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Problems of Virology

ISSN 0507-4088 (Print) ISSN 2411-2097 (Online)
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Keywords Bunyaviridae COVID-19 ELISA HIV HIV-1 Ixodidae SARS-CoV-2 antiviral
activity hemagglutinin herpes simplex virus human immunodeficiency virus
influenza influenza virus monoclonal antibodies phylogenetic analysis polymerase
chain reaction review sequencing tick-borne encephalitis virus vaccination
vaccine
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Keywords Bunyaviridae COVID-19 ELISA HIV HIV-1 Ixodidae SARS-CoV-2 antiviral
activity hemagglutinin herpes simplex virus human immunodeficiency virus
influenza influenza virus monoclonal antibodies phylogenetic analysis polymerase
chain reaction review sequencing tick-borne encephalitis virus vaccination
vaccine
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Home > Problems of Virology


PROBLEMS OF VIROLOGY




International peer-reviewed scientific and practical journal "Problems of
Virology" (Russian title “Voprosy virusologii”, ISSN (Print) 0507-4088, ISSN
(Online) 2411-2097) acquaints readers with the achievements of Russian and
international virology, publishes articles on the study of viruses and viral
diseases of humans, animals and plants. A prominent place in the journal is
given to the publication of the results of experimental studies on various
fields in fundamental and applied virology.

The journal publishes materials that contribute to the implementation in
practice of the achievements of virological science in eliminating and reducing
the prevalence of infectious diseases, as well as its diagnosis, prevention and
treatment.

The review articles summarize the latest advances in virology. In order to
attract the attention of virologists to the most actual issues requiring further
study, the journal publishes editorial notes and book reviews. The reader will
find in the journal a description of new research methods, new equipment,
diagnostic and treatment tools.

The journal is intended for virologists (medical and veterinary),
epidemiologists, parasitologists, pharmacologists, biochemists and other
specialists.

«Problems of Virology» is an open access journal that does not charge for the
publication of scientific articles.

The journal is presented in SCOPUS database (Q4).

The journal is included in the recommended by the Higher Attestation Commission
"List of peer-reviewed scientific publications in which the main scientific
results of dissertations for the doctoral degree (PhD), for the degree of doctor
of science should be published" (in accordance with paragraph 5 of the Rules for
the formation of the List, as part of the international abstract database and
citation systems Scopus) in the following specialties:

 * 02.02 Epidemiology (medical and biological sciences)
 * 01.09 Infectious diseases
 * 03.07 Chemotherapy and antibiotics
 * 02.02 Virology (medical and biological sciences)
 * 02.03 Microbiology (medical and biological sciences)

The journal is presented in the following international bibliographic databases
and information and reference systems: RSCI (on the platform WoS), Abstract
Journals, AIDS & Cancer Research, Biocontrol News and Information, Biological
Sciences, Chemical Abstracts, EBSCOhost Biological Abstracts, EBSCOhost Wildlife
& Ecology Studies Worldwide, Elsevier BV Scopus, Elsevier BV EMBASE, Index
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Medicine PubMed, Parasitology Database, Poultry Abstracts, Review of Medical and
Veterinary Entomology, Thomson Reuters Biological Abstracts, Thomson Reuters
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Reuters Web of Science, Tropical Diseases Bulletin, Veterinary Science Database,
Virology and AIDS Abstracts, ROAD, DOAJ.

Content is available under license Creative Commons — Attribution 4.0
International, CC-BY.

Each article published in the journal is assigned a digital object identifier
(DOI).

All articles, reviews and lectures published in the journal undergo mandatory
double-blind peer review by members of the editorial board and invited experts.

Articles by foreign authors, as well as Russian-language articles separately
recommended by the editorial board, are published in Russian and English under a
single DOI. Native-language translation and its scientific editing is carried
out at the expense of the Editorial Board.

The journal is registered with the Federal Service for Supervision of
Communications, Information Technology and Mass Communications. Certificate PI
No. FS77-77676.

The journal is published once every 2 months (6 issues per year).

The journal is a printed edition of the All-Russian public organization “The
All-Russian Scientific and Practical Society of Epidemiologists, Microbiologists
and Parasitologists”.

Founders:

 * FBIS Central Research Institute of Epidemiology of the Federal Service for
   Supervision of Consumer Rights Protection and Human Welfare,
 * All-Russian public organization "All-Russian Scientific and Practical Society
   of Epidemiologists, Microbiologists and Parasitologists".

Publisher:

 * FBIS Central Research Institute of Epidemiology of the Federal Service for
   Supervision of Consumer Rights Protection and Human Welfare.

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CURRENT ISSUE


VOL 69, NO 4 (2024)

 * Year: 2024
 * Published: 26.09.2024
 * Articles: 10
 * URL: https://virusjour.crie.ru/jour/issue/view/135

FULL ISSUE

(Russian)

ORIGINAL RESEARCH

MOLECULAR DETECTION OF HIGH-RISK PAPILLOMAVIRUSES AND VACCINATION STATUS IN
NORMAL CYTOLOGY IN CONGO

Ngombe Mouabata D.F., Boumba A.L., Iloukou Mayakia P.J., Massengo N.R., Takale
R.P., Moukassa D., Ennaji M.M.

ABSTRACT

Objective: The aim of this study was to identify the molecular prevalence of
high-risk HPV infection and the distribution of genotypes present in normal
cytology, as well as to determine the vaccination status of our study
population.

Methods: 110 cervical samples were taken from individuals, and 1 ml of each
sample was added to the Xpert HPV cartridge in the sample compartment before it
was placed in the Cepheid GeneXpert system. Detection was performed
simultaneously via amplification of the E6 and E7 genes in five fluorescent
channels (HPV16, HPV18/45, HPV31/33/35/52/58, HPV51/59, and HPV39/56/66/68a).

Results: 36/110 (33%) of all samples tested were positive for HPV DNA. The
predominant genotypes were HPV16 (12.7%) and other pooled HR-HPV types (8.2%).
All women who received the Gardasil-9 vaccine (3.6%) had HPV, and infection was
associated with travel outside Africa. 96.4% of the screened individuals had not
received any HPV vaccine.

Conclusion: Our research confirms a widespread HR-HPV infection in our
population and extends the importance of studies on the molecular prevalence of
HPV, particularly in women with normal cytology and apparent good health, in
view of the cruel lack of public awareness of HPV infections.

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Problems of Virology. 2024;69(4):301-308
301-308 259

(Eng)

(JATS XML)

THE EFFECT OF SODIUM DEOXYRIBONUCLEATE WITH IRON COMPLEX ON THE EXPRESSION OF
SURFACE MARKERS OF MT-4 CELLS INFECTED WITH HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
(HIV-1) (RETROVIRIDAE: PRIMATE LENTIVIRUS GROUP)

Nosik D.N., Kalnina L.B., Selimova L.M., Kaplina E.N.

ABSTRACT

Introduction. The persistence of immune dysfunction during therapy has serious
consequences for the health of HIV-infected people. Therefore, an important
direction is the search for drugs that can reduce the inflammatory potential of
the immune system and serve as an additional component of antiviral therapy.

Aim ‒ to study the effect of the immunomodulatory drug Sodium deoxyribonucleate
with iron complex (DNA-Na-Fe) on the expression of activation markers in MT-4
cells infected with HIV-1.

Materials and methods. Expression levels of CD4, CD28, CD38, CD62L and HLA-DR
proteins on the plasma membrane were measured in cells. To assess viral
activity, the p24 protein was quantified by ELISA.

Results and discussion. The two cell variants with different replicative
activity were analyzed. Control cells, cells with DNA-Na-Fe, infected cells and
infected cells with DNA-Na-Fe were tested. Based on the results obtained, it can
be concluded that antiviral activity of the drug in MT-4 cells infected with
HIV-1 is associated with immunomodulatory activity that enhances the expression
of membrane proteins CD4, CD28, CD38 and CD62L. Diversity in the effect of
DNA-Na-Fe on the studied surface proteins expression in two cell lines indicates
that they depend on the characteristics of the combined molecular biological
processes occurring in cells. And the increased effects observed in a system
with changes in replicative activity assumes its active participation in virus
replication at the stages of virus penetration and budding.

Conclusion. Studies have shown that DNA-Na-Fe has antiviral and immunomodulatory
activity.

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Problems of Virology. 2024;69(4):309-319
309-319 207

(Rus)

(Eng)

(JATS XML)

SEROPOSITIVITY OF WEST NILE VIRUS AMONG ACUTE FEBRILE PATIENTS IN ILORIN,
NIGERIA

Odebisi-Omokanye M.B., Suleiman M.M., Sulaiman M.K., Atolagbe S.A.

ABSTRACT

Introduction. West Nile Virus (WNV), a member of Flaviviridae family, is one of
the most widely distributed arboviruses in the world. In developing countries
like Nigeria, fever resulting from the WNV infection is often presumptively
ascribed to malaria or typhoid due to misdiagnosis and low-level awareness of
the viral infection. This study determined the prevalence of WNV IgM and IgG
antibodies among febrile patients in the Ilorin metropolis.

Materials and methods. A total of two hundred (200) blood samples were collected
from consenting patients and each serum was screened for anti-WNV IgM and IgG
antibodies using indirect enzyme-linked immunosorbent assay (ELISA). Statistical
correlation and logistic regression analysis were conducted.

Results. Overall, 6% (12/200) anti-WNV IgM seropositivity rate was recorded
amongst the acute febrile patients with higher prevalence (6.30%) in females
than in males (5.45%). Anti-WNV IgG positivity rate of 52% (104/200) was
recorded, with 50.67% positivity rate in males and 38.95% in female
participants. The convalescence phase posited by the 5.4% (11/200) co-detection
of anti-WNV IgG and IgM antibodies among the participants was recorded. A
statistical correlation was noticed with the age and religion of respondents to
WNV serological positivity while gender, occupation, use of mosquito nets and
formal education had no positive correlation at p < 0.05. However, based on odd
ratio at 95% CI and logistic regression coefficients, the evaluated risk factors
such as blood transfusion, residency, malaria parasite, and proximity to
stagnant water and bush were significant to anti-WNV IgG and IgM positivity.

Conclusion. The findings of this study show the circulation of WNV in the study
area. There is an urgent need for clinicians/physicians to include screening for
the West Nile virus in cases of febrile patients before the commencement of
treatment.

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Problems of Virology. 2024;69(4):320-328
320-328 221

(Eng)

(JATS XML)

THE MOLECULAR AND BIOLOGICAL PATTERNS UNDERLYING SUSTAINED SARS-COV-2
CIRCULATION IN THE HUMAN POPULATION

Kustova D.D., Pochtovyi A.A., Shpakova O.G., Shtinova I.A., Kuznetsova N.A.,
Kleimenov D.A., Komarov A.G., Gushchin V.A.

ABSTRACT

Introduction. For four years, SARS-CoV-2, the etiological agent of COVID-19, has
been circulating among humans. By the end of the second year, an absence of
immunologically naive individuals was observed, attributable to extensive
immunization efforts and natural viral exposure. This study focuses on
delineating the molecular and biological patterns that facilitate the
persistence of SARS-CoV-2, thereby informing predictions on the epidemiological
trajectory of COVID-19 toward refining pandemic countermeasures.

The aim of this study was to describe the molecular biological patterns
identified that contribute to the persistence of the virus in the human
population.

Materials and methods. For over three years since the beginning of the COVID-19
pandemic, molecular genetic monitoring of SARS-CoV-2 has been conducted, which
included the collection of nasopharyngeal swabs from infected individuals,
assessment of viral load, and subsequent whole-genome sequencing.

Results. We discerned dominant genetic lineages correlated with rising disease
incidence. We scrutinized amino acid substitutions across SARS-CoV-2 proteins
and quantified viral loads in swab samples from patients with emerging COVID-19
variants. Our findings suggest a model of viral persistence characterized by 1)
periodic serotype shifts causing substantial diminutions in serum
virus-neutralizing activity (> 10-fold), 2) serotype-specific accrual of point
mutations in the receptor-binding domain (RBD) to modestly circumvent
neutralizing antibodies and enhance receptor affinity, and 3) a gradually
increasing amount of virus being shed in mucosal surfaces within a single
serotype.

Conclusion. This model aptly accounts for the dynamics of COVID-19 incidence in
Moscow. For a comprehensive understanding of these dynamics, acquiring
population-level data on immune tension and antibody neutralization relative to
genetic lineage compositions is essential.

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Problems of Virology. 2024;69(4):329-340
329-340 495

(Rus)

(Eng)

(JATS XML)

DEVELOPMENT, STUDY, AND COMPARISON OF MODELS OF CROSS-IMMUNITY TO THE INFLUENZA
VIRUS USING STATISTICAL METHODS AND MACHINE LEARNING

Asatryan M.N., Shmyr I.S., Timofeev B.I., Shcherbinin D.N., Agasaryan V.G.,
Timofeeva T.A., Ershov I.F., Gerasimuk E.R., Nozdracheva A.V., Semenenko T.A.,
Logunov D.Y., Gintsburg A.L.

ABSTRACT

Introduction. The World Health Organization considers the values of antibody
titers in the hemagglutination inhibition assay as one of the most important
criteria for assessing successful vaccination. Mathematical modeling of
cross-immunity allows for identification on a real-time basis of new antigenic
variants, which is of paramount importance for human health.

Materials and methods. This study uses statistical methods and machine learning
techniques from simple to complex: logistic regression model, random forest
method, and gradient boosting. The calculations used the AAindex matrices in
parallel to the Hamming distance. The calculations were carried out with
different types and values of antigenic escape thresholds, on four data sets.
The results were compared using common binary classification metrics.

Results. Significant differentiation is shown depending on the data sets used.
The best results were demonstrated by all three models for the forecast autumn
season of 2022, which were preliminary trained on the February season of the
same year (Auroc 0.934; 0.958; 0.956, respectively). The lowest results were
obtained for the entire forecast year 2023, they were set up on data from two
seasons of 2022 (Aucroc 0.614; 0.658; 0.775). The dependence of the results on
the types of thresholds used and their values turned out to be insignificant.
The additional use of AAindex matrices did not significantly improve the results
of the models without introducing significant deterioration.

Conclusion. More complex models show better results. When developing
cross-immunity models, testing on a variety of data sets is important to make
strong claims about their prognostic robustness.

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Problems of Virology. 2024;69(4):349-362
349-362 351

(Rus)

(Eng)

(JATS XML)

MOLECULAR STUDY OF VARICELLA ZOSTER VIRUS IN CEREBROSPINAL FLUID FROM STROKE
PATIENTS OF THI-QAR PROVINCE

Salim Z.F., Hamad B.J.

ABSTRACT

Introduction: Varicella zoster virus (VZV) is a type of alpha-herpesvirus that
specifically targets the nervous system. The initial infection, typically
occurring during childhood, results in varicella (commonly known as chickenpox),
after which the virus enters a dormant state in cranial nerve ganglia, dorsal
root ganglia, and autonomic ganglia throughout the entire neuroaxis.

Aim of the study: Molecular and genetic studies of viruses are an important tool
for virus development and identifying viral treatments to combat the diseases.
The aim of the study was to determine the whole ORF4 sequence of the local VZV
strains for phylogenetic analysis to determine the variability in the viral
sequence.

Material and methods: Ten samples of VZV DNA were subjected to the sequencing of
the whole ORF4 region following identification using the PCR method.

Results: Sequences from five samples have been successfully analyzed. All
clinical strains were discovered to possess a genome with a length of 124,884
base pairs. The sequences exhibited the occurrence of two distinct mutations,
one being a transversion and the other a transition, with the latter resulting
in an alteration of the amino acid. A phylogenetic tree was constructed using
the maximum likelihood method based on the sequences of five nucleotide
sequences from clinical samples and nine reference VZV strains. The tree
displayed the evolutionary distances between these sequences. The analysis of
the phylogenetic tree revealed the presence of five primary clades, with four of
them originating from India (isolates S1, S2, S4, S5), while S3 exhibited
similarity to a strain from the United Kingdom.

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Problems of Virology. 2024;69(4):341-348
341-348 261

(Eng)

(JATS XML)

UNUSUAL BA222-LIKE STRAINS OF ROTAVIRUS A (SEDOREOVIRIDAE: ROTAVIRUS: ROTAVIRUS
A): MOLECULAR AND GENETIC ANALYSIS BASED ON ALL GENOME SEGMENTS

Velikzhanina E.I., Sashina T.A., Morozova O.V., Kashnikov A.Y., Epifanova N.V.,
Novikova N.A.

ABSTRACT

Introduction. Rotavirus infection is the major cause of severe dehydrating
diarrhea requiring hospitalization in young children worldwide. Due to their
segmented genome, rotaviruses are capable of gene reassortment, which makes the
emergence and spread of genetically novel strains possible. The purpose of this
study was to search for unusual rotaviruses circulating in Nizhny Novgorod in
2021‒2023 and their molecular genetic characterization based on all genome
segments.

Materials and methods. Rotavirus-positive stool samples of children were
examined by PCR genotyping and electrophoresis in PAAG. cDNA fragments of each
of the 11 genes (VP1‒VP4, VP6, VP7, NSP1‒NSP5), 570 to 850 nucleotide pairs in
length were sequenced for the selected strains. The phylogenetic analysis was
performed in the MEGA X program.

Results. In the study period 2021‒2023, 11 G[P] combinations with a predominance
of G3P[8] (59.5%) were identified. Six atypical Rotavirus А (RVA) strains were
identified: 2 strains of the G2P[4] genotype
(G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E2-H3, G2-P[4]-I2-R2-C2-M2-A3-N2-T3-E3-H2) and 4
G3P[9] strains (all strains had the genotype
G3-P[9]-I2-R2-C2-M2-A3-N2-T3-E3-H3). Phylogenetic analysis based on all genes
showed an evolutionary relationship between rotaviruses similar to rotaviruses
of cats and dogs (BA222-like) and unusual strains of the G2P[4] genotype, for
which a mixed combination of genotypes was identified and characterized for the
first time.

Discussion. The results obtained expand the understanding of the diversity of
reassortant RVAs, as well as complement the data on the genotypic structure of
the rotavirus population in Nizhny Novgorod.

Conclusion. The wide genetic diversity of reassortant RVA can help rotaviruses
overcome the immunological pressure provided by natural and vaccine-induced
immunity. In this regard, to control the emergence of new variants and assess
changes in the virulence of rotaviruses after reassortment processes, continuous
molecular monitoring for circulating RVA is necessary.

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Problems of Virology. 2024;69(4):363-376
363-376 206

(Rus)

(Eng)

(JATS XML)

FIRST DETECTION OF INFLUENZA A VIRUS SUBTYPES H1N1 AND H3N8 IN THE ANTARCTIC
REGION: KING GEORGE ISLAND, 2023

Ohlopkova O.V., Goncharov A.E., Aslanov B.I., Fadeev A.V., Davidyuk Y.N.,
Moshkin A.D., Stolbunova K.A., Stepanyuk M.A., Sobolev I.A., Tyumentseva M.A.,
Tyumentsev A.I., Shestopalov A.M., Akimkin V.G.

ABSTRACT

Relevance. Influenza A virus is characterized by a segmented single-stranded RNA
genome. Such organization of the virus genome determines the possibility of
reassortment, which can lead to the emergence of new virus variants. The main
natural reservoir of most influenza A virus subtypes are wild waterfowl.
Seasonal migrations gather waterfowl from all major migration routes to nesting
areas near the northern and southern polar circles. This makes intercontinental
spread of influenza A viruses possible.

Objective ‒ to conduct molecular genetic monitoring and study the phylogenetic
relationships of influenza A virus variants circulating in Antarctica in 2023.

Materials and methods. We studied 84 samples of biological material obtained
from birds and marine mammals in April‒May 2023 in coastal areas of Antarctica.
For 3 samples, sequencing was performed on the Miseq, Illumina platform and
phylogenetic analysis of the obtained nucleotide sequences of the influenza A
virus genomes was performed.

Results. The circulation of avian influenza virus in the Antarctic region was
confirmed. Heterogeneity of the pool of circulating variants of the influenza A
virus (H3N8, H1N1) was revealed. Full-length genomes of the avian influenza
virus were sequenced and posted in the GISAID database (EPI_ISL_19032103,
19174530, 19174467).

Conclusion. The study of the genetic diversity of influenza A viruses
circulating in the polar regions of the Earth and the identification of the
conditions for the emergence of new genetic variants is a relevant task for the
development of measures to prevent biological threats.

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Problems of Virology. 2024;69(4):377-389
377-389 699

(Rus)

(Eng)

(JATS XML)

BOOK REVIEW

REVIEW OF THE COLLECTIVE MONOGRAPH EDITED BY ACADEMICIAN OF THE RUSSIAN ACADEMY
OF SCIENCES V.I. ZLOBIN «TICK-BORNE ENCEPHALITIS IN THE 21ST CENTURY»

Zhirnov O.P.
Problems of Virology. 2024;69(4):390-391
390-391 88

(Rus)

(JATS XML)

OBITUARY

LYUDMILA V. KOLOBUKHINA

Problems of Virology. 2024;69(4):392-392
392-392 95

(Rus)

(JATS XML)




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СМИ зарегистрировано Федеральной службой по надзору в сфере связи,
информационных технологий и массовых коммуникаций (Роскомнадзор).
Регистрационный номер и дата принятия решения о регистрации СМИ: серия ПИ №
ФС77-77676 от 29.01.2020.


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