Publications by authors named "Jumpei Ito"
The era of big data has begun in life sciences, and virology is no exception. Especially since COVID-19, virology has become one of the most genome data-rich fields in life sciences. In this article, I will introduce the new paradigm of "understanding and predicting viral epidemics and evolution, " made possible by the emergence of vast amounts of genome data, focusing on my research to date.
View Article and Find Full Text PDFTransposable elements (TEs) are mobile parasitic sequences that have expanded within the host genome. It has been hypothesized that host organisms have expanded the Krüppel-associated box-containing zinc finger proteins (KRAB-ZFPs), which epigenetically suppress TEs, to counteract disorderly TE transpositions. This process is referred to as the evolutionary arms race.
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- Since 2019, SARS-CoV-2 has mutated, leading to various pandemic and epidemic waves that involve changes in its spike protein, which is key for the virus's entry into cells.
- Researchers studied the spike proteins from variants BA.2.86 and JN.1, discovering structures where ACE2 receptor binds to the spike protein in both up and down conformations.
- Their findings suggest that the down-conformation of the receptor-binding domain (RBD) is an important intermediate state that helps facilitate the virus's entry, with specific mutations like K356T impacting infectivity and resistance to neutralizing antibodies.
Due to the incessant emergence of various SARS-CoV-2 variants with enhanced fitness in the human population, controlling the COVID-19 pandemic has been challenging. Understanding how the virus enhances its fitness during a pandemic could offer valuable insights for more effective control of viral epidemics. In this manuscript, we review the evolution of SARS-CoV-2 from early 2022 to the end of 2023-from Omicron BA.
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- A new variant of SARS-CoV-2, called EG.5.1, is spreading rapidly and has been studied using various scientific methods to understand its features.
- Key mutations in EG.5.1, specifically S:F456L and ORF9b:I5T, enhance its viral fitness compared to other variants like XBB.1.5.
- Structural differences were found in the spike proteins of EG.5.1 versus XBB.1.5, and the research helps us understand the evolution of emerging viruses that can affect human health.
Article Synopsis
- Researchers isolated a coronavirus called BANAL-20-236 (B236) from Malayan horseshoe bats and found it lacks a key site in its spike protein that is present in SARS-CoV-2.
- * They compared B236's characteristics using human-derived cells and hamster infection experiments, discovering it's less pathogenic and grows slower in respiratory cells compared to SARS-CoV-2, but grows better in intestinal cells.
- * The study suggests that SC2r-CoVs like B236 may primarily replicate in the intestines rather than the respiratory system, supporting prior findings about its behavior in other models.
A primary reason for the ongoing spread of coronavirus disease 2019 (COVID-19) is the continuous acquisition of mutations by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the mechanism of acquiring mutations is not fully understood. In this study, we isolated SARS-CoV-2 from an immunocompromized patient persistently infected with Omicron strain BF.
View Article and Find Full Text PDFBackground: PlMERS-CoV is a coronavirus known to cause severe disease in humans, taxonomically classified under the subgenus Merbecovirus. Recent findings showed that the close relatives of MERS-CoV infecting vespertillionid bats (family Vespertillionidae), named NeoCoV and PDF-2180, use their hosts' ACE2 as their entry receptor, unlike the DPP4 receptor usage of MERS-CoV. Previous research suggests that this difference in receptor usage between these related viruses is a result of recombination.
View Article and Find Full Text PDFA feature of the SARS-CoV-2 Omicron subvariants BF.5 and BF.7 that recently circulated mainly in China and Japan was the high prevalence of the ORF7a: H47Y mutation, in which the 47th residue of ORF7a has been mutated from a histidine (H) to a tyrosine (Y).
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- The emergence of a new Variant of Interest, XBB.1.5, is linked to mutations from the pre-existing variant XBB.1, specifically an S486P spike mutation and a nonsense mutation in ORF8.
- Phylogenetic analysis indicates that XBB.1.5 maintains similar immune escape abilities compared to XBB.1, and structural studies reveal that the spike proteins of both variants are largely similar.
- Research involving hamsters shows that the ORF8 nonsense mutation in XBB.1.5 reduces MHC suppression and results in lower virulence in this variant compared to XBB.1.
The pandemic HIV-1, HIV-1 group M, emerged from a single spillover event of its ancestral lentivirus from a chimpanzee. During human-to-human spread worldwide, HIV-1 diversified into multiple subtypes. Here, our interdisciplinary investigation mainly sheds light on the evolutionary scenario of the viral budding system of HIV-1 subtype C (HIV-1C), a most successfully spread subtype.
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- In late 2023, the SARS-CoV-2 BA.2.86 variant emerged alongside the dominant XBB descendants like EG.5.1, distinguishing itself with over 30 mutations in its spike protein.
- Modeling showed BA.2.86 has a higher reproduction number compared to EG.5.1, suggesting it spreads more easily.
- Despite its increased spread, BA.2.86 demonstrated lower pathogenicity and replication capacity in hamsters, indicating it may be less severe, while remaining sensitive to four existing antiviral treatments.
Most SARS-CoV-2 proteins are translated from subgenomic RNAs (sgRNAs). While the majority of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. One example is the ORF3a sgRNA that also encodes ORF3c, an enigmatic 41-amino-acid peptide.
View Article and Find Full Text PDFBackground: Bats harbor various viruses without severe symptoms and act as their natural reservoirs. The tolerance of bats against viral infections is assumed to originate from the uniqueness of their immune system. However, how immune responses vary between primates and bats remains unclear.
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- Most research on SARS-CoV-2 variants has concentrated on mutations in spike proteins that influence how the virus infects and spreads.
- This study highlights that there are also significant mutations outside of the spike protein that can affect the virus's behavior.
- Specifically, the study found that certain mutations in the Omicron BA.2 variant, including one in the spike protein and another further down the gene, play crucial roles in defining its characteristics.