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Infectious diseases are associated with considerable morbidity and mortality worldwide. Although human, financial, substantial, and time resources are limited, it is unknown whether such resources are used effectively in research to manage diseases. The correlation between the disability-adjusted life years to represent disease burden and number of publications as a surrogate for research activity was investigated to measure burden-adjusted research intensity for 52 infectious diseases at global and country levels. There was significantly low research intensity for paratyphoid fever and high intensity for influenza, HIV/acquired immunodeficiency syndrome, hepatitis C, and tuberculosis considering their disease burden. We identified the infectious diseases that have received the most attention from researchers and those that have been relatively disregarded. Interestingly, not all so-called neglected tropical diseases were subject to low burden-adjusted research intensity. Analysis of the intensity of infectious disease research at a country level revealed characteristic patterns. These findings provided a basis for further discussion of the more appropriate allocation of resources for research into infectious diseases.

Recent studies about the transcriptome-wide presence of RNA modifications have revealed their importance in many cellular functions. Nevertheless, information about RNA modifications in viral RNA is scarce, especially for negative-strand RNA viruses. Here we provide a catalog of RNA modifications including m1A, ac4C, m7G, inosine, and pseudouridine on RNA derived from an influenza A virus infected into A549 cells, as studied by RNA immunoprecipitation followed by deep-sequencing. Possible regions with RNA modifications were found in the negative-strand segments of viral genomic RNA. In addition, our analyses of previously published data revealed that the expression levels of the host factors for RNA modifications were affected by an infection with influenza A virus, and some of the host factors likely have a proviral effect. RNA modification is a novel aspect of host–virus interactions leading to the discovery of previously unrecognized viral pathogenicity mechanisms and has the potential to aid the development of novel antivirals.

Nonpharmaceutical and pharmaceutical public health interventions are important to mitigate the coronavirus disease 2019 (COVID-19) epidemic. However, it is still unclear how the effectiveness of these interventions changes with the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) novel variants. This simulation study utilized data from Japan and investigated how the characteristic properties of the Omicron variant, which emerged in late 2021, influence the effectiveness of public health interventions, including vaccination, the reduction of interpersonal contact, and the early isolation of infectious people. Although the short generation time of the Omicron variant increases the effectiveness of vaccination and the reduction of interpersonal contact, it decreases the effectiveness of early isolation. The latter feature may make the containment of case clusters difficult. The increase of infected children during the Omicron-dominant epidemic diminishes the effects of previously adult-targeted interventions. These findings underscore the importance of monitoring viral evolution and consequent changes in epidemiological characteristics. An assessment and adaptation of public health measures against COVID-19 are required as SARS-CoV-2 novel variants continue to emerge.

The novel variants of the SARS-CoV-2 are a great global concern for the ongoing COVID-19 pandemic. However, how the novel variants predominate and replace existing strains remains elusive. In this study, I simulated the infection spread to investigate what kinds of viral, immunological, and epidemiological factors affect the predominance of SARS-CoV-2 novel variants. The results showed that the increase of the transmissibility of the novel variant substantially enhanced the predominance probability. In addition, the increasing trend of the infection spread, the large case number of the epidemic, and the ability of immune escape of the novel variant increased the predominance probability. A small number of cases and a decreasing trend of an entire epidemic, including not only the novel variant but also earlier strains, are especially important to reduce the chance of the predominance of the novel variant and delay the process. Good control of the COVID-19 epidemic could make the disease burden small and sequester the spread of the SARS-CoV-2 novel variants.

During the COVID-19 pandemic, a large number of research papers were published, and some of them were retracted. The present study aims to reveal the characteristics of retracted papers before and during the pandemic. The study investigated 24,542,394 publications from 1999 to 2022 and analyzed the profiles of retracted papers from the perspectives of year, disease category, country, and journal. Retraction rates were generally increasing at least until 2019, and were the highest for \"Neoplasms.\" The number of publications for \"Infections\" and \"Respiratory Tract Diseases\" dramatically rose during the COVID-19 pandemic; however, the retraction rates in the two categories or of COVID-19-related papers were not especially high compared to other diseases. The association with retraction was strongest for China in most disease categories, whereas for COVID-19 papers, other countries showed higher retraction rates than China. In recent years, retracted papers have become less likely to be published in high-impact journals. The COVID-19 pandemic does not seem to affect the retractions of research papers much. We should keep monitoring retractions and analyze the effects of pandemics for better science.

COVID-19 continues to impose significant morbidity and mortality in Japan even after implementing the vaccination program. It would remain elusive if restrictions for its mitigation were to be lifted or relaxed in the future. A simulation study that explored possible vaccination coverage scenarios and changes in the intensity of nonpharmaceutical intervention restrictions was performed to assess the impact of COVID-19 based on death count. Assuming the basic reproduction number of circulating viruses was 5.0, vaccines could prevent 90% of infections and 95% of deaths, and the vaccination coverage rate was high (75%, 80%, and 90% in people aged 12-39 years, 40-59 years, ≥60 years, respectively), approximately 50 000 deaths would occur over 150 days in Japan if all restrictions were lifted. Most deaths would occur among older adults, even if their vaccination coverage was assumed to be especially high. A low vaccination coverage scenario (45%, 60%, and 80% in people aged 12-39 years, 40-59 years, ≥60 years, respectively) would require periodic implementation of strict measures even if the modified lifestyle observed in 2020 was sustained and vaccines were very effective. Some restrictions could be relaxed under high vaccination coverage. However, in the worst-case scenario where vaccines had decreased efficacy, as we have observed for the Delta variant, and people lived a relaxed lifestyle, our simulation suggests that even high vaccination coverage would occasionally require strict measures. We should carefully explore a manageable degree of restrictions and their relaxation. We will have to keep bracing for occasional surges of COVID-19 infection, which could lead to strict measures, such as those under a state of emergency. Such strategies are essential even after a wide rollout of vaccination.

We analyzed 3,184 cases of coronavirus disease in Japan and identified 61 case-clusters in healthcare and other care facilities, restaurants and bars, workplaces, and music events. We also identified 22 probable primary case-patients for the clusters; most were 20-39 years of age and presymptomatic or asymptomatic at virus transmission.

In biology, research on evolution is important to understand the significance of genetic mutation. When there is a significantly beneficial mutation, a population of species with the mutation prospers and predominates, in a process called “selective sweep.” However, there are few methods that can find such a mutation causing selective sweep from genetic data. Genetic mutations play a central role in evolution. For a significantly beneficial mutation, a one-time mutation event suffices for the species to prosper and predominate through the process called “monophyletic selective sweep.” However, existing methods that rely on counting the number of mutation events to detect selection are unable to find such a mutation in selective sweep. We here introduce a method to detect mutations at the single amino acid/nucleotide level that could be responsible for monophyletic selective sweep evolution. The method identifies a genetic signature associated with selective sweep using the population genetic test statistic Tajima’s D . We applied the algorithm to ebolavirus, influenza A virus, and severe acute respiratory syndrome coronavirus 2 to identify known biologically significant mutations and unrecognized mutations associated with potential selective sweep. The method can detect beneficial mutations, possibly leading to discovery of previously unknown biological functions and mechanisms related to those mutations. IMPORTANCE In biology, research on evolution is important to understand the significance of genetic mutation. When there is a significantly beneficial mutation, a population of species with the mutation prospers and predominates, in a process called “selective sweep.” However, there are few methods that can find such a mutation causing selective sweep from genetic data. We here introduce a novel method to detect such mutations. Applying the method to the genomes of ebolavirus, influenza viruses, and the novel coronavirus, we detected known biologically significant mutations and identified mutations the importance of which is previously unrecognized. The method can deepen our understanding of molecular and evolutionary biology.