high mutation rate of the influenza virus. An extracellular domain of Matrix 2 protein (M2e) is among the most attractive target for the universal influenza [...] Read more.

The development of an influenza vaccine with broad protection and durability remains an attractive idea due to the high mutation rate of the influenza virus. An extracellular domain of Matrix 2 protein (M2e) is among the most attractive target for the universal influenza vaccine owing to its high conservancy rate. Here, we generated two recombinant live attenuated influenza vaccine (LAIV) candidates encoding four M2e epitopes representing consensus sequences of human, avian and swine influenza viruses, and studied them in a preclinical ferret model. Both LAIV+4M2e viruses induced higher levels of M2e-specific antibodies compared to the control LAIV strain, with the LAIV/HA+4M2e candidate being significantly more immunogenic than the LAIV/NS+4M2e counterpart. A high-dose heterosubtypic influenza virus challenge revealed the highest degree of protection after immunization with LAIV/HA+4M2e strain, followed by the NS-modified LAIV and the classical LAIV virus. Furthermore, only the immune sera from the LAIV/HA+4M2e-immunized ferrets protected mice from a panel of lethal influenza viruses encoding M genes of various origins. These data suggest that the improved cross-protection of the LAIV/HA+4M2e universal influenza vaccine candidate was mediated by the M2e-targeted antibodies. Taking into account the safety profile and improved cross-protective potential, the LAIV/HA+4M2e vaccine warrants its further evaluation in a phase I clinical trial. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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17 pages, 2294 KiB

Open AccessArticle

Different Neutralization Sensitivity of SARS-CoV-2 Cell-to-Cell and Cell-Free Modes of Infection to Convalescent Sera

by Natalia Kruglova, Andrei Siniavin, Vladimir Gushchin and Dmitriy Mazurov

Viruses 2021, 13(6), 1133; https://doi.org/10.3390/v13061133 - 12 Jun 2021

Cited by 17 | Viewed by 4192

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 has posed a global threat to human lives and economics. One of the best ways to determine protection against the infection is to quantify the neutralizing activity of serum antibodies. Multiple assays have been developed to validate [...] Read more.

The COVID-19 pandemic caused by SARS-CoV-2 has posed a global threat to human lives and economics. One of the best ways to determine protection against the infection is to quantify the neutralizing activity of serum antibodies. Multiple assays have been developed to validate SARS-CoV-2 neutralization; most of them utilized lentiviral or vesicular stomatitis virus-based particles pseudotyped with the spike (S) protein, making them safe and acceptable to work with in many labs. However, these systems are only capable of measuring infection with purified particles. This study has developed a pseudoviral assay with replication-dependent reporter vectors that can accurately quantify the level of infection directly from the virus producing cell to the permissive target cell. Comparative analysis of cell-free and cell-to-cell infection revealed that the neutralizing activity of convalescent sera was more than tenfold lower in cell cocultures than in the cell-free mode of infection. As the pseudoviral system could not properly model the mechanisms of SARS-CoV-2 transmission, similar experiments were performed with replication-competent coronavirus, which detected nearly complete SARS-CoV-2 cell-to-cell infection resistance to neutralization by convalescent sera. These findings suggest that the cell-to-cell mode of SARS-CoV-2 transmission, for which the mechanisms are largely unknown, could be of great importance for treatment and prevention of COVID-19. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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10 pages, 3707 KiB

Open AccessCommunication

Characterization of a Novel SARS-CoV-2 Genetic Variant with Distinct Spike Protein Mutations

by Anna Gladkikh, Anna Dolgova, Vladimir Dedkov, Valeriya Sbarzaglia, Olga Kanaeva, Anna Popova and Areg Totolian

Viruses 2021, 13(6), 1029; https://doi.org/10.3390/v13061029 - 29 May 2021

Cited by 3 | Viewed by 4856

Abstract

The COVID-19 pandemic, which began in Wuhan (Hubei, China), has been ongoing for about a year and a half. An unprecedented number of people around the world have been infected with SARS-CoV-2, the etiological agent of COVID-19. Despite the fact that the mortality [...] Read more.

The COVID-19 pandemic, which began in Wuhan (Hubei, China), has been ongoing for about a year and a half. An unprecedented number of people around the world have been infected with SARS-CoV-2, the etiological agent of COVID-19. Despite the fact that the mortality rate for COVID-19 is relatively low, the total number of deaths has currently already reached more than three million and continues to increase due to high incidence. Since the beginning of the pandemic, a large number of sequences have been obtained and many genetic variants have been identified. Some of them bear significant mutations that affect biological properties of the virus. These genetic variants, currently Variants of Concern (VoC), include the so-called United Kingdom variant (20I/501Y), the Brazilian variant (20J/501Y.V3), and the South African variant (20H/501Y.V2). We describe here a novel SARS-CoV-2 variant with distinct spike protein mutations, first obtained at the end of January 2021 in northwest Russia. Therefore, it is necessary to pay attention to the dynamics of its spread among patients with COVID-19, as well as to study in detail its biological properties. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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14 pages, 870 KiB

Open AccessArticle

Diversity and Reassortment Rate of Influenza A Viruses in Wild Ducks and Gulls

by Yulia Postnikova, Anastasia Treshchalina, Elizaveta Boravleva, Alexandra Gambaryan, Aydar Ishmukhametov, Mikhail Matrosovich, Ron A. M. Fouchier, Galina Sadykova, Alexey Prilipov and Natalia Lomakina

Viruses 2021, 13(6), 1010; https://doi.org/10.3390/v13061010 - 27 May 2021

Cited by 10 | Viewed by 2603

Abstract

Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. [...] Read more.

Influenza A viruses (IAVs) evolve via point mutations and reassortment of viral gene segments. The patterns of reassortment in different host species differ considerably. We investigated the genetic diversity of IAVs in wild ducks and compared it with the viral diversity in gulls. The complete genomes of 38 IAVs of H1N1, H1N2, H3N1, H3N2, H3N6, H3N8, H4N6, H5N3, H6N2, H11N6, and H11N9 subtypes isolated from wild mallard ducks and gulls resting in a city pond in Moscow, Russia were sequenced. The analysis of phylogenetic trees showed that stable viral genotypes do not persist from year to year in ducks owing to frequent gene reassortment. For comparison, similar analyses were carried out using sequences of IAVs isolated in the same period from ducks and gulls in The Netherlands. Our results revealed a significant difference in diversity and rates of reassortment of IAVs in ducks and gulls. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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11 pages, 2463 KiB

Open AccessArticle

The Photosensitizer Octakis(cholinyl)zinc Phthalocyanine with Ability to Bind to a Model Spike Protein Leads to a Loss of SARS-CoV-2 Infectivity In Vitro When Exposed to Far-Red LED

by Kirill Sharshov, Mariya Solomatina, Olga Kurskaya, Ilya Kovalenko, Ekaterina Kholina, Vladimir Fedorov, Gennady Meerovich, Andrew Rubin and Marina Strakhovskaya

Viruses 2021, 13(4), 643; https://doi.org/10.3390/v13040643 - 09 Apr 2021

Cited by 22 | Viewed by 3054

Abstract

Photodynamic inactivation of pathogenic microorganisms can be successfully used to eradicate pathogens in localized lesions, infected liquid media, and on various surfaces. This technique utilizes the photosensitizer (PS), light, and molecular oxygen to produce reactive oxygen species that kill pathogens. Here, we used [...] Read more.

Photodynamic inactivation of pathogenic microorganisms can be successfully used to eradicate pathogens in localized lesions, infected liquid media, and on various surfaces. This technique utilizes the photosensitizer (PS), light, and molecular oxygen to produce reactive oxygen species that kill pathogens. Here, we used the PS, water soluble octakis(cholinyl)zinc phthalocyanine (Zn-PcChol₈₊), to inactivate an initial 4.75–5.00 IgTCID50/mL titer of SARS-CoV-2, thereby preventing viral infection when tested in Vero E6 cell cultures. Zn-PcChol₈₊ in a minimally studied concentration, 1 µM and LED 3.75 J/cm², completely destroyed the infectivity of SARS-CoV-2. To detect possible PS binding sites on the envelope of SARS-CoV-2, we analyzed electrostatic potential and simulated binding of Zn-PcChol₈₊ to the spike protein of this coronavirus by means of Brownian dynamics software, ProKSim (Protein Kinetics Simulator). Most of the Zn-PcChol₈₊ molecules formed clusters at the upper half of the stalk within a vast area of negative electrostatic potential. Positioning of the PS on the surface of the spike protein at a distance of no more than 10 nm from the viral membrane may be favorable for the oxidative damage. The high sensitivity of SARS-CoV-2 to photodynamic inactivation by Zn-PcChol₈₊ is discussed with respect to the application of this PS to control the spread of COVID-19. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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10 pages, 1648 KiB

Open AccessBrief Report

Ferristatin II Efficiently Inhibits SARS-CoV-2 Replication in Vero Cells

by Alexey Sokolov, Irina Isakova-Sivak, Natalia Grudinina, Daria Mezhenskaya, Elena Litasova, Valeria Kostevich, Ekaterina Stepanova, Alexandra Rak, Ivan Sychev, Olga Kirik and Larisa Rudenko

Viruses 2022, 14(2), 317; https://doi.org/10.3390/v14020317 - 03 Feb 2022

Cited by 9 | Viewed by 2433

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to have a significant impact on global public health. Multiple mechanisms for SARS-CoV-2 cell entry have been described; however, the role of transferrin receptor 1 (TfR1) in SARS-CoV-2 infection has received little attention. We used [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to have a significant impact on global public health. Multiple mechanisms for SARS-CoV-2 cell entry have been described; however, the role of transferrin receptor 1 (TfR1) in SARS-CoV-2 infection has received little attention. We used ferristatin II to induce the degradation of TfR1 on the surface of Vero cells and to study the consequences of such treatment on the viability of the cells and the replication of SARS-CoV-2. We demonstrated that ferristatin II is non-toxic for Vero cells in concentrations up to 400 µM. According to confocal microscopy data, the distribution of the labeled transferrin and receptor-binding domain (RBD) of Spike protein is significantly affected by the 18h pretreatment with 100 µM ferristatin II in culture medium. The uptake of RBD protein is nearly fully inhibited by ferristatin II treatment, although this protein remains bound on the cell surface. The findings were well confirmed by the significant inhibition of the SARS-CoV-2 infection of Vero cells by ferristatin II with IC₅₀ values of 27 µM (for Wuhan D614G virus) and 40 µM (for Delta virus). A significant reduction in the infectious titer of the Omicron SARS-CoV-2 variant was noted at a ferristatin II concentration as low as 6.25 µM. We hypothesize that ferristatin II blocks the TfR1-mediated SARS-CoV-2 host cell entry; however, further studies are needed to elucidate the full mechanisms of this virus inhibition, including the effect of ferristatin II on other SARS-CoV-2 receptors, such as ACE2, Neuropilin-1 and CD147. The inhibition of viral entry by targeting the receptor on the host cells, rather than the viral mutation-prone protein, is a promising COVID-19 therapeutic strategy. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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14 pages, 431 KiB

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The Value of Rapid Antigen Tests for Identifying Carriers of Viable SARS-CoV-2

by Elena V. Shidlovskaya, Nadezhda A. Kuznetsova, Elizaveta V. Divisenko, Maria A. Nikiforova, Andrei E. Siniavin, Daria A. Ogarkova, Aleksandr V. Shagaev, Maria A. Semashko, Artem P. Tkachuk, Olga A. Burgasova and Vladimir A. Gushchin

Viruses 2021, 13(10), 2012; https://doi.org/10.3390/v13102012 - 06 Oct 2021

Cited by 10 | Viewed by 2419

Abstract

The search for effective methods to detect patients who excrete a viable virus is one of the urgent tasks of modern biomedicine. In the present study, we examined the diagnostic value of two antigen tests, BIOCREDIT COVID-19 Ag (RapiGEN Inc., Anyang, Korea) and [...] Read more.

The search for effective methods to detect patients who excrete a viable virus is one of the urgent tasks of modern biomedicine. In the present study, we examined the diagnostic value of two antigen tests, BIOCREDIT COVID-19 Ag (RapiGEN Inc., Anyang, Korea) and SGTI-flex COVID-19 Ag (Sugentech Inc., Cheongju, Korea), for their diagnostic value in identifying patients who excrete viable SARS-CoV-2. As part of the study, we examined samples from 106 patients who had just been admitted to the hospital and who had undergone quantitative RT-PCR and assessment of viability of SARS-CoV-2 using cell culture. Assessment of the tests’ value for detecting samples containing viable virus showed high sensitivity for both tests. Sensitivity was 78.6% (95% CI, from 49.2% to 95.3%) for SGTI-flex COVID-19 Ag and 100% (95% CI, from 76.8% to 100%) for Biocredit COVID-19 Ag. The specificity of rapid tests was significantly higher than that of RT-PCR and was 66.3% (95% CI, from 55.7% to 75.8%) and 67.4% (95% CI, from 56.8% to 76.8%) for SGTI-flex COVID-19 Ag and Biocredit COVID-19 Ag versus 30.4% (95% CI, from 21.3% to 40.9%) obtained for PCR. Thus, for tasks of identifying viable SARS-CoV-2 during screening of conditionally healthy people, as well as monitoring those quarantined, rapid tests show significantly better results. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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9 pages, 628 KiB

Open AccessBrief Report

Detection of IFNγ-Secreting CD4⁺ and CD8⁺ Memory T Cells in COVID-19 Convalescents after Stimulation of Peripheral Blood Mononuclear Cells with Live SARS-CoV-2

by Victoria Matyushenko, Irina Isakova-Sivak, Igor Kudryavtsev, Arina Goshina, Anna Chistyakova, Ekaterina Stepanova, Polina Prokopenko, Ivan Sychev and Larisa Rudenko

Viruses 2021, 13(8), 1490; https://doi.org/10.3390/v13081490 - 29 Jul 2021

Cited by 18 | Viewed by 3106

Abstract

Background: New coronavirus SARS-CoV-2, a causative agent of the COVID-19 pandemic, has been circulating among humans since November 2019. Multiple studies have assessed the qualitative and quantitative characteristics of virus-specific immunity in COVID-19 convalescents, however, some aspects of the development of memory T-cell [...] Read more.

Background: New coronavirus SARS-CoV-2, a causative agent of the COVID-19 pandemic, has been circulating among humans since November 2019. Multiple studies have assessed the qualitative and quantitative characteristics of virus-specific immunity in COVID-19 convalescents, however, some aspects of the development of memory T-cell responses after natural SARS-CoV-2 infection remain uncovered. Methods: In most of published studies T-cell immunity to the new coronavirus is assessed using peptides corresponding to SARS-CoV-1 or SARS-CoV-2 T-cell epitopes, or with peptide pools covering various parts of the viral proteins. Here, we determined the level of CD4⁺ and CD8⁺ memory T-cell responses in COVID-19 convalescents by stimulating PBMCs collected 1 to 6 months after recovery with sucrose gradient-purified live SARS-CoV-2. IFNγ production by the central and effector memory helper and cytotoxic T cells was assessed by intracellular cytokine staining assay and flow cytometry. Results: Stimulation of PBMCs with live SARS-CoV-2 revealed IFNγ-producing T-helper effector memory cells with CD4⁺CD45RA⁻CCR7⁻ phenotype, which persisted in circulation for up to 6 month after COVID-19. In contrast, SARS-CoV-2-specific IFNγ-secreting cytotoxic effector memory T cells were found at significant levels only shortly after the disease, but rapidly decreased over time. Conclusion: The stimulation of immune cells with live SARS-CoV-2 revealed a rapid decline in the pool of effector memory CD8⁺, but not CD4⁺, T cells after recovery from COVID-19. These data provide additional information on the development and persistence of cellular immune responses after natural infection, and can inform further development of T cell-based SARS-CoV-2 vaccines. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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11 pages, 1210 KiB

Open AccessBrief Report

The Significance of Phenotyping and Quantification of Plasma Extracellular Vesicles Levels Using High-Sensitivity Flow Cytometry during COVID-19 Treatment

by Igor Kudryavtsev, Olga Kalinina, Vadim Bezrukikh, Olesya Melnik and Alexey Golovkin

Viruses 2021, 13(5), 767; https://doi.org/10.3390/v13050767 - 27 Apr 2021

Cited by 22 | Viewed by 3020

Abstract

New investigation results point to the potential participation of extracellular vesicles (EVs) in the pathogenesis of coronavirus infection, its progression, and mechanisms of the therapy effectiveness. This dictates the necessity to transfer scientific testing technologies to medical practice. Here, we demonstrated the method [...] Read more.

New investigation results point to the potential participation of extracellular vesicles (EVs) in the pathogenesis of coronavirus infection, its progression, and mechanisms of the therapy effectiveness. This dictates the necessity to transfer scientific testing technologies to medical practice. Here, we demonstrated the method of phenotyping and quantitative analysis of plasma EVs based on differential centrifugation, immunostaining, and high-sensitivity multicolor flow cytometry. We used EV markers that were potentially associated with SARS-CoV-2 dissemination via vesicles and cell-origination markers, characterizing objects from different cell types that could influence clinical manifestation of COVID-19. Plasma levels of CD235a+ and CD14+ EVs in patients with moderate infection were significantly increased while CD8+ and CD19+ EVs were decreased comparing with HD. Patients with severe infection had lower levels of CD4+, CD19+, and CD146+ EVs than HD. These findings demonstrate that EV concentrations in COVID-19 are severity related. Moreover, the three-point dynamic assessment demonstrated significant loss of CD63+ and CD147+ plasma EVs. The used method can be a convenient tool for vital infection pathogenesis investigation and for COVID-19 diagnostics. Full article

(This article belongs to the Special Issue State-of-the-Art Respiratory Viruses Research in Russia)

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