Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths

Prevalence of Respiratory Viral Infections in Deceased Persons during the COVID-19 Pandemic Season 2021-2022: A Population-Based Observational Study

Although the omicron variant of SARS-CoV-2 circulated intensely during the 2021-2022 season, many patients with severe acute respiratory disease tested negative for COVID-19. The aim of this study was to assess the presence of different respiratory viruses in deceased persons. The proportion of deceased persons with respiratory viral infections in the 2021-2022 season in Navarre, Spain, was estimated considering all deaths caused by confirmed COVID-19 according to the epidemiological surveillance and the results of multiplex PCR tests for respiratory viruses performed in a sample of deceased persons with a cause of death other than COVID-19. Of 3578 deaths, 324 (9.1%) were initially reported as caused by pre-mortem confirmed COVID-19. A sample of 242 persons who died by causes other than COVID-19 were tested post-mortem; 64 (26.4%) of them were positive for any respiratory virus: 11.2% for SARS-CoV-2, 5.8% for rhinovirus, 3.7% for human coronavirus, 2.5% for metapneumovirus, 1.7% for respiratory syncytial virus, 1.7% for parainfluenza, 1.2% for influenza, and less than 1% each for adenovirus and bocavirus. Combining both approaches, we estimated that 34.4% of all deceased persons during the study period had a respiratory viral infection and 19.2% had SARS-CoV-2. Only 33.3% (9/27) of SARS-CoV-2 and 5.0% (2/40) of other viruses detected post-mortem had previously been confirmed pre-mortem. In a period with very intense circulation of SARS-CoV-2 during the pandemic, other respiratory viruses were also frequently present in deceased persons. Some SARS-CoV-2 infections and most other viral infections were not diagnosed pre-mortem. Several respiratory viruses may contribute to excess mortality in winter.

An Investigation of Severe Influenza Cases in Russia during the 2022-2023 Epidemic Season and an Analysis of HA-D222G/N Polymorphism in Newly Emerged and Dominant Clade 6B.1A.5a.2a A(H1N1)pdm09 Viruses

In Russia, during the COVID-19 pandemic, a decrease in influenza circulation was initially observed. Influenza circulation re-emerged with the dominance of new clades of A(H3N2) viruses in 2021-2022 and A(H1N1)pdm09 viruses in 2022-2023. In this study, we aimed to characterize influenza viruses during the 2022-2023 season in Russia, as well as investigate A(H1N1)pdm09 HA-D222G/N polymorphism associated with increased disease severity. PCR testing of 780 clinical specimens showed 72.2% of them to be positive for A(H1N1)pdm09, 2.8% for A(H3N2), and 25% for influenza B viruses. The majority of A(H1N1)pdm09 viruses analyzed belonged to the newly emerged 6B.1A.5a.2a clade. The intra-sample predominance of HA-D222G/N virus variants was observed in 29% of the specimens from A(H1N1)pdm09 fatal cases. The D222N polymorphic variant was registered more frequently than D222G. All the B/Victoria viruses analyzed belonged to the V1A.3a.2 clade. Several identified A(H3N2) viruses belonged to one of the four subclades (2a.1b, 2a.3a.1, 2a.3b, 2b) within the 3C.2a1b.2a.2 group. The majority of antigenically characterized viruses bore similarities to the corresponding 2022-2023 NH vaccine strains. Only one influenza A(H1N1)pdm09 virus showed reduced inhibition by neuraminidase inhibitors. None of the influenza viruses analyzed had genetic markers of reduced susceptibility to baloxavir.

Systematic review of influenza vaccine effectiveness against laboratory-confirmed influenza among older adults living in aged care facilities

We estimated the effectiveness of influenza vaccines in preventing laboratory-confirmed influenza among older adults in aged care. Electronic database searches were conducted using search terms, and studies were selected as per the selection criteria. Fourteen studies were included for final review. The studies exhibited considerable variation in reported vaccine effectiveness (VE) across different seasons. Among the observational studies, VE ranged from 7.2% to 89.8% against laboratory-confirmed influenza across different vaccines. Randomized clinical trials demonstrated a 17% reduction in infection rates with the adjuvanted trivalent vaccine. The limitations include the small number of included studies conducted in different countries or regions, varied seasons, variations in diagnostic testing methods, a focus on the A/H3N2 strain, and few studies available on the effectiveness of enhanced influenza vaccines in aged care settings. Despite challenges associated with achieving optimal protection, the studies showed the benefits of influenza vaccination in the elderly residents.

COVID-19-Related Age Profiles for SARS-CoV-2 Variants in England and Wales and States of the USA (2020 to 2022): Impact on All-Cause Mortality

Since 2020, COVID-19 has caused serious mortality around the world. Given the ambiguity in establishing COVID-19 as the direct cause of death, we first investigate the effects of age and sex on all-cause mortality during 2020 and 2021 in England and Wales. Since infectious agents have their own unique age profile for death, we use a 9-year time series and several different methods to adjust single-year-of-age deaths in England and Wales during 2019 (the pre-COVID-19 base year) to a pathogen-neutral single-year-of-age baseline. This adjusted base year is then used to confirm the widely reported higher deaths in males for most ages above 43 in both 2020 and 2021. During 2020 (+COVID-19 but no vaccination), both male and female population-adjusted deaths significantly increased above age 35. A significant reduction in all-cause mortality among both males and females aged 75+ could be demonstrated in 2021 during the widespread COVID-19 vaccination period; however, deaths below age 75 progressively increased. This finding arises from a mix of vaccination coverage and year-of-age profiles of deaths for the different SARS-CoV-2 variants. In addition, specific effects of age around puberty were demonstrated, where females had higher deaths than males. There is evidence that year-of-birth cohorts may also be involved, indicating that immune priming to specific pathogen outbreaks in the past may have led to lower deaths for some birth cohorts. To specifically identify the age profile for the COVID-19 variants from 2020 to 2023, we employ the proportion of total deaths at each age that are potentially due to or 'with' COVID-19. The original Wuhan strain and the Alpha variant show somewhat limited divergence in the age profile, with the Alpha variant shifting to a moderately higher proportion of deaths below age 84. The Delta variant specifically targeted individuals below age 65. The Omicron variants showed a significantly lower proportion of overall mortality, with a markedly higher relative proportion of deaths above age 65, steeply increasing with age to a maximum around 100 years of age. A similar age profile for the variants can be seen in the age-banded deaths in US states, although they are slightly obscured by using age bands rather than single years of age. However, the US data shows that higher male deaths are greatly dependent on age and the COVID variant. Deaths assessed to be 'due to' COVID-19 (as opposed to 'involving' COVID-19) in England and Wales were especially overestimated in 2021 relative to the change in all-cause mortality. This arose as a by-product of an increase in COVID-19 testing capacity in late 2020. Potential structure-function mechanisms for the age-specificity of SARS-CoV-2 variants are discussed, along with potential roles for small noncoding RNAs (miRNAs). Using data from England, it is possible to show that the unvaccinated do indeed have a unique age profile for death from each variant and that vaccination alters the shape of the age profile in a manner dependent on age, sex, and the variant. The question is posed as to whether vaccines based on different variants carry a specific age profile.

Changes in the Epidemiology of Rubella: The Influence of Vaccine-Introducing Methods and COVID-19

Rubella is an infectious disease caused by the rubella virus. Congenital rubella syndrome is a risk for all newborns if pregnant women are infected with rubella, raising an important public health issue. Rubella is a vaccine-preventable disease, and routine immunization has been conducted in Japan. The timing of the vaccine approval did not differ from that in the United States. In 2004, endemic rubella was eliminated in the United States. However, recent rubella outbreaks have occurred in Japan. This may be related to differences in the introduction of routine rubella immunization. In Japan, routine rubella immunization was initially introduced only for junior high school girls, and the rate of susceptibility is high among males who have not received rubella vaccination, causing an outbreak. Therefore, in Japan, measures have been taken to decrease the number of susceptible males in the vaccination-free generation. The coronavirus pandemic has also affected the epidemiology of rubella as well as other infectious diseases.

Serum Metabolic Correlates of the Antibody Response in Subjects Receiving the Inactivated COVID-19 Vaccine

BACKGROUND

Metabolites are involved in biological process that govern the immune response to infection and vaccination. Knowledge of how metabolites interact with the immune system during immunization with the COVID-19 vaccine is limited. Here, we report that the serum metabolites are correlated with the magnitude of the antibody response in recipients receiving the inactivated COVID-19 vaccine, which provides critical information for studying metabolism regarding the human immune response to vaccination.

METHODS

106 healthy volunteers without history of SARS-CoV-2 infection or vaccination were prospectively enrolled to receive the primary series of two doses of inactivated whole-virion SARS-CoV-2 vaccine. The serum samples were collected 2-4 weeks after the second dose. The magnitude of the anti-RBD antibody was quantified using surrogate virus neutralization tests. The profile of metabolites in serum was identified using untargeted metabolomics analysis.

RESULTS

The level of anti-RBD antibody 14-28 days after the second dose was significantly elevated and its interpersonal variability was diverse in a wide range. Thirty-two samples at extremes of the anti-RBD antibody titer were selected to discover the metabolic correlates. Two hundred and fifteen differential metabolites associated with antibody response independent of body mass index were identified. Pregnenolone and sphingolipid metabolism might be involved in the modulation of the human antibody response to the inactivated COVID-19 vaccine.

CONCLUSION

We discovered key metabolites as well as those with a related functional significance that might modulate the human immune response to vaccination.

A Model to Compare International Hospital Bed Numbers, including a Case Study on the Role of Indigenous People on Acute 'Occupied' Bed Demand in Australian States

Comparing international or regional hospital bed numbers is not an easy matter, and a pragmatic method has been proposed that plots the number of beds per 1000 deaths versus the log of deaths per 1000 population. This method relies on the fact that 55% of a person's lifetime hospital bed utilization occurs in the last year of life-irrespective of the age at death. This is called the nearness to death effect. The slope and intercept of the logarithmic relationship between the two are highly correlated. This study demonstrates how lines of equivalent bed provision can be constructed based on the value of the intercept. Sweden looks to be the most bed-efficient country due to long-term investment in integrated care. The potential limitations of the method are illustrated using data from English Clinical Commissioning Groups. The main limitation is that maternity, paediatric, and mental health care do not conform to the nearness to death effect, and hence, the method mainly applies to adult acute care, especially medical and critical care bed numbers. It is also suggested that sensible comparison can only be made by comparing levels of occupied beds rather than available beds. Occupied beds measure the expressed bed demand (although often constrained by access to care issues), while available beds measure supply. The issue of bed supply is made complex by the role of hospital size on the average occupancy margin. Smaller hospitals are forced to operate at a lower average occupancy; hence, countries with many smaller hospitals such as Germany and the USA appear to have very high numbers of available beds. The so-called 85% occupancy rule is an "urban myth" and has no fundamental basis whatsoever. The very high number of "hospital" beds in Japan is simply an artefact arising from "nursing home" beds being counted as a "hospital" bed in this country. Finally, the new method is applied to the expressed demand for occupied acute beds in Australian states. Using data specific to acute care, i.e., excluding mental health and maternity, a long-standing deficit of beds was identified in Tasmania, while an unusually high level of occupied beds in the Northern Territory (NT) was revealed. The high level of demand for beds in the NT appears due to an exceptionally large population of indigenous people in this state, who are recognized to have elevated health care needs relative to non-indigenous Australians. In this respect, indigenous Australians use 3.5 times more occupied bed days per 1000 deaths (1509 versus 429 beds per 1000 deaths) and 6 times more occupied bed days per 1000 population (90 versus 15 beds per 1000 population) than their non-indigenous counterparts. The figure of 1509 beds per 1000 deaths (or 4.13 occupied beds per 1000 deaths) for indigenous Australians is indicative of a high level of "acute" nursing care in the last months of life, probably because nursing home care is not readily available due to remoteness. A lack of acute beds in the NT then results in an extremely high average bed occupancy rate with contingent efficiency and delayed access implications.