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1. Excess mortality in the United States during the first three months of the COVID-19 pandemic

   https://doi.org/10.1017/S0950268820002617  

   Rivera, R. ; Rosenbaum, J. E. ; Quispe, W. ( January 2020 , Epidemiology and Infection)

   null (Ed.)

   Abstract Deaths are frequently under-estimated during emergencies, times when accurate mortality estimates are crucial for emergency response. This study estimates excess all-cause, pneumonia and influenza mortality during the coronavirus disease 2019 (COVID-19) pandemic using the 11 September 2020 release of weekly mortality data from the United States (U.S.) Mortality Surveillance System (MSS) from 27 September 2015 to 9 May 2020, using semiparametric and conventional time-series models in 13 states with high reported COVID-19 deaths and apparently complete mortality data: California, Colorado, Connecticut, Florida, Illinois, Indiana, Louisiana, Massachusetts, Michigan, New Jersey, New York, Pennsylvania and Washington. We estimated greater excess mortality than official COVID-19 mortality in the U.S. (excess mortality 95% confidence interval (CI) 100 013–127 501 vs. 78 834 COVID-19 deaths) and 9 states: California (excess mortality 95% CI 3338–6344) vs. 2849 COVID-19 deaths); Connecticut (excess mortality 95% CI 3095–3952) vs. 2932 COVID-19 deaths); Illinois (95% CI 4646–6111) vs. 3525 COVID-19 deaths); Louisiana (excess mortality 95% CI 2341–3183 vs. 2267 COVID-19 deaths); Massachusetts (95% CI 5562–7201 vs. 5050 COVID-19 deaths); New Jersey (95% CI 13 170–16 058 vs. 10 465 COVID-19 deaths); New York (95% CI 32 538–39 960 vs. 26 584 COVID-19 deaths); and Pennsylvania (95% CI 5125–6560 vs. 3793 COVID-19 deaths). Conventional model results were consistent with semiparametric results but less precise. Significant excess pneumonia deaths were also found for all locations and we estimated hundreds of excess influenza deaths in New York. We find that official COVID-19 mortality substantially understates actual mortality, excess deaths cannot be explained entirely by official COVID-19 death counts. Mortality reporting lags appeared to worsen during the pandemic, when timeliness in surveillance systems was most crucial for improving pandemic response. 

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2. Using excess deaths and testing statistics to determine COVID-19 mortalities

   https://doi.org/10.1007/s10654-021-00748-2  

   Böttcher, Lucas ; D’Orsogna, Maria R. ; Chou, Tom ( May 2021 , European Journal of Epidemiology)

   null (Ed.)

   Abstract Factors such as varied definitions of mortality, uncertainty in disease prevalence, and biased sampling complicate the quantification of fatality during an epidemic. Regardless of the employed fatality measure, the infected population and the number of infection-caused deaths need to be consistently estimated for comparing mortality across regions. We combine historical and current mortality data, a statistical testing model, and an SIR epidemic model, to improve estimation of mortality. We find that the average excess death across the entire US from January 2020 until February 2021 is 9 $$\%$$ % higher than the number of reported COVID-19 deaths. In some areas, such as New York City, the number of weekly deaths is about eight times higher than in previous years. Other countries such as Peru, Ecuador, Mexico, and Spain exhibit excess deaths significantly higher than their reported COVID-19 deaths. Conversely, we find statistically insignificant or even negative excess deaths for at least most of 2020 in places such as Germany, Denmark, and Norway. 

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3. Low‐frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled‐edged sword

   https://doi.org/10.1002/jmv.27726  

   Magalis, Brittany R. ; Mavian, Carla ; Tagliamonte, Massimiliano ; Rich, Shannan N. ; Cash, Melanie ; Riva, Alberto ; Loeb, Julia C. ; Norris, Michael ; Amador, David M. ; Zhang, Yanping ; et al ( April 2022 , Journal of Medical Virology)

   The emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) variants of concern (VOC) has raised questions regarding vaccine protection against SARS‐CoV‐2 infection, transmission, and ongoing virus evolution. Twenty‐three mildly symptomatic “vaccination breakthrough” infections were identified as early as January 2021 in Alachua County, Florida, among individuals fully vaccinated with either the BNT162b2 (Pfizer) or the Ad26 (Janssen/J&J) vaccines. SARS‐CoV‐2 genomes were successfully generated for 11 of the vaccine breakthroughs, and 878 individuals in the surrounding area and were included for reference‐based phylogenetic investigation. These 11 individuals were characterized by infection with VOCs, but also low‐frequency variants present within the surrounding population. Low‐frequency mutations were observed, which have been more recently identified as mutations of interest owing to their location within targeted immune epitopes (P812L) and association with increased replicative capacity (L18F). We present these results to posit the nature of the efficacy of vaccines in reducing symptoms as both a blessing and a curse—as vaccination becomes more widespread and self‐motivated testing reduced owing to the absence of severe symptoms, we face the challenge of early recognition of novel mutations of potential concern. This case study highlights the critical need for continued testing and monitoring of infection and transmission among individuals regardless of vaccination status.

    

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4. Contact tracing reveals community transmission of COVID-19 in New York City

   https://doi.org/10.1038/s41467-022-34130-x  

   Pei, Sen ; Kandula, Sasikiran ; Cascante Vega, Jaime ; Yang, Wan ; Foerster, Steffen ; Thompson, Corinne ; Baumgartner, Jennifer ; Ahuja, Shama Desai ; Blaney, Kathleen ; Varma, Jay K. ; et al ( October 2022 , Nature Communications)

   Understanding SARS-CoV-2 transmission within and among communities is critical for tailoring public health policies to local context. However, analysis of community transmission is challenging due to a lack of high-resolution surveillance and testing data. Here, using contact tracing records for 644,029 cases and their contacts in New York City during the second pandemic wave, we provide a detailed characterization of the operational performance of contact tracing and reconstruct exposure and transmission networks at individual and ZIP code scales. We find considerable heterogeneity in reported close contacts and secondary infections and evidence of extensive transmission across ZIP code areas. Our analysis reveals the spatial pattern of SARS-CoV-2 spread and communities that are tightly interconnected by exposure and transmission. We find that locations with higher vaccination coverage and lower numbers of visitors to points-of-interest had reduced within- and cross-ZIP code transmission events, highlighting potential measures for curtailing SARS-CoV-2 spread in urban settings.

    

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5. Parasitic infection increases risk-taking in a social, intermediate host carnivore

   https://doi.org/10.1038/s42003-022-04122-0  

   Meyer, Connor J. ; Cassidy, Kira A. ; Stahler, Erin E. ; Brandell, Ellen E. ; Anton, Colby B. ; Stahler, Daniel R. ; Smith, Douglas W. ( November 2022 , Communications Biology)

   Toxoplasma gondiiis a protozoan parasite capable of infecting any warm-blooded species and can increase risk-taking in intermediate hosts. Despite extensive laboratory research on the effects ofT. gondiiinfection on behaviour, little is understood about the effects of toxoplasmosis on wild intermediate host behavior. Yellowstone National Park, Wyoming, USA, has a diverse carnivore community including gray wolves (Canis lupus) and cougars (Puma concolor), intermediate and definitive hosts ofT. gondii, respectively. Here, we used 26 years of wolf behavioural, spatial, and serological data to show that wolf territory overlap with areas of high cougar density was an important predictor of infection. In addition, seropositive wolves were more likely to make high-risk decisions such as dispersing and becoming a pack leader, both factors critical to individual fitness and wolf vital rates. Due to the social hierarchy within a wolf pack, we hypothesize that the behavioural effects of toxoplasmosis may create a feedback loop that increases spatial overlap and disease transmission between wolves and cougars. These findings demonstrate that parasites have important implications for intermediate hosts, beyond acute infections, through behavioural impacts. Particularly in a social species, these impacts can surge beyond individuals to affect groups, populations, and even ecosystem processes.

    

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