Clinical evidence that the pandemic from 1889 to 1891 commonly called the Russian flu might have been an earlier coronavirus pandemic

Development of Primer Panels for Whole-Genome Amplification and Sequencing of Human Seasonal Coronaviruses: hCoV-OC43, hCoV-HKU1, hCoV-229E, and hCoV-NL63

Human seasonal coronaviruses (hCoVs) are a group of viruses that affect the upper respiratory tract. While seasonal patterns and the annual variability of predominant hCoV species are well-documented, their genetic and species diversity in St. Petersburg and across Russia remains largely unexplored. In this study, we developed a two-pool, long-amplicon (900-1100 bp) PCR primer panel for the whole-genome sequencing of four seasonal hCoV species. The panel was validated using nasopharyngeal swab samples collected within the Global Influenza Hospital Surveillance Network (GIHSN) project. Over a period of six epidemiological seasons from 2017 to 2023, we retrospectively analyzed 14,704 nasopharyngeal swabs collected from patients hospitalized in St. Petersburg clinics. Of these samples, 5010 (34.07%) tested positive for respiratory viruses, with 424 (2.88% of all samples) identified as seasonal human coronaviruses. The assessment of species diversity showed that predominant hCoV species alternate between seasons. Whole-genome sequences for 85 seasonal human coronaviruses (hCoVs) with >70% genome coverage were obtained, including 23 hCoV-OC43, 6 hCoV-HKU1, 39 hCoV-229E, and 17 hCoV-NL63. These represent the first near-complete genomes of seasonal hCoVs from the Russian Federation, addressing a significant gap in the genomic epidemiology of these viruses. A detailed phylogenetic analysis of the sequenced genomes was conducted, highlighting the emergence of hCoV-229E subclades 7b.1 and 7b.2, which carry numerous substitutions in the Spike protein. Additionally, we sequenced a historical hCoV-229E isolate collected in the USSR in 1979, the oldest sequenced 229E virus from Eurasia, and demonstrated that it belongs to Genotype 2. The newly developed PCR-based sequencing protocol for seasonal hCoVs is straightforward and well-suited for genomic surveillance, providing a valuable tool to enhance our understanding of the genetic diversity of human seasonal coronaviruses.

The health and demographic impacts of the "Russian flu" pandemic in Switzerland in 1889/1890 and in the years thereafter

Our study aims to enhance future pandemic preparedness by leveraging insights from historical pandemics, focusing on the multidimensional analysis of past outbreaks. In this study, we digitised and analysed for the first time aggregated mortality and morbidity data series from the Russian flu in Switzerland in 1889/1890 and subsequent years to assess its comprehensive impact. The strongest effects were observed in January 1890, showing significant monthly excess mortality from all causes compared to the preceding five years (58.9%, 95% CI 36.6 to 81.0). Even though the whole of Switzerland was affected, the impact varied regionally due to ecological variations. Deaths from other conditions such as tuberculosis and heart disease also increased during this period. A significant drop in birth occurred 9 months later, in the autumn of 1890. Morbidity estimates by physicians suggest that around 60% of the Swiss population fell ill, with regional discrepancies and earlier outbreaks among postal workers (1-2 weeks earlier than the rest of the population). A subsequent spike in all-cause excess and influenza mortality was recorded in January 1894 but more localized than in 1890. Our findings show no cross-protection between the 1890 and 1894 outbreaks.

Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness

The COVID-19 pandemic highlights the ongoing risk of zoonotic transmission of coronaviruses to global health. To prepare for future pandemics, it is essential to develop effective antivirals targeting a broad range of coronaviruses. Targeting the essential and clinically validated coronavirus main protease (Mpro), we constructed a structurally diverse Mpro panel by clustering all known coronavirus sequences by Mpro active site sequence similarity. Through screening, we identified a potent covalent inhibitor that engaged the catalytic cysteine of SARS-CoV-2 Mpro and used structure-based medicinal chemistry to develop compounds in the pyrazolopyrimidine sulfone series that exhibit submicromolar activity against multiple Mpro homologues. Additionally, we solved the first X-ray cocrystal structure of Mpro from the human-infecting OC43 coronavirus, providing insights into potency differences among compound-target pairs. Overall, the chemical compounds described in this study serve as starting points for the development of antivirals with broad-spectrum activity, enhancing our preparedness for emerging human-infecting coronaviruses.

Will COVID-19 become mild, like a cold?

Several recent studies conclude that an increase in the pathogenicity of SARS-CoV-2 cannot be ruled out. However, it should be noted that SARS-CoV-2 is a 'direct' respiratory virus - meaning it is usually spread by the respiratory route but does not routinely pass through the lymphatics like measles and smallpox. Providing its tropism does not change, it will be unique if its pathogenicity does not decrease until it becomes similar to common cold viruses. Ewald noted in the 1980s that respiratory viruses may evolve mildness because their spread benefits from the mobility of their hosts. This review examines factors that usually lower respiratory viruses' severity, including heat sensitivity (which limits replication in the warmer lungs) and changes to the virus's surface proteins. Other factors may, however, increase pathogenicity, such as replication in the lymphatic system and spreading via solid surfaces or faecal matter. Furthermore, human activities and political events could increase the harmfulness of SARS-CoV-2, including the following: large-scale testing, especially when the results are delayed; transmission in settings where people are close together and not free to move around; poor hygiene facilities; and social, political, or cultural influences that encourage sick individuals to remain active, including crises such as wars. If we can avoid these eventualities, SARS-CoV-2 is likely to evolve to be milder, although the timescale is uncertain. Observations of influenza-like pandemics suggest it may take around two decades for COVID-19 to become as mild as seasonal colds.

One hundred years of influenza A evolution

Leveraging the simplicity of nucleotide mismatch distributions, we provide an intuitive window into the evolution of the human influenza A 'nonstructural' (NS) gene segment. In an analysis suggested by the eminent Danish biologist Freddy B. Christiansen, we illustrate the existence of a continuous genetic "backbone" of influenza A NS sequences, steadily increasing in nucleotide distance to the 1918 root over more than a century. The 2009 influenza A/H1N1 pandemic represents a clear departure from this enduring genetic backbone. Utilizing nucleotide distance maps and phylogenetic analyses, we illustrate remaining uncertainties regarding the origin of the 2009 pandemic, highlighting the complexity of influenza evolution. The NS segment is interesting precisely because it experiences less pervasive positive selection, and departs less strongly from neutral evolution than e.g. the HA antigen. Consequently, sudden deviations from neutral diversification can indicate changes in other genes via the hitchhiking effect. Our approach employs two measures based on nucleotide mismatch counts to analyze the evolutionary dynamics of the NS gene segment. The rooted Hamming map of distances between a reference sequence and all other sequences over time, and the unrooted temporal Hamming distribution which captures the distribution of genotypic distances between simultaneously circulating viruses, thereby revealing patterns of nucleotide diversity and epi-evolutionary dynamics.

Transcriptome dynamics of the BHK21 cell line in response to human coronavirus OC43 infection

The progress of viral infection involves numerous transcriptional regulatory events. The identification of the newly synthesized transcripts helps us to understand the replication mechanisms and pathogenesis of the virus. Here, we utilized a time-resolved technique called metabolic RNA labeling approach called thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) to differentially elucidate the levels of steady-state and newly synthesized RNAs of BHK21 cell line in response to human coronavirus OC43 (HCoV-OC43) infection. Our results showed that the Wnt/β-catenin signaling pathway was significantly enriched with the newly synthesized transcripts of BHK21 cell line in response to HCoV-OC43 infection. Moreover, inhibition of the Wnt pathway promoted viral replication in the early stage of infection, but inhibited it in the later stage of infection. Furthermore, remdesivir inhibits the upregulation of the Wnt/β-catenin signaling pathway induced by early infection with HCoV-OC43. Collectively, our study showed the diverse roles of Wnt/β-catenin pathway at different stages of HCoV-OC43 infection, suggesting a potential target for the antiviral treatment. In addition, although infection with HCoV-OC43 induces cytopathic effects in BHK21 cells, inhibiting apoptosis does not affect the intracellular replication of the virus. Monitoring newly synthesized RNA based on such time-resolved approach is a highly promising method for studying the mechanism of viral infections.

Mild Primary or Breakthrough SARS-CoV-2 Infection Promotes Autoantibody Production in Individuals with and without Neuro-PASC

Patients with long COVID can develop humoral autoimmunity after severe acute SARS-CoV-2 infection. However, whether similar increases in autoantibody responses occur after mild infection and whether vaccination prior to SARS-CoV-2 breakthrough infection can limit autoantibody responses is unknown. In this study, we demonstrate that mild SARS-CoV-2 infection increases autoantibodies associated with rheumatic autoimmune diseases and diabetes in most individuals, regardless of vaccination status prior to infection. However, patients with long COVID and persistent neurologic and fatigue symptoms (neuro-PASC) have substantially higher autoantibody responses than convalescent control subjects at an average of 8 mo postinfection. Furthermore, high titers of systemic lupus erythematosus- and CNS-associated autoantibodies in patients with neuro-PASC are associated with impaired cognitive performance and greater symptom severity. In summary, we found that mild SARS-CoV-2 primary and breakthrough infections can induce persistent humoral autoimmunity in both patients with neuro-PASC and healthy COVID convalescents, suggesting that a reappraisal of mitigation strategies against SARS-CoV-2 is warranted to prevent transmission and potential development of autoimmunity.

Differences and similarities between innate immune evasion strategies of human coronaviruses

So far, seven coronaviruses have emerged in humans. Four recurring endemic coronaviruses cause mild respiratory symptoms. Infections with epidemic Middle East respiratory syndrome-related coronavirus or severe acute respiratory syndrome coronavirus (SARS-CoV)-1 are associated with high mortality rates. SARS-CoV-2 is the causative agent of the coronavirus disease 2019 pandemic. To establish an infection, coronaviruses evade restriction by human innate immune defenses, such as the interferon system, autophagy and the inflammasome. Here, we review similar and distinct innate immune manipulation strategies employed by the seven human coronaviruses. We further discuss the impact on pathogenesis, zoonotic emergence and adaptation. Understanding the nature of the interplay between endemic/epidemic/pandemic coronaviruses and host defenses may help to better assess the pandemic potential of emerging coronaviruses.

A systematic review on the incidence of influenza viruses in wastewater matrices: Implications for public health

Influenza viruses pose a significant public health threat, necessitating comprehensive surveillance strategies to enhance early detection and preventive measures. This systematic review investigates the incidence of influenza viruses in wastewater matrices, aiming to elucidate the potential implications for public health. The study synthesizes existing literature, employing rigorous inclusion criteria to identify relevant studies conducted globally. The essence of the problem lies in the gaps of traditional surveillance methods, which often rely on clinical data and may underestimate the true prevalence of influenza within communities. Wastewater-based epidemiology offers a novel approach to supplementing these conventional methods, providing a broader and more representative assessment of viral circulation. This review systematically examines the methodologies employed in the selected studies, including virus concentration techniques and molecular detection methods, to establish a standardized framework for future research. Our findings reveal a consistent presence of influenza viruses in diverse wastewater matrices across different geographic locations and seasons. Recommendations for future research include the standardization of sampling protocols, improvement of virus concentration methods, and the integration of wastewater surveillance into existing public health frameworks. In conclusion, this systematic review contributes to the understanding of influenza dynamics in wastewater matrices, offering valuable insights for public health practitioners and policymakers. Implementation of wastewater surveillance alongside traditional methods can enhance the resilience of public health systems and better prepare communities for the challenges posed by influenza outbreaks.

Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes

Betacoronaviruses are a genus within the Coronaviridae family of RNA viruses. They are capable of infecting vertebrates and causing epidemics as well as global pandemics in humans. Mitigating the threat posed by Betacoronaviruses requires an understanding of their molecular diversity. The development of novel antivirals hinges on understanding the key regulatory elements within the viral RNA genomes, in particular the 5'-proximal region, which is pivotal for viral protein synthesis. Using a combination of cryo-electron microscopy, atomic force microscopy, chemical probing, and computational modeling, we determined the structures of 5'-proximal regions in RNA genomes of Betacoronaviruses from four subgenera: OC43-CoV, SARS-CoV-2, MERS-CoV, and Rousettus bat-CoV. We obtained cryo-electron microscopy maps and determined atomic-resolution models for the stem-loop-5 (SL5) region at the translation start site and found that despite low sequence similarity and variable length of the helical elements it exhibits a remarkable structural conservation. Atomic force microscopy imaging revealed a common domain organization and a dynamic arrangement of structural elements connected with flexible linkers across all four Betacoronavirus subgenera. Together, these results reveal common features of a critical regulatory region shared between different Betacoronavirus RNA genomes, which may allow targeting of these RNAs by broad-spectrum antiviral therapeutics.

An Unwanted but Long-Known Company: Post-Viral Symptoms in the Context of Past Pandemics in Switzerland (and Beyond)

Objectives: Some people do not fully recover from an acute viral infection and experience persistent symptoms or incomplete recovery for months or even years. This is not unique to the SARS-CoV-2 virus and history shows that post-viral conditions like post COVID-19 condition, also referred to as Long Covid, are not new. In particular, during and after pandemics caused by respiratory viruses in which large parts of the population were infected or exposed, professional and public attention was increased, not least because of the large number of people affected. Methods: Given the current relevance of the topic, this article aims to narratively review and summarize the literature on post-viral symptoms during past pandemics and to supplement and illustrate it with Swiss examples from the pandemics of 1890, 1918-1920 and later. Results: Post-viral diseases were an increasingly emphasised health topic during and after past pandemics triggered by respiratory infections over the last 150 years. Conclusion: In the next pandemic, it should not be surprising that post-viral conditions will again play a role, and pandemic plans should reflect this.

The post-COVID-19 population has a high prevalence of cross-reactive antibodies to spikes from all Orthocoronavirinae genera

IMPORTANCE

As demonstrated by severe acute respiratory syndrome coronavirus 2, coronaviruses pose a significant pandemic threat. Here, we show that coronavirus disease 2019 mRNA vaccination can induce significant levels of cross-reactive antibodies against diverse coronavirus spike proteins. While these antibodies are binding antibodies that likely have little neutralization capacity and while their contribution to cross-protection is unclear, it is possible that they may play a role in protection from progression to severe disease with novel coronaviruses.

Determinants of species-specific utilization of ACE2 by human and animal coronaviruses

Utilization of human ACE2 allowed several bat coronaviruses (CoVs), including the causative agent of COVID-19, to infect humans directly or via intermediate hosts. However, the determinants of species-specific differences in ACE2 usage and the frequency of the ability of animal CoVs to use human ACE2 are poorly understood. Here we applied VSV pseudoviruses to analyze the ability of Spike proteins from 26 human or animal CoVs to use ACE2 receptors across nine reservoir, potential intermediate and human hosts. We show that SARS-CoV-2 Omicron variants evolved towards more efficient ACE2 usage but mutation of R493Q in BA.4/5 and XBB Spike proteins disrupts utilization of ACE2 from Greater horseshoe bats. Variations in ACE2 residues 31, 41 and 354 govern species-specific differences in usage by coronaviral Spike proteins. Mutation of T403R allows the RaTG13 bat CoV Spike to efficiently use all ACE2 orthologs for viral entry. Sera from COVID-19 vaccinated individuals neutralize the Spike proteins of various bat Sarbecoviruses. Our results define determinants of ACE2 receptor usage of diverse CoVs and suggest that COVID-19 vaccination may protect against future zoonoses of bat coronaviruses.

A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus

The repeated emergence of zoonotic human betacoronaviruses (β-CoVs) dictates the need for broad therapeutics and conserved epitope targets for countermeasure design. Middle East respiratory syndrome (MERS)-related coronaviruses (CoVs) remain a pressing concern for global health preparedness. Using metagenomic sequence data and CoV reverse genetics, we recovered a full-length wild-type MERS-like BtCoV/li/GD/2014-422 (BtCoV-422) recombinant virus, as well as two reporter viruses, and evaluated their human emergence potential and susceptibility to currently available countermeasures. Similar to MERS-CoV, BtCoV-422 efficiently used human and other mammalian dipeptidyl peptidase protein 4 (DPP4) proteins as entry receptors and an alternative DPP4-independent infection route in the presence of exogenous proteases. BtCoV-422 also replicated efficiently in primary human airway, lung endothelial, and fibroblast cells, although less efficiently than MERS-CoV. However, BtCoV-422 shows minor signs of infection in 288/330 human DPP4 transgenic mice. Several broad CoV antivirals, including nucleoside analogs and 3C-like/Mpro protease inhibitors, demonstrated potent inhibition against BtCoV-422 in vitro. Serum from mice that received a MERS-CoV mRNA vaccine showed reduced neutralizing activity against BtCoV-422. Although most MERS-CoV-neutralizing monoclonal antibodies (mAbs) had limited activity, one anti-MERS receptor binding domain mAb, JC57-11, neutralized BtCoV-422 potently. A cryo-electron microscopy structure of JC57-11 in complex with BtCoV-422 spike protein revealed the mechanism of cross-neutralization involving occlusion of the DPP4 binding site, highlighting its potential as a broadly neutralizing mAb for group 2c CoVs that use DPP4 as a receptor. These studies provide critical insights into MERS-like CoVs and provide candidates for countermeasure development.

An extended period of elevated influenza mortality risk follows the main waves of influenza pandemics

Understanding the extent and evolution of pandemic-induced mortality risk is critical given its wide-ranging impacts on population health and socioeconomic outcomes. We examine empirically the persistence and scale of influenza mortality risk following the main waves of influenza pandemics, a quantitative analysis of which is required to understand the true scale of pandemic-induced risk. We provide evidence from municipal public health records that multiple recurrent outbreaks followed the main waves of the 1918-19 pandemic in eight large cities in the UK, a pattern we confirm using data for the same period in the US and data for multiple influenza pandemics during the period 1838-2000 in England and Wales. To estimate the persistence and scale of latent post-pandemic influenza mortality risk, we model the stochastic process of mortality rates as a sequence of bounded Pareto distributions whose tail indexes evolves over time. Consistently across pandemics and locations, we find that influenza mortality risk remains elevated for around two decades after the main pandemic waves before more rapid convergence to background influenza mortality, amplifying the impact of pandemics. Despite the commonality in duration, there is heterogeneity in the persistence and scale of risk across the cities, suggesting effects of both immunity and socioeconomic conditions.

Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T-cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2

Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but the T-cell response to seasonal coronaviruses remains largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal coronavirus OC43. We identified MHC-bound peptides derived from each of the viral structural proteins (spike, nucleoprotein, hemagglutinin-esterase, membrane, and envelope) as well as non-structural proteins nsp3, nsp5, nsp6, and nsp12. Eighty MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. Fewer and less abundant MHC-I bound OC43-derived peptides were observed, possibly due to MHC-I downregulation induced by OC43 infection. The MHC-II peptides elicited low-abundance recall T-cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T-cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T-cell lines. Among the validated epitopes, spike protein S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. Nucleoprotein N54-68 and hemagglutinin-esterase HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow CD4 T-cell cross-reactivity after infection or vaccination, and to guide selection of epitopes for inclusion in pan-coronavirus vaccines.

Viral infections at the animal-human interface-Learning lessons from the SARS-CoV-2 pandemic

This Lilliput explores the current epidemiological and virological arguments for a zoonotic origin of the COVID-19 pandemic. While the role of bats, pangolins and racoon dogs as viral reservoirs has not yet been proven, a spill-over of a coronavirus infection from animals into humans at the Huanan food market in Wuhan has a much greater plausibility than alternative hypotheses such as a laboratory virus escape, deliberate genetic engineering or introduction by cold chain food products. This Lilliput highlights the dynamic nature of the animal-human interface for viral cross-infections from humans into feral white tail deer or farmed minks (reverse zoonosis). Surveillance of viral infections at the animal-human interface is an urgent task since live animal markets are not the only risks for future viral spill-overs. Climate change will induce animal migration which leads to viral exchanges between animal species that have not met in the past. Environmental change and deforestation will also increase contact between animals and humans. Developing an early warning system for emerging viral infections becomes thus a societal necessity not only for human but also for animal and environmental health (One Health concept). Microbiologists have developed tools ranging from virome analysis in key suspects such as viral reservoirs (bats, wild game animals, bushmeat) and in humans exposed to wild animals, to wastewater analysis to detect known and unknown viruses circulating in the human population and sentinel studies in animal-exposed patients with fever. Criteria need to be developed to assess the virulence and transmissibility of zoonotic viruses. An early virus warning system is costly and will need political lobbying. The accelerating number of viral infections with pandemic potential over the last decades should provide the public pressure to extend pandemic preparedness for the inclusion of early viral alert systems.

Influenza pandemics and macroeconomic fluctuations 1871-2016

This paper documents the short-run macroeconomic impacts of influenza pandemics across 16 countries spanning 1871-2016 using the Jordà-Schularick-Taylor Macrohistory Database and the Human Mortality Database. We find pandemic-induced mortality contributed meaningfully to business cycle fluctuations in the post 1870 era. We identify negative causal impacts on the cyclical component of GDP using pandemics to instrument for working-age mortality. The analysis of short-run economic outcomes extends literature dominated by long-run economic growth outcomes and case studies of several specific health shocks such as the Black Death, Spanish Flu or COVID-19. Our findings illustrate that less catastrophic pandemics still have important economic implications.

Complement and COVID-19: Three years on, what we know, what we don't know, and what we ought to know

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus was identified in China in 2019 as the causative agent of COVID-19, and quickly spread throughout the world, causing over 7 million deaths, of which 2 million occurred prior to the introduction of the first vaccine. In the following discussion, while recognising that complement is just one of many players in COVID-19, we focus on the relationship between complement and COVID-19 disease, with limited digression into directly-related areas such as the relationship between complement, kinin release, and coagulation. Prior to the 2019 COVID-19 outbreak, an important role for complement in coronavirus diseases had been established. Subsequently, multiple investigations of patients with COVID-19 confirmed that complement dysregulation is likely to be a major driver of disease pathology, in some, if not all, patients. These data fuelled evaluation of many complement-directed therapeutic agents in small patient cohorts, with claims of significant beneficial effect. As yet, these early results have not been reflected in larger clinical trials, posing questions such as who to treat, appropriate time to treat, duration of treatment, and optimal target for treatment. While significant control of the pandemic has been achieved through a global scientific and medical effort to comprehend the etiology of the disease, through extensive SARS-CoV-2 testing and quarantine measures, through vaccine development, and through improved therapy, possibly aided by attenuation of the dominant strains, it is not yet over. In this review, we summarise complement-relevant literature, emphasise its main conclusions, and formulate a hypothesis for complement involvement in COVID-19. Based on this we make suggestions as to how any future outbreak might be better managed in order to minimise impact on patients.

Reinfections and Cross-Protection in the 1918/19 Influenza Pandemic: Revisiting a Survey Among Male and Female Factory Workers

Objectives: The COVID-19 pandemic highlights questions regarding reinfections and immunity resulting from vaccination and/or previous illness. Studies addressing related questions for historical pandemics are limited. Methods: We revisit an unnoticed archival source on the 1918/19 influenza pandemic. We analysed individual responses to a medical survey completed by an entire factory workforce in Western Switzerland in 1919. Results: Among the total of n = 820 factory workers, 50.2% reported influenza-related illness during the pandemic, the majority of whom reported severe illness. Among male workers 47.4% reported an illness vs. 58.5% of female workers, although this might be explained by varied age distribution for each sex (median age was 31 years old for men, vs. 22 years old for females). Among those who reported illness, 15.3% reported reinfections. Reinfection rates increased across the three pandemic waves. The majority of subsequent infections were reported to be as severe as the first infection, if not more. Illness during the first wave, in the summer of 1918, was associated with a 35.9% (95%CI, 15.7-51.1) protective effect against reinfections during later waves. Conclusion: Our study draws attention to a forgotten constant between multi-wave pandemics triggered by respiratory viruses: Reinfection and cross-protection have been and continue to be a key topic for health authorities and physicians in pandemics, becoming increasingly important as the number of waves increases.

Autoantibody production is enhanced after mild SARS-CoV-2 infection despite vaccination in individuals with and without long COVID

Long COVID patients who experienced severe acute SARS-CoV-2 infection can present with humoral autoimmunity. However, whether mild SARS-CoV-2 infection increases autoantibody responses and whether vaccination can decrease autoimmunity in long COVID patients is unknown. Here, we demonstrate that mild SARS-CoV-2 infection increases autoantibodies associated with systemic lupus erythematosus (SLE) and inflammatory myopathies in long COVID patients with persistent neurologic symptoms to a greater extent than COVID convalescent controls at 8 months post-infection. Furthermore, high titers of SLE-associated autoantibodies in long COVID patients are associated with impaired cognitive performance and greater symptom severity, and subsequent vaccination/booster does not decrease autoantibody titers. In summary, we found that mild SARS-CoV-2 infection can induce persistent humoral autoimmunity in both long COVID patients and healthy COVID convalescents, suggesting that a reappraisal of vaccination and mitigation strategies is warranted.

Cross-species transmission of coronaviruses with a focus on severe acute respiratory syndrome coronavirus 2 infection in animals: a review for the veterinary practitioner

AbstractIn 2019 a novel coronavirus termed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged from an unidentified source and spread rapidly among humans worldwide. While many human infections are mild, some result in severe clinical disease that in a small proportion of infected people is fatal. The pandemic spread of SARS-CoV-2 has been facilitated by efficient human-to-human transmission of the virus, with no data to indicate that animals contributed to this global health crisis. However, a range of domesticated and wild animals are also susceptible to SARS-CoV-2 infection under both experimental and natural conditions. Humans are presumed to be the source of most animal infections thus far, although natural transmission between mink and between free-ranging deer has occurred, and occasional natural transmission between cats cannot be fully excluded. Considering the ongoing circulation of the virus among people, together with its capacity to evolve through mutation and recombination, the risk of the emergence of animal-adapted variants is not negligible. If such variants remain infectious to humans, this could lead to the establishment of an animal reservoir for the virus, which would complicate control efforts. As such, minimising human-to-animal transmission of SARS-CoV-2 should be considered as part of infection control efforts. The aim of this review is to summarise what is currently known about the species specificity of animal coronaviruses, with an emphasis on SARS-CoV-2, in the broader context of factors that facilitate cross-species transmission of viruses.

Monkeypox virus: A review

While monkeypox was previously found in Africa, the bulk of occurrences in the present outbreak are being reported in many countries. It is not yet known how this outbreak began, and as the COVID-19 crisis begins to abate, numerous nations throughout the world are now contending with a novel outbreak. Monkeypox is a transmissible virus between animals and humans, belonging to the Orthopoxvirus genus of the Poxviridae family. In the 1970s, cases of monkeypox began increasing due to the cessation of vaccination against smallpox, which drew international attention. The virus was named monkeypox because it was first observed in macaque monkeys. It is thought to be transmitted by several different rodents and small mammals, though the origin of the virus is not known. Monkeypox, while occasionally transmitted from one human to another, can be disseminated through the inhalation of droplets or through contact with the skin lesions of an infected individual. Unfortunately, there is no definitive cure for monkeypox; however, supportive care can be offered to ameliorate its symptoms. In severe cases, medications like tecovirimat may be administered. However, there are no established guidelines for symptom management in monkeypox cases. In this article we have discussed about different aspects of monkeypox including viral structure, transmission, replication, clinical manifestations, vaccination, treatment and current prevalence in the world to understand it better and give insight to the future studies.

Health disparities in past influenza pandemics: A scoping review of the literature

Objective

The COVID-19 pandemic has exacerbated existing health disparities. To provide a historical perspective on health disparities for pandemic acute respiratory viruses, we conducted a scoping review of the public health literature of health disparities in influenza outcomes during the 1918, 1957, 1968, and 2009 influenza pandemics.

Methods

We searched for articles examining socioeconomic or racial/ethnic disparities in any population, examining any influenza-related outcome (e.g., incidence, hospitalizations, mortality), during the 1918, 1957, 1968, and 2009 influenza pandemics. We conducted a structured search of English-written articles in PubMed supplemented by a snowball of articles meeting inclusion criteria.

Results

A total of 29 articles met inclusion criteria, all but one focusing exclusively on the 1918 or 2009 pandemics. Individuals of low socioeconomic status, or living in low socioeconomic status areas, experienced higher incidence, hospitalizations, and mortality in the 1918 and 2009 pandemics. There were conflicting results regarding racial/ethnic disparities during the 1918 pandemic, with differences in magnitude and direction by outcome, potentially due to issues in data quality by race/ethnicity. Racial/ethnic minorities had generally higher incidence, mortality, and hospitalization rates in the 1957 and 2009 pandemics.

Conclusion

Individuals of low socioeconomic status and racial/ethnic minorities have historically experienced worse influenza outcomes during pandemics. These historical patterns can inform current research to understand disparities in the ongoing COVID-19 pandemic and future pandemics.

Evaluating the Virology and Evolution of Seasonal Human Coronaviruses Associated with the Common Cold in the COVID-19 Era

Approximately 15-30% of all cases of the common cold are due to human coronavirus infections. More recently, the emergence of the more severe respiratory coronaviruses, SARS-CoV and MERS-CoV, have highlighted the increased pathogenic potential of emergent coronaviruses. Lastly, the current emergence of SARS-CoV-2 has demonstrated not only the potential for significant disease caused by emerging coronaviruses, but also the capacity of novel coronaviruses to promote pandemic spread. Largely driven by the global response to the COVID-19 pandemic, significant research in coronavirus biology has led to advances in our understanding of these viruses. In this review, we evaluate the virology, emergence, and evolution of the four endemic coronaviruses associated with the common cold, their relationship to pandemic SARS-CoV-2, and discuss the potential for future emergent human coronaviruses.

The health of influenza surveillance and pandemic preparedness in the wake of the COVID-19 pandemic

The COVID-19 pandemic is the first to have emerged when Next Generation Sequencing was readily available and it has played the major role in following evolution of the causative agent, Severe Acute Respiratory Syndrome Coronavirus 2. Response to the pandemic was greatly facilitated though use of existing influenza surveillance networks: World Health Organization (WHO) Global Influenza Surveillance and Response System (GISRS), focussing largely on human influenza, and the OFFLU network of expertise on avian influenza established by the Food and Agricultural Organization of the United Nations (FAO) and the World Organization for Animal Health (WOAH). Data collection/deposition platforms associated with these networks, notably WHO's FluNet and the Global Initiative on Sharing All Influenza Data (GISAID) were/are being used intensely. Measures introduced to combat COVID-19 resulted in greatly decreased circulation of human seasonal influenza viruses for approximately 2 years, but circulation continued in the animal sector with an upsurge in the spread of highly pathogenic avian influenza subtype H5N1 with large numbers of wild bird deaths, culling of many poultry flocks and sporadic spill over into mammalian species, including humans, thereby increasing pandemic risk potential. While there are proposals/implementations to extend use of GISRS and GISAID to other infectious disease agents (e.g. Respiratory Syncytial Virus and Monkeypox), there is need to ensure that influenza surveillance is maintained and improved in both human and animal sectors in a sustainable manner to be truly prepared (early detection) for the next influenza pandemic.

Candidate historical events for the emergence of Human Coronavirus OC43: A critical reassessment of the molecular evidence

The "Russian Influenza"-coronavirus theory (RICT) proposes that the pandemic of 1889-1892, conventionally regarded as an influenza pandemic, was caused by the emergence of human coronavirus OC43 (HCoV-OC43) as a zoonosis of bovine coronavirus (BCoV). RICT is based on a Bayesian phylogenetic calculation of the date of the most recent common ancestor (MRCA) of HCoV-OC43 and BCoV. The theory also draws on comparison of both symptoms and some epidemiological parameters of the best studied coronavirus pandemic, i.e. COVID-19, with those reported in 1889-1892. The case is completed with circumstantial evidence involving a panzoonotic among cattle in the decade prior to the "Russian Influenza", with characteristics suggesting it may have been caused by BCoV. In this paper, we review the Bayesian phylogenetic evidence for RICT, replicating previous studies and adding our own, in each case critically reviewing the suitability of the datasets used and the parameters applied. We conclude that the most probable date for the MRCA of HCoV-OC43 and BCoV is 1898-1902. This is a decade too late for compatibility with RICT but happens to coincide with another serious outbreak of respiratory illness, reported in both the USA and the UK, in the winter of 1899-1900.

Encephalitis lethargica. What is still wrong?

Encephalitis lethargica developed in epidemic from 1919 to 1926 in Europe and throughout the world. From the clinical point of view, the disturbances of consciousness and alertness and the possible outcomes of a postencephalitic Parkinsonism has attracted much attention. For a long time, it was thought that such a disease may still occur sporadically. In this review, the authors examined historical and current pictures of epidemics that may be related to Encephalitis lethargica. The previous Nona and Russian Influenza exhibited frequent neurological symptoms. The Spanish flu, formerly related to Encephalitis lethargica, would appear an epidemic that had its development in a partially overlapping period. The current pandemic linked to COVID-19 sometimes has aspects that can resemble Encephalitis lethargica. Based on historical analysis and the more recent immunological data, it could be suggested that Encephalitis lethargica was an autoimmune encephalitis that arose in a secondary form to the action of a viral agent. It cannot be ruled out that this agent was a coronavirus. From the nosological point of view, the term Encephalitis lethargica should be abolished in designating autoimmune encephalitis pictures that run sporadically.

Olfactory dysfunction in COVID-19: new insights into the underlying mechanisms

The mechanisms of olfactory dysfunction in COVID-19 are still unclear. In this review, we examine potential mechanisms that may explain why the sense of smell is lost or altered. Among the current hypotheses, the most plausible is that death of infected support cells in the olfactory epithelium causes, besides altered composition of the mucus, retraction of the cilia on olfactory receptor neurons, possibly because of the lack of support cell-derived glucose in the mucus, which powers olfactory signal transduction within the cilia. This mechanism is consistent with the rapid loss of smell with COVID-19, and its rapid recovery after the regeneration of support cells. Host immune responses that cause downregulation of genes involved in olfactory signal transduction occur too late to trigger anosmia, but may contribute to the duration of the olfactory dysfunction.

A Proposal to Refer to Four Coronaviruses of Limited Human Virulence "Common Cold Coronaviruses"

We propose the term "common cold coronaviruses," or ccCoV, to describe the four human coronaviruses commonly associated with upper respiratory tract disease - coronaviruses 229E, OC43, NL63, and HKU1. This will differentiate these previously described coronaviruses from those causing more severe disease in humans - including the viruses severe acute respiraotry syndrome coronavirus (SARS-CoV), the Middle East respiratory syndrome coronavirus (MERS-CoV) and SARS-CoV-2.

Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2

Seasonal "common-cold" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S 903-917 presented by DPA1*01:03/DPB1*04:01 and S 1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N 54-68 and HE 128-142 presented by DRB1*15:01 and HE 259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines.

Author Summary

There is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.

Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats

Public health emergencies like SARS, MERS, and COVID-19 have prioritized surveillance of zoonotic coronaviruses, resulting in extensive genomic characterization of coronavirus diversity in bats. Sequencing viral genomes directly from animal specimens remains a laboratory challenge, however, and most bat coronaviruses have been characterized solely by PCR amplification of small regions from the best-conserved gene. This has resulted in limited phylogenetic resolution and left viral genetic factors relevant to threat assessment undescribed. In this study, we evaluated whether a technique called hybridization probe capture can achieve more extensive genome recovery from surveillance specimens. Using a custom panel of 20,000 probes, we captured and sequenced coronavirus genomic material in 21 swab specimens collected from bats in the Democratic Republic of the Congo. For 15 of these specimens, probe capture recovered more genome sequence than had been previously generated with standard amplicon sequencing protocols, providing a median 6.1-fold improvement (ranging up to 69.1-fold). Probe capture data also identified five novel alpha- and betacoronaviruses in these specimens, and their full genomes were recovered with additional deep sequencing. Based on these experiences, we discuss how probe capture could be effectively operationalized alongside other sequencing technologies for high-throughput, genomics-based discovery and surveillance of bat coronaviruses.

Racial Disparities in Mortality During the 1918 Influenza Pandemic in United States Cities

Against a backdrop of extreme racial health inequality, the 1918 influenza pandemic resulted in a striking reduction of non-White to White influenza and pneumonia mortality disparities in United States cities. We provide the most complete account to date of these reduced racial disparities, showing that they were unexpectedly uniform across cities. Linking data from multiple sources, we then examine potential explanations for this finding, including city-level sociodemographic factors such as segregation, implementation of nonpharmaceutical interventions, racial differences in exposure to the milder spring 1918 "herald wave," and racial differences in early-life influenza exposures, resulting in differential immunological vulnerability to the 1918 flu. While we find little evidence for the first three explanations, we offer suggestive evidence that racial variation in childhood exposure to the 1889-1892 influenza pandemic may have shrunk racial disparities in 1918. We also highlight the possibility that differential behavioral responses to the herald wave may have protected non-White urban populations. By providing a comprehensive description and examination of racial inequality in mortality during the 1918 pandemic, we offer a framework for understanding disparities in infectious disease mortality that considers interactions between the natural histories of particular microbial agents and the social histories of those they infect.

Seven Months after Mild COVID-19: A Single-Centre Controlled Follow-Up Study in the District of Constance (FSC19-KN)

Objective

The primary aim of the study was to investigate the rate of hospitalization and admission diagnoses in severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) positive patients seven months after initial infection. Secondarily, measurement of long-term effects on physical performance, quality of life, and functional outcome was intended.

Design

The study is designed as a controlled follow-up of COVID-19 cases in the district of Constance (FSC19-KN). Setting. A controlled setting is provided due to the recruitment of an equally sized cohort consisting of age- and gender-matched subjects featuring similar cardiovascular risk profiles and negative SARS-CoV-2 antibody titers. Participants. The study examines 206 subjects after polymerase chain reaction (PCR) confirmed SARS-CoV-2 infection seven months after initial infection. Exposure. Infection in the SARS-CoV-2 positive group occurred between March and December 2020. Main Outcome and Measures. The frequency of inpatient admission during the observational period including the related diagnosis was defined as the primary endpoint. Secondary endpoints were health-related quality of life, physical performance, and functional outcome measured by European Quality of Life-5-Dimensions-5-Level (EQ-5D-5L), Short Form Health 36 (SF-36), Six-Minute Walk Test (6MWT), and Post-COVID-19 Functional Status (PCFS).

Results

The study population consisted of mainly nonhospitalized subjects. During the first seven months of observation, frequency of inpatient admission was low and did not differ significantly between both groups (2.4% vs. 2.9% controls: OR 0.8, 95% CI 0.2 to 2.8). Calculation of six-minute walk distance ratios showed no significant difference between both cohorts (0.97 ± 0.17 vs. 0.98 ± 0.16 controls; mean difference -0.01; 95% CI -0.04 to 0.02). However, SARS-CoV-2-positive subjects achieved significantly lower EQ-5D-5L index scores (0.92 ± 0.12 vs. 0.95 ± 0.1 controls; mean difference -0.03, 95% CI -0.05 to -0.01) and SF-36 subscores. Reduced PCFS was reported significantly more often in the SARS-CoV-2 positive cohort (30.6% vs 14.6% controls: OR 2.6, 95% CI 1.6 to 4.2).

Conclusion

The results suggest that mild COVID-19 has no impact on the hospitalization rate during the first seven months after infection. Despite unimpaired performance in cardiopulmonary exercise, SARS-CoV-2-positive subjects reported reduced quality of life and functional sequelae. Underlying psychoneurological mechanisms need further investigation. Trial Registration. This trial is registered with clinicaltrials.gov (identifier: NCT04724434) and German Clinical Trials Register (identifier: DKRS00022409).

Molecular adaptations during viral epidemics

In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.

Twenty-first century bioarchaeology: Taking stock and moving forward

This article presents outcomes from a Workshop entitled "Bioarchaeology: Taking Stock and Moving Forward," which was held at Arizona State University (ASU) on March 6-8, 2020. Funded by the National Science Foundation (NSF), the School of Human Evolution and Social Change (ASU), and the Center for Bioarchaeological Research (CBR, ASU), the Workshop's overall goal was to explore reasons why research proposals submitted by bioarchaeologists, both graduate students and established scholars, fared disproportionately poorly within recent NSF Anthropology Program competitions and to offer advice for increasing success. Therefore, this Workshop comprised 43 international scholars and four advanced graduate students with a history of successful grant acquisition, primarily from the United States. Ultimately, we focused on two related aims: (1) best practices for improving research designs and training and (2) evaluating topics of contemporary significance that reverberate through history and beyond as promising trajectories for bioarchaeological research. Among the former were contextual grounding, research question/hypothesis generation, statistical procedures appropriate for small samples and mixed qualitative/quantitative data, the salience of Bayesian methods, and training program content. Topical foci included ethics, social inequality, identity (including intersectionality), climate change, migration, violence, epidemic disease, adaptability/plasticity, the osteological paradox, and the developmental origins of health and disease. Given the profound changes required globally to address decolonization in the 21st century, this concern also entered many formal and informal discussions.

Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance

Coronaviruses can evolve and spread rapidly to cause severe disease morbidity and mortality, as exemplified by SARS-CoV-2 variants of the COVID-19 pandemic. Although currently available vaccines remain mostly effective against SARS-CoV-2 variants, additional treatment strategies are needed. Inhibitors that target essential viral enzymes, such as proteases and polymerases, represent key classes of antivirals. However, clinical use of antiviral therapies inevitably leads to emergence of drug resistance. In this study we implemented a strategy to pre-emptively address drug resistance to protease inhibitors targeting the main protease (Mpro) of SARS-CoV-2, an essential enzyme that promotes viral maturation. We solved nine high-resolution cocrystal structures of SARS-CoV-2 Mpro bound to substrate peptides and six structures with cleavage products. These structures enabled us to define the substrate envelope of Mpro, map the critical recognition elements, and identify evolutionarily vulnerable sites that may be susceptible to resistance mutations that would compromise binding of the newly developed Mpro inhibitors. Our results suggest strategies for developing robust inhibitors against SARS-CoV-2 that will retain longer-lasting efficacy against this evolving viral pathogen.

The past, current and future epidemiological dynamic of SARS-CoV-2

SARS-CoV-2, the agent of the COVID-19 pandemic, emerged in late 2019 in China, and rapidly spread throughout the world to reach all continents. As the virus expanded in its novel human host, viral lineages diversified through the accumulation of around two mutations a month on average. Different viral lineages have replaced each other since the start of the pandemic, with the most successful Alpha, Delta and Omicron variants of concern (VoCs) sequentially sweeping through the world to reach high global prevalence. Neither Alpha nor Delta was characterized by strong immune escape, with their success coming mainly from their higher transmissibility. Omicron is far more prone to immune evasion and spread primarily due to its increased ability to (re-)infect hosts with prior immunity. As host immunity reaches high levels globally through vaccination and prior infection, the epidemic is expected to transition from a pandemic regime to an endemic one where seasonality and waning host immunization are anticipated to become the primary forces shaping future SARS-CoV-2 lineage dynamics. In this review, we consider a body of evidence on the origins, host tropism, epidemiology, genomic and immunogenetic evolution of SARS-CoV-2 including an assessment of other coronaviruses infecting humans. Considering what is known so far, we conclude by delineating scenarios for the future dynamic of SARS-CoV-2, ranging from the good-circulation of a fifth endemic 'common cold' coronavirus of potentially low virulence, the bad-a situation roughly comparable with seasonal flu, and the ugly-extensive diversification into serotypes with long-term high-level endemicity.

Coronavirus as the Possible Causative Agent of the 1889-1894 Pandemic

Using new and original nineteenth-century sources, we analysed the epidemiology, clinical features and virology of the 1889 pandemic, which was referred to at the time as ‘Russian flu’ or ‘Asiatic flu’. However, we rejected this identification of the disease as an ‘influenza’, which we believe to have been based on insufficient knowledge of the causative agent and instead posit that the pandemic was caused by a coronavirus. We provide a new account of the 1889–1893 pandemic, with a more detailed chronology that included at least four epidemiological waves. At the end of 1889, a new virus appeared in Europe, which could be identified as the coronavirus HCoV-OC43, causing crude death rates of 1.3 per 1000 population in St Petersburg; 2.1 per 1000 in Paris; 2.8 per 1000 in Bilbao and on the French–Spanish border; between 2.9 and 5.2 per 1000 in small towns in the Basque Country; and 5.8 deaths per 1000 in Madrid, which had the highest death rate. The clinical features of the disease differed from classical influenza pandemics in terms of the latency phase, duration, symptomatology, convalescence, immunity, age and death rates. Another factor to be considered was the neurotropic capacity of the disease. The most frequent form of the 1889 pandemic was the ‘nervous form’, with specific symptoms such as ‘heavy headache’ (céphalalgie gravative), tiredness, fever and delirium. There are strong parallels between the 1889–1894 pandemic and the COVID-19 pandemic, and a better understanding of the former may therefore help us to better manage the latter.

Viruses as Living Systems—A Metacybernetic View

The debate over whether viruses are living organisms tends to be paradigmatically determined. The metabolic paradigm denies that they are, while new research evidences the opposite. The purpose of this paper is to deliver a generic model for viral contexts that explains why viruses are alive. It will take a systems biology approach, with a qualitative part (using metacybernetics) to provide deeper explanations of viral contexts, and a quantitative part (using Fisher Information deriving from the variational principle of Extreme Physical Information) which is in principle able to take measurements and predict outcomes. The modelling process provides an extended view of the epigenetic processes of viruses. The generic systems biology model will depict viruses as autonomous entities with metaphysical processes of autopoietic self-organisation and adaptation, enabling them to maintain their physical viability and hence, within their populations, mutate and evolve. The autopoietic epigenetic processes are shown to describe their capability to change, and these are both qualitatively and quantitatively explored, the latter providing an approach to make measurements of physical phenomena under uncertainty. Viruses maintain their fitness when they are able to maintain their stability, and this is indicated by information flow efficacy. A brief case study is presented on the COVID-19 virus from the perspective that it is a living system, and this includes outcome predictions given Fisher Information conditions for known contexts.

Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes

Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1_A domain, but, remarkably, also to S1_B. The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1_B epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2.

Human coronavirus OC43 causes respiratory disease and is maintained in the human population through recurring infections. Here, by extensive structural analyses, the authors provide insights into the binding sites and breadth of neutralizing antibodies against this endemic coronavirus.

Palaeoserology - teeth put into ancient plagues and pandemics

Based on archived medical records and evolutionary modelling, a Coronavirus has been hypothesized as root and causative agent of the so‐called ‘Russian Flu’ pandemic that surged in 1889–1890. In a Correspondence published in this volume of Microbial Biotechnology, Ramassy and colleagues try to support historical evidence by true experimental data using 'palaeoserology', a novel approach combining archaeology and modern immunological analysis. This Opinion piece tries to weigh arguments how strong such data may be, and where a refinement of methodology might be desirable before textbooks of medical history switch to call the 1890s pandemic ‘Russian Corona’.

Viral and cellular translation during SARS‐CoV‐2 infection

SARS‐CoV‐2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid‐19 pandemic. This enveloped virus contains a large positive‐sense single‐stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non‐structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non‐structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.

Antiviral Activity of Contemporary Contact Lens Care Solutions against Two Human Seasonal Coronavirus Strains

Background: Given that reports have suggested SARS-CoV-2 can be transmitted via conjunctiva, the ability of contact lens (CL) care products to reduce the infectiousness of two seasonal human coronavirus (HCoV) (HCoV-229E and HCoV-OC43) surrogates for SARS-CoV-2 was investigated. Methods: Biotrue and Boston Simplus (Bausch&Lomb), OPTI-FREE Puremoist and Clear Care (Alcon), and cleadew and cleadew GP (Ophtecs) were tested. Their ability to inactivate HCoV was evaluated using contact times of 4 and 6 h as well as 1% and 10% of virus inoculum. Results: Non-oxidative systems (Biotrue, Boston Simplus, and OPTI-FREE) did not exhibit a significant log10 reduction compared to controls for the two viral strains for either incubation time (all p > 0.05) when 10% tests were performed. For the 1% test, while Boston Simplus and OPTI-FREE exhibited a significant log10 reduction of both HCoV-229E (after 6 h) and HCoV-OC43 (after either 4 or 6 h incubation), those products showed less than 1 log10 reduction of the two infectious viruses. Oxidative systems based on hydrogen peroxide or povidone-iodine showed a significant log10 reduction compared with the controls for both HCoV-229E and HCoV-OC43 in all tested conditions (all p < 0.01). Clear Care led to virus inactivation to below the limit of quantification for tests performed with 1% of inoculum after 6 h incubation, while cleadew and cleadew GP led to inactivation of the two viruses to below the limit of quantification in all tested conditions. Conclusion: Oxidative CL disinfection systems showed significant virucidal activity against HCoV-229E and HCoV-OC43, while non-oxidative systems showed minimal ability to inactivate the HCoV species examined.

Historically High Excess Mortality During the COVID-19 Pandemic in Switzerland, Sweden, and Spain

BACKGROUND

Excess mortality quantifies the overall mortality impact of a pandemic. Mortality data have been accessible for many countries in recent decades, but few continuous data have been available for longer periods.

OBJECTIVE

To assess the historical dimension of the COVID-19 pandemic in 2020 for 3 countries with reliable death count data over an uninterrupted span of more than 100 years.

DESIGN

Observational study.

SETTING

Switzerland, Sweden, and Spain, which were militarily neutral and not involved in combat during either world war and have not been affected by significant changes in their territory since the end of the 19th century.

PARTICIPANTS

Complete populations of these 3 countries.

MEASUREMENTS

Continuous series of recorded deaths (from all causes) by month from the earliest available year (1877 for Switzerland, 1851 for Sweden, and 1908 for Spain) were jointly modeled with annual age group-specific death and total population counts using negative binomial and multinomial models, which accounted for temporal trends and seasonal variability of prepandemic years. The aim was to estimate the expected number of deaths in a pandemic year for a nonpandemic scenario and the difference in observed and expected deaths aggregated over the year.

RESULTS

In 2020, the number of excess deaths recorded per 100 000 persons was 100 (95% credible interval [CrI], 60 to 135) for Switzerland, 75 (CrI, 40 to 105) for Sweden, and 155 (CrI, 110 to 195) for Spain. In 1918, excess mortality was 6 to 7 times higher. In all 3 countries, the peaks of monthly excess mortality in 2020 were greater than most monthly excess mortality since 1918, including many peaks due to seasonal influenza and heat waves during that period.

LIMITATION

Historical vital statistics might be affected by minor completeness issues before the beginning of the 20th century.

CONCLUSION

In 2020, the COVID-19 pandemic led to the second-largest infection-related mortality disaster in Switzerland, Sweden, and Spain since the beginning of the 20th century.

PRIMARY FUNDING SOURCE

Foundation for Research in Science and the Humanities at the University of Zurich, Swiss National Science Foundation, and National Institute of Allergy and Infectious Diseases.

The beginning and ending of a respiratory viral pandemic-lessons from the Spanish flu

The COVID‐19 pandemic goes into its third year and the world population is longing for an end to the pandemic. Computer simulations of the future development of the pandemic have wide error margins and predictions on the evolution of new viral variants of SARS‐CoV‐2 are uncertain. It is thus tempting to look into the development of historical viral respiratory pandemics for insight into the dynamic of pandemics. The Spanish flu pandemic of 1918 caused by the influenza virus H1N1 can here serve as a potential model case. Epidemiological observations on the shift of influenza mortality from very young and old subjects to high mortality in young adults delimitate the pandemic phase of the Spanish flu from 1918 to 1920. The identification and sequencing of the Spanish flu agent allowed following the H1N1 influenza virus after the acute pandemic phase. During the 1920s H1N1 influenza virus epidemics with substantial mortality were still observed. As late as 1951, H1N1 strains of high virulence evolved but remained geographically limited. Until 1957, the H1N1 virus evolved by accumulation of mutations (‘antigenic drift’) and some intratypic reassortment. H1N1 viruses were then replaced by the pandemic H2N2 influenza virus from 1957, which was in 1968 replaced by the pandemic H3N2 influenza virus; both viruses were descendants from the Spanish flu agent but showed the exchange of entire gene segments (‘antigenic shift’). In 1977, H1N1 reappeared from an unknown source but caused only mild disease. However, H1N1 achieved again circulation in the human population and is now together with the H3N2 influenza virus an agent of seasonal influenza winter epidemics.

SARS-CoV-2: tracing the origin, tracking the evolution

The origin of SARS-CoV-2 is uncertain. Findings support a "bat origin" but results are not highly convincing. Studies found evidence that SARS-CoV-2 was around for many years before the pandemic outbreak. Evidence has been published that the progenitor of SARS-CoV-2 already had the capability to bind strongly to the human ACE2 receptor. This may be an indication that many other animal viruses are capable to jump to humans, having already affinity for a human receptor. This is quite worrying since current ecosystems' collapse brings people to high proximity with animals, increasing probabilities for random viral transitions. On the other hand, future adaptation of SARS-CoV-2 is of great concern. Virus-host interactions are complicated and unfortunately, we still do not have accurate tools for predicting viruses' future evolution. Viral adaptation is a multifactorial process and probably SARS-CoV-2 will not become soon, as we wish, a harmless infection. However, humanity is currently under the largest vaccination program and it's of great interest to see if vaccinations will change the evolutionary game against the virus.

Can a combination of vaccination and face mask wearing contain the COVID-19 pandemic?

The COVID‐19 pandemic is going into its third year with Europe again being the focus of major epidemic activity. The present review tries to answer the question whether one can come to grip with the pandemic by a combination of vaccinations and non‐pharmaceutical interventions (NPIs). Several COVID‐19 vaccines are of remarkable efficacy and achieve high protection rates against symptomatic disease, especially severe disease, but mathematical models suggest that the current vaccination coverage in many countries is insufficient to achieve pandemic control. NPIs are needed as complementary measures because recent research has also revealed the limits of vaccination alone. Here, we review the evidence for efficacy of face mask wearing in various settings. Overall pooled analysis showed significant reduction in COVID‐19 incidence with mask wearing, although heterogeneity between studies was substantial. Controlled trials of mask wearing are difficult to conduct, separating mask wearing effects in population studies from the impact of other NPIs is challenging and the efficacy of masks depend on mask material and mask fit. The combination of vaccination and mask wearing is potentially synergistic since vaccination protects so far well from disease development (the omicron variant is currently an unknown) but immunity from infection wanes over few months after vaccination. In comparison, masks interfere with the virus transmission process at a level of a physical barrier independent of coronavirus variant. Vaccination and masks are much less costly to apply than other NPI measures which are associated with high economic and social costs, but paradoxically both measures are the target of a vocal opposition by a sizable minority of the society. In parallel with biomedical research, we need more social science research into this opposition to guide political decisions on how to end the pandemic.

The present review tries to answer the question whether one can control the pandemic by a combination of vaccinations and non‐pharmaceutical interventions. The combination of vaccination and mask wearing is potentially synergistic since vaccination protects so far well from disease while masks interfere with the virus transmission process as a physical barrier against any type of coronavirus variant.