SARS-CoV-2 と COVID-19 に関する備忘録 Vol.19――ORF7aと抗ウイルス性自然免疫回避、コロナの“エンデミック化”で葬られる公衆衛生…etc.

SARS-CoV-2 と COVID-19 に関するメモ・備忘録

SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-γ and NK cells【nature immunology 2023年11月2日】


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA generally becomes undetectable in upper airways after a few days or weeks postinfection. Here we used a model of viral infection in macaques to address whether SARS-CoV-2 persists in the body and which mechanisms regulate its persistence. Replication-competent virus was detected in bronchioalveolar lavage (BAL) macrophages beyond 6 months postinfection. Viral propagation in BAL macrophages occurred from cell to cell and was inhibited by interferon-γ (IFN-γ). IFN-γ production was strongest in BAL NKG2r+CD8+ T cells and NKG2Alo natural killer (NK) cells and was further increased in NKG2Alo NK cells after spike protein stimulation. However, IFN-γ production was impaired in NK cells from macaques with persisting virus. Moreover, IFN-γ also enhanced the expression of major histocompatibility complex (MHC)-E on BAL macrophages, possibly inhibiting NK cell-mediated killing. Macaques with less persisting virus mounted adaptive NK cells that escaped the MHC-E-dependent inhibition. Our findings reveal an interplay between NK cells and macrophages that regulated SARS-CoV-2 persistence in macrophages and was mediated by IFN-γ.


SARS-CoV-2 ORF7a blocked autophagy flux by intervening in the fusion between autophagosome and lysosome to promote viral infection and pathogenesis【WILEY Online Library 2023年11月2日】


The coronavirus disease 2019 (COVID-19) continues to pose a major threat to public health worldwide. Although many studies have clarified the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection process, the underlying mechanisms of viral invasion and immune evasion were still unclear. This study focused on SARS-CoV-2 ORF7a (open reading frame-7a), one of the essential open reading frames (ORFs) in infection and pathogenesis. First, by analyzing its physical and chemical characteristics, SARS-CoV-2 ORF7a is an unstable hydrophobic transmembrane protein. Then, the ORF7a transmembrane domain three-dimensional crystal structure model was predicted and verified. SARS-CoV-2 ORF7a localized in the endoplasmic reticulum and participated in the autophagy-lysosome pathway via interacting with p62. In addition, we elucidated the underlying molecular mechanisms by which ORF7a intercepted autophagic flux, promoted double membrane vesicle formation, and evaded host autophagy-lysosome degradation and antiviral innate immunity. This study demonstrated that ORF7a could be a therapeutic target, and Glecaprevir may be a potential drug against SARS-CoV-2 by targeting ORF7a. A comprehensive understanding of ORF7a’s functions may contribute to developing novel therapies and clinical drugs against COVID-19.


Double-Membrane Vesicles as Platforms for Viral Replication【Cell Trends in Microbiology 2020年6月11日】


Positive-sense RNA viruses utilize host membranes to generate viral replication organelles (ROs), inducing either invaginated spherules or double-membrane vesicles (DMVs) to support viral RNA synthesis.
DMVs have emerged as a recurrent RO motif among important human pathogenic viruses. These include picornaviruses such as enteroviruses and poliovirus, hepatitis C virus, noroviruses, and coronaviruses such as Middle East respiratory syndrome (MERS)- and severe acute respiratory syndrome (SARS)-coronaviruses.
Virus-induced DMVs appear to derive from membranes of the secretory pathway and form via several membrane remodelling steps coordinated by specific viral nonstructural proteins and host factors.
Recent evidence demonstrates that DMVs are a central hub for the synthesis of viral RNA (vRNA), making them attractive targets for novel antiviral interventions.
Viruses, as obligate intracellular parasites, exploit cellular pathways and resources in a variety of fascinating ways. A striking example of this is the remodelling of intracellular membranes into specialized structures that support the replication of positive-sense ssRNA (+RNA) viruses infecting eukaryotes. These distinct forms of virus-induced structures include double-membrane vesicles (DMVs), found during viral infections as diverse and notorious as those of coronaviruses, enteroviruses, noroviruses, or hepatitis C virus. Our understanding of these DMVs has evolved over the past 15 years thanks to advances in imaging techniques and modern molecular biology tools. In this article, we review contemporary understanding of the biogenesis, structure, and function of virus-induced DMVs as well as the open questions posed by these intriguing structures.


‘Endemic’ SARS-CoV-2 and the death of public health【John Snow Project Editorial 2023年11月6日】

SARS-CoV-2 is now circulating out of control worldwide. The only major limitation on transmission is the immune environment the virus faces. The disease it causes, COVID-19, is now a risk faced by most people as part of daily life.

While some are better than others, no national or regional government is making serious efforts towards infection prevention and control, and it seems likely this laissez-faire policy will continue for the foreseeable future. The social, political, and economic movements that worked to achieve this mass infection environment can rejoice at their success.

Those schooled in public health, immunology or working on the front line of healthcare provision know we face an uncertain future, and are aware the implications of recent events stretch far beyond SARS-CoV-2. The shifts that have taken place in attitudes and public health policy will likely damage a key pillar that forms the basis of modern civilized society, one that was built over the last two centuries; the expectation of a largely uninterrupted upwards trajectory of ever-improving health and quality of life, largely driven by the reduction and elimination of infectious diseases that plagued humankind for thousands of years. In the last three years, that trajectory has reversed.

The upward trajectory of public health in the last two centuries

Control of infectious disease has historically been a priority for all societies. Quarantine has been in common use since at least the Bronze Age and has been the key method for preventing the spread of infectious diseases ever since. The word “quarantine” itself derives from the 40-day isolation period for ships and crews that was implemented in Europe during the late Middle Ages to prevent the introduction of bubonic plague epidemics into cities.

Modern public health traces its roots to the middle of the 19th century thanks to converging scientific developments in early industrial societies:

  1. The germ theory of diseases was firmly established in the mid-19th century, in particular after Louis Pasteur disproved the spontaneous generation hypothesis. If diseases spread through transmission chains between individual humans or from the environment/animals to humans, then it follows that those transmission chains can be interrupted, and the spread stopped.
  2. The science of epidemiology appeared, its birth usually associated with the 1854 Broad Street cholera outbreak in London during which the British physician John Snow identified contaminated water as the source of cholera, pointing to improved sanitation as the way to stop cholera epidemics.
  3. Vaccination technology began to develop, initially against smallpox, and the first mandatory smallpox vaccination campaigns began, starting in England in the 1850s.
  4. The early industrial era generated horrendous workplace and living conditions for working class populations living in large industrial cities, dramatically reducing life expectancy and quality of life (life expectancy at birth in key industrial cities in the middle of the 19th century was often in the low 30s or even lower2). This in turn resulted in a recognition that such environmental factors affect human health and life spans. The long and bitter struggle for workers’ rights in subsequent decades resulted in much improved working conditions, workplace safety regulations, and general sanitation, and brought sharp increases in life expectancy and quality of life, which in turn had positive impacts on productivity and wealth.
  5. Florence Nightingale reemphasized the role of ventilation in healing and preventing illness, ‘The very first canon of nursing… : keep the air he breathes as pure as the external air, without chilling him,’ a maxim that influenced building design at the time.

These trends continued in the 20th century, greatly helped by further technological and scientific advances. Many diseases – diphtheria, pertussis, hepatitis B, polio, measles, mumps, rubella, etc. – became things of the past thanks to near-universal highly effective vaccinations, while others that used to be common are no longer of such concern for highly developed countries in temperate climates – malaria, typhus, typhoid, leprosy, cholera, tuberculosis, and many others – primarily thanks to improvements in hygiene and the implementation of non-pharmaceutical measures for their containment.

Furthermore, the idea that infectious diseases should not just be reduced, but permanently eliminated altogether began to be put into practice in the second half of the 20th century on a global level, and much earlier locally. These programs were based on the obvious consideration that if an infectious agent is driven to extinction, the incalculable damage to people’s health and the overall economy by a persisting and indefinite disease burden will also be eliminated.

The ambition of local elimination grew into one of global eradication for smallpox, which was successfully eliminated from the human population in the 1970s (this had already been achieved locally in the late 19th century by some countries), after a heroic effort to find and contain the last remaining infectious individuals. The other complete success was rinderpest in cattle, globally eradicated in the early 21st century.

When the COVID-19 pandemic started, global eradication programs were very close to succeeding for two other diseases – polio and dracunculiasis. Eradication is also globally pursued for other diseases, such as yaws, and regionally for many others, e.g. lymphatic filariasis, onchocerciasis, measles and rubella. The most challenging diseases are those that have an external reservoir outside the human population, especially if they are insect borne, and in particular those carried by mosquitos. Malaria is the primary example, but despite these difficulties, eradication of malaria has been a long-standing global public health goal and elimination has been achieved in temperate regions of the globe, even though it involved the ecologically destructive widespread application of polluting chemical pesticides to reduce the populations of the vectors. Elimination is also a public goal for other insect borne diseases such as trypanosomiasis.

In parallel with pursuing maximal reduction and eventual eradication of the burden of existing endemic infectious diseases, humanity has also had to battle novel infectious diseases, which have been appearing at an increased rate over recent decades. Most of these diseases are of zoonotic origin, and the rate at which they are making the jump from wildlife to humans is accelerating, because of the increased encroachment on wildlife due to expanding human populations and physical infrastructure associated with human activity, the continued destruction of wild ecosystems that forces wild animals towards closer human contact, the booming wildlife trade, and other such trends.

Because it is much easier to stop an outbreak when it is still in its early stages of spreading through the population than to eradicate an endemic pathogen, the governing principle has been that no emerging infectious disease should be allowed to become endemic. This goal has been pursued reasonably successfully and without controversy for many decades.

The most famous newly emerging pathogens were the filoviruses (Ebola, Marburg), the SARS and MERS coronaviruses, and paramyxoviruses like Nipah. These gained fame because of their high lethality and potential for human-to-human spread, but they were merely the most notable of many examples.

Such epidemics were almost always aggressively suppressed. Usually, these were small outbreaks, and because highly pathogenic viruses such as Ebola cause very serious sickness in practically all infected people, finding and isolating the contagious individuals is a manageable task. The largest such epidemic was the 2013-16 Ebola outbreak in West Africa, when a filovirus spread widely in major urban centers for the first time. Containment required a wartime-level mobilization, but that was nevertheless achieved, even though there were nearly 30,000 infections and more than 11,000 deaths.

SARS was also contained and eradicated from the human population back in 2003-04, and the same happened every time MERS made the jump from camels to humans, as well as when there were Nipah outbreaks in Asia.

The major counterexample of a successful establishment in the human population of a novel highly pathogenic virus is HIV. HIV is a retrovirus, and as such it integrates into the host genome and is thus nearly impossible to eliminate from the body and to eradicate from the population (unless all infected individuals are identified and prevented from infecting others for the rest of their lives). However, HIV is not an example of the containment principle being voluntarily abandoned as the virus had made its zoonotic jump and established itself many decades before its eventual discovery and recognition, and long before the molecular tools that could have detected and potentially fully contained it existed.

Still, despite all these containment success stories, the emergence of a new pathogen with pandemic potential was a well understood and frequently discussed threat, although influenza viruses rather than coronaviruses were often seen as the most likely culprit. The eventual appearance of SARS-CoV-2 should therefore not have been a huge surprise, and should have been met with a full mobilization of the technical tools and fundamental public health principles developed over the previous decades.