Article
Microbiology
Weiwen Liang, Timothy J. C. Tan, Yiquan Wang, Huibin Lv, Yuanxin Sun, Roberto Bruzzone, Chris K. P. Mok, Nicholas C. Wu
Summary: Influenza hemagglutinin (HA) often undergoes adaptive mutations during egg-based vaccine production. These mutations can vary in their impact on HA antigenicity and are strain-dependent.
Article
Veterinary Sciences
Xueyun Li, Jia Liu, Zengzhao Qiu, Qijun Liao, Yani Peng, Yongkun Chen, Yuelong Shu
Summary: The study identified 54 canine-adaptive signatures in H3N2 CIVs and found that IAVs can establish persistent transmission more easily in lower mammals compared to higher mammals. Additionally, 25 common adaptation signatures of H3 IAVs were observed in diverse avian-mammals comparison.
FRONTIERS IN VETERINARY SCIENCE
(2021)
Article
Medicine, Research & Experimental
Feng Liu, F. Liaini Gross, Stacie N. Jefferson, Crystal Holiday, Yaohui Bai, Li Wang, Bin Zhou, Min Z. Levine
Summary: The effectiveness of A(H3N2) influenza vaccine was found to be low during the 2016-19 seasons and varied by age. It was observed that antibody responses to cell and egg-propagated vaccine viruses differed due to egg-adapted changes in the vaccine hemagglutinins. The impact of vaccine egg adaptation on antibody responses varied across different age groups.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Microbiology
Fucheng Guo, Ayan Roy, Ruichen Wang, Jinjin Yang, Zhipeng Zhang, Wen Luo, Xuejuan Shen, Rui-Ai Chen, David M. Irwin, Yongyi Shen
Summary: The avian-origin H3N2 canine influenza virus experiences higher selection pressure and accumulates more non-synonymous substitutions than synonymous substitutions compared to avian reservoir viruses. Convergent evolution has been observed in different lineages of canine influenza viruses with certain substitutions facilitating transmission across species barriers. These adaptive changes have helped H3N2 CIV spread from South Asia to North America and enhance adaptation to host cellular systems.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Johanna West, Juliane Roeder, Tatyana Matrosovich, Jana Beicht, Jan Baumann, Nancy Mounogou Kouassi, Jennifer Doedt, Nicolai Bovin, Gianpiero Zamperin, Michele Gastaldelli, Annalisa Salviato, Francesco Bonfante, Sergei Kosakovsky Pond, Sander Herfst, Ron Fouchier, Jochen Wilhelm, Hans-Dieter Klenk, Mikhail Matrosovich
Summary: This study revealed the evolutionary pathway of the HA of the 1968 pandemic influenza virus, predicting its origin from wild duck virus and identifying key amino acid substitutions affecting HA binding and stability. The addition of N-glycan at specific positions was also found to be a common marker of avian-to-mammalian adaptation, highlighting the importance of studying past pandemic IAVs for influenza risk assessment and preparedness.
Article
Multidisciplinary Sciences
Frederik Broszeit, Rosanne J. van Beek, Luca Unione, Theo M. Bestebroer, Digantkumar Chapla, Jeong-Yeh Yang, Kelley W. Moremen, Sander Herfst, Ron A. M. Fouchier, Robert P. de Vries, Geert-Jan Boons
Summary: Recent studies have shown that A/H3N2 viruses have evolved binding specificity to certain receptors, leading to inability to agglutinate erythrocytes. Glycan remodeling approach enables installation of functional receptors on erythrocytes, facilitating vaccine design.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Chika Kikuchi, Aristotelis Antonopoulos, Shengyang Wang, Tadashi Maemura, Rositsa Karamanska, Chiara Lee, Andrew J. Thompson, Anne Dell, Yoshihiro Kawaoka, Stuart M. Haslam, James C. Paulson
Summary: The evolution of human H3N2 influenza viruses has led to a limited specificity of the hemagglutinin to a subset of glycan receptors, presenting challenges for virus recognition and vaccine production. By studying glyco-engineered cell lines, the authors demonstrate the importance of extended glycan receptors for the growth of recent H3N2 viruses and their relevance to vaccine production.
NATURE COMMUNICATIONS
(2023)
Article
Immunology
Ashley M. Price, Brendan Flannery, H. Keipp Talbot, Carlos G. Grijalva, Karen J. Wernli, C. Hallie Phillips, Arnold S. Monto, Emily T. Martin, Edward A. Belongia, Huong Q. McLean, Manjusha Gaglani, Manohar Mutnal, Krissy Moehling Geffel, Mary Patricia Nowalk, Sara Y. Tartof, Ana Florea, Callie McLean, Sara S. Kim, Manish M. Patel, Jessie R. Chung
Summary: In the 2021-2022 season, influenza activity in the United States was mild enough to estimate the effectiveness of the influenza vaccine. Researchers found that the vaccine had an effectiveness of 36% against outpatient acute illness caused by A(H3N2) viruses.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Medicine, General & Internal
Hyun-Jong Lee, Gwanghui Ryu, Ki-Il Lee
Summary: This study compared the symptomatic characteristics of influenza A/H3N2 and A/H1N1 subtypes in primary healthcare settings in Korea. The results showed that the H3N2-dominant season had higher average body temperature and more patients with high fever compared to the H1N1-dominant season. On the other hand, symptoms such as myalgia, cough, and sore throat were more common in the H1N1-dominant season. Antiviral drugs were prescribed to the majority of febrile patients in both seasons.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Immunology
Min Kang, Mark Zanin, Sook-San Wong
Summary: H3N2 influenza A viruses have been dominant in the Western Pacific region since the H1N1 pandemic. Low vaccine effectiveness, especially for A(H3N2), has been reported due to antigenic mismatch between the vaccine and circulating viral strains. Strategies to improve this include new vaccine platforms that may provide better protection.
Article
Biochemistry & Molecular Biology
Chang Shu, Qinglan Sun, Guomei Fan, Kesheng Peng, Zhengfei Yu, Yingfeng Luo, Shenghan Gao, Juncai Ma, Tao Deng, Songnian Hu, Linhuan Wu
Summary: The VarEPS-Influ database is a risk assessment system for influenza virus variations that comprehensively evaluates various aspects of mutations, including physical and chemical properties, structural features, receptor affinity, antibody binding capacity, etc., and considers factors such as time and spatial distribution and host species distribution. It accurately evaluates and predicts the risk of influenza virus variations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Michael Lutz, Jordana Schmierer, Toru Takimoto
Summary: Avian species are the main source of pandemic influenza A viruses that can infect humans. This study found that avian influenza A virus genes, including PA, PB1, and PB2, need to undergo host-adaptive mutations in order to replicate and transmit in humans. It was discovered that the PA gene from the 2009 pH1N1 strain had host-adaptive mutations that enhanced viral replication by increasing translation efficiency. This was achieved through increased cytosolic accumulation of viral mRNA, which depended on the host RNA binding protein GRSF1. Mutations to the GRSF1 binding site and knockdown of GRSF1 reduced viral mRNA accumulation and translation efficiency. These findings reveal a previously unrecognized mechanism by which host-adaptive mutations in PA regulate viral replication and host adaptation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Jiayu Wu, Yanan Wang, Yu An, Changyu Tian, Lingfeng Wang, Zuhong Liu, Desheng Qi
Summary: This study compared the gene expression differences in liver tissues of laying hens at different ages using RNA sequencing, and found that the transport and metabolism of amino acids changed during the growing period, which influenced the growth and development of the hens.
Article
Virology
Elien Vandoorn, Wojciech Stadejek, Anna Parys, Sharon Chepkwony, Koen Chiers, Kristien Van Reeth
Summary: The study found that the H3N2 LAIV strain lvTX98 is only partly attenuated in pigs and is excreted at significant titers after intranasal vaccination. Attenuation and restricted replication of lvTX98 in vivo seemed to be associated with the loss of NS1 functions other than type I IFN antagonism.
JOURNAL OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Gopal Kalwan, Parichita Priyadarshini, Kuldeep Kumar, Yashwant Kumar Yadava, Sheel Yadav, Deshika Kohli, Sarvajeet Singh Gill, Kishor Gaikwad, Venkatraman Hegde, Pradeep Kumar Jain
Summary: This study comprehensively analyzes the AAT gene family in chickpea and identifies 109 AAT genes, which play important roles in plant growth, stress resilience, and nutritional quality enhancement.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Aleksandra Bezmenova, Elena A. Zvyagina, Anna Fedotova, Artem S. Kasianov, Tatiana Neretina, Aleksey A. Penin, Georgii A. Bazykin, Alexey S. Kondrashov
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Elena Nabieva, Satyarth Mishra Sharma, Yermek Kapushev, Sofya K. Garushyants, Anna Fedotova, Viktoria N. Moskalenko, Tatyana E. Serebrenikova, Eugene Glazyrina, Ilya Kanivets, Denis Pyankov, Tatyana Neretina, Maria D. Logacheva, Georgii A. Bazykin, Dmitry Yarotsky
EUROPEAN JOURNAL OF HUMAN GENETICS
(2020)
Article
Evolutionary Biology
Valentina Burskaia, Sergey Naumenko, Mikhail Schelkunov, Daria Bedulina, Tatyana Neretina, Alexey Kondrashov, Lev Yampolsky, Georgii A. Bazykin
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Genetics & Heredity
Alexey D. Neverov, Anfisa V. Popova, Gennady G. Fedonin, Evgeny A. Cheremukhin, Galya V. Klink, Georgii A. Bazykin
Summary: The study analyzes the evolution rates and methods of protein sites in detail, finding that co-evolving sites cluster in protein structures and are influenced by epistasis and selection events. Additionally, they discovered that proteins consist of co-evolving structural blocks with specific functions.
Article
Biochemistry & Molecular Biology
Sergei A. Slavskii, Ivan A. Kuznetsov, Tatiana I. Shashkova, Georgii A. Bazykin, Tatiana I. Axenovich, Fyodor A. Kondrashov, Yurii S. Aulchenko
Summary: The study found that as the height of hundreds of thousands of individuals is analyzed, the complexity of the model needs to be increased to include non-additive interactions between sex, environment, and genes. Alternatively, the use of log-normal approximation allowed researchers to still use the additive effects model.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Multidisciplinary Sciences
Andrey B. Komissarov, Ksenia R. Safina, Sofya K. Garushyants, Artem Fadeev, Mariia Sergeeva, Anna A. Ivanova, Daria M. Danilenko, Dmitry Lioznov, Olga Shneider, Nikita Shvyrev, Vadim Spirin, Dmitry Glyzin, Vladimir Shchur, Georgii A. Bazykin
Summary: The study analyzed the emergence of SARS-CoV-2 in Russia in 2020, finding that of the 67 introductions, only one was from China, indicating that border closure may have helped delay the spread of the virus in Russia.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Dmitry Biba, Galya Klink, Georgii A. Bazykin
Summary: Insertions and deletions of lengths not divisible by 3 in protein-coding sequences can cause frameshifts and high fitness costs. However, a compensatory indel can partially offset this cost. This study examines the prevalence of compensatory frameshifting mutations (pCFMs) in the divergence of vertebrate and insect protein-coding genes. The results show that pCFMs can lead to novel variations in amino acid sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemical Research Methods
Galya Klink, Olga Kalinina, Georgii Bazykin
Summary: Fitness conferred by the same allele may differ between genotypes and environments, and these differences shape variation and evolution. In this study, a new method is developed to detect individual amino acids that confer different fitness in different groups of species. The method combines sequence and phylogenetic data, and is validated using simulated evolution and applied to HIV-1 and influenza A. The results are consistent with fitness differences observed in experiments.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Genetics & Heredity
Wentai Ma, Jing Yang, Haoyi Fu, Chao Su, Caixia Yu, Qihui Wang, Ana Tereza Ribeiro de Vasconcelos, Georgii A. Bazykin, Yiming Bao, Mingkun Li
Summary: This study analyzed the viral genome of the Omicron variant and found it to have numerous mutations, especially in the Spike gene. These mutations may affect the replication, infectivity, and antigenicity of SARS-CoV-2. The Omicron variant has 53 mutations compared to its closest sequences in public databases, many of which are rare. Strengthening global genomic surveillance and data sharing is crucial for detecting and tracking the source of new variants.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biology
Anastasia Stolyarova, Tatiana Neretina, Elena A. Zvyagina, Anna Fedotova, Alexey S. Kondrashov, Georgii A. Bazykin
Summary: Studying patterns of genetic variation in hyperpolymorphic species, such as the fungus Schizophyllum commune, can reveal large-scale properties of the fitness landscape that are difficult to detect in species with ordinary levels of genetic variation. In S. commune, short-range linkage disequilibrium tends to be higher between pairs of nonsynonymous variants, especially those located within the same gene and covered by haploblocks, which are segments of the genome consisting of two highly divergent haplotypes and a signature of balancing selection. LD is also higher for pairs of nonsynonymous variants encoding interacting amino acids within the protein. Additionally, there is a correlation between LDs at the same pairs of nonsynonymous mutations in different populations.
Article
Biotechnology & Applied Microbiology
Olgo A. Mukhina, Daria S. Fomina, Vasiliy V. Parshin, Vladimir A. Gushchin, Inna V. Dolzhikova, Alexey M. Shchetinin, Dmitriy M. Chudakov, Evgeniia Alekseeva, Dmitriy Korostin, Georgii A. Bazykin, Galya Klink, Denis Yu. Logunov, Maryana A. Lysenko
Summary: The article discusses the case of a patient with long-term SARS-CoV-2 infection and secondary immunodeficiency. The analysis shows a mutation in the S-protein that may affect its binding ability to cellular receptors. Treatment with a COVID-19-globulin preparation resulted in rapid improvement, elimination of the virus, and passive immunization for at least 30 days.
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2022)
Article
Biology
Artem Mikelov, Evgeniia Alekseeva, Ekaterina A. Komech, Dmitry B. Staroverov, Maria A. Turchaninova, Mikhail Shugay, Dmitriy M. Chudakov, Georgii A. Bazykin, Ivan Zvyagin
Summary: The study analyzes the longitudinal dynamics of immune memory B cells and reveals a high degree of clonal persistence within memory B cell subsets. There is convergence between memory B cells and antibody-secreting cells (ASCs) among individuals. The study identifies two clusters of expanded clonal lineages with different prevalence and persistence, suggesting the reactivation of memory B cells during proliferation and differentiation into ASCs.
Article
Multidisciplinary Sciences
Alina Matsvay, Galya K. Klink, Ksenia Safina, Elena A. Nabieva, Sofya M. Garushyants, Dmitry V. Biba, Georgii I. Bazykin, Ivan O. Mikhaylov, Anna S. Say, Anastasiya A. Zakamornaya, Anastasiya S. Khakhina, Tatiana A. Lisitsa, Andrey B. Ayginin, Ivan U. Abramov, Sergey F. Bogdan, Kseniya A. Kolbutova, Daria M. Oleynikova, Tatiana I. Avdeenko, German Shipulin, Sergey Yudin, Veronika Skvortsova
Summary: In 2020, SARS-CoV-2 quickly spread worldwide, and most countries were unable to prevent or delay its transmission. The impact of limitations on trans-border passenger traffic on the global spread of COVID-19 strains is uncertain. A study analyzed 3206 whole-genome sequences of SARS-CoV-2 samples from 78 regions in Russia before the spread of variants of concern. The results showed that partial border closure had little effect on trans-border transmission of variants, contributing to the rapid global spread of newly arising SARS-CoV-2 variants.
Article
Infectious Diseases
Grigorii A. Sukhorukov, Alexey I. V. Paramonov, Oksana Lisak, Irina V. V. Kozlova, Georgii A. Bazykin, Alexey D. V. Neverov, Lyudmila S. Karan
Summary: This study found that a group of viruses obtained near Lake Baikal in Russia have a mosaic genome, with some parts related to the Siberian group and others related to the Far Eastern group. This pattern likely arose through recombination, a process where infected cells produce hybrid viral progeny with genetic material from both parents. These findings suggest that the mixing of genetic information from different sources can increase the genetic diversity of these viruses and potentially accelerate their adaptation. Additionally, this study also discovered that the tick-borne encephalitis virus undergoes frequent recombination during evolution, expanding our understanding of the role of recombination in the evolution of this human pathogen.
PLOS NEGLECTED TROPICAL DISEASES
(2023)
Article
Evolutionary Biology
Nurislam M. Shaikhutdinov, Galya Klink, Sofya K. Garushyants, Olga S. Kozlova, Alexander Cherkasov, Takahiro Kikawada, Takashi Okuda, Dylo Pemba, Elena Shagimardanova, Aleksey A. Penin, Ruslan M. Deviatiiarov, Guzel R. Gazizova, Richard Cornette, Oleg A. Gusev, Georgii A. Bazykin
Summary: The genome analysis of two chironomid species, Polypedilum vanderplanki and Polypedilum pembai, reveals the evolution of anhydrobiosis and the amplification of protective genes in P. pembai. Positive selection and changes in gene architecture are observed, suggesting ongoing adaptation to desiccation tolerance.
GENOME BIOLOGY AND EVOLUTION
(2023)