Novel data streams (NDS), such as web search data or social media updates, hold promise for enhan... more Novel data streams (NDS), such as web search data or social media updates, hold promise for enhancing the capabilities of public health surveillance. In this paper, we outline a conceptual framework for integrating NDS into current public health surveillance. Our approach focuses on two key questions: What are the opportunities for using NDS and what are the minimal tests of validity and utility that must be applied when using NDS? Identifying these opportunities will necessitate the involvement of public health authorities and an appreciation of the diversity of objectives and scales across agencies at different levels (local, state, national, international). We present the case that clearly articulating surveillance objectives and systematically evaluating NDS and comparing the performance of NDS to existing surveillance data and alternative NDS data is critical and has not sufficiently been addressed in many applications of NDS currently in the literature.
medRxiv (Cold Spring Harbor Laboratory), Jan 6, 2021
Long-term care facilities (LTCFs) bear disproportionate burden of COVID-19 and are prioritized fo... more Long-term care facilities (LTCFs) bear disproportionate burden of COVID-19 and are prioritized for vaccine deployment. LTCF outbreaks could continue occurring during vaccine rollout due to incomplete population coverage, and the effect of vaccines on viral transmission are currently unknown. Declining adherence to non-pharmaceutical interventions (NPIs) against withinfacility transmission could therefore limit the effectiveness of vaccination. We built a stochastic model to simulate outbreaks in LTCF populations with differing vaccination coverage and NPI adherence to evaluate their interacting effects. Vaccination combined with strong NPI adherence produced the least morbidity and mortality. Healthcare worker vaccination improved outcomes in unvaccinated LTCF residents but was less impactful with declining NPI adherence. To prevent further illness and deaths, there is a continued need for NPIs in LTCFs during vaccine rollout. MAIN The COVID-19 pandemic has been particularly devastating for residents of LTCFs (skilled nursing homes and assisted living facilities). While there has been a shift of disease burden to. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The first ever case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported in Se... more The first ever case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported in September 2012. This report describes the approaches taken by CDC, in collaboration with the World Health Organization (WHO) and other partners, to respond to this novel virus, and outlines the agency responses prior to the first case appearing in the United States in May 2014. During this time, CDC's response integrated multiple disciplines and was divided into three distinct phases: before, during, and after the initial activation of its Emergency Operations Center. CDC's response to MERS-CoV required a large effort, deploying at least 353 staff members who worked in the areas of surveillance, laboratory capacity, infection control guidance, and travelers' health. This response built on CDC's experience with previous outbreaks of other pathogens and provided useful lessons for future emerging threats.
The findings and conclusions in this report are those of the authors and do not necessarily repre... more The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
BackgroundAdult respiratory syncytial virus (RSV) vaccines are in late stages of development. A c... more BackgroundAdult respiratory syncytial virus (RSV) vaccines are in late stages of development. A comprehensive synthesis of adult RSV burden is needed to inform public health decision-making.MethodsWe performed a systematic review and meta-analysis of studies describing the incidence of medically-attended RSV (MA-RSV) among US adults. We also identified studies reporting nasopharyngeal (NP) or nasal swab RT-PCR results with paired serology (four-fold-rise) or sputum (RT-PCR) to calculate RSV detection ratios quantifying improved diagnostic yield after adding a second specimen type (ie, serology or sputum).ResultsWe identified 14 studies with 15 unique MA-RSV incidence estimates, all based on NP or nasal swab RT-PCR testing alone. Pooled annual RSV-associated incidence per 100,000 adults ≥65 years of age was 178 (95%CI: 152‒204; n=8 estimates) hospitalizations (4 prospective studies: 189; 4 model-based studies: 157), 133 (95%CI: 0‒319, n=2) emergency department (ED) admissions, and 1519 (95%CI: 1109‒1929, n=3) outpatient visits. Based on 6 studies, RSV detection was ∼1.5 times higher when adding paired serology or sputum. After adjustment for this increased yield, annual RSV-associated rates per 100,000 adults ≥65 years were 267 hospitalizations (UI: 228‒306) (prospective: 282; model-based: 236), 200 ED admissions (UI: 0‒478), and 2278 outpatient visits (UI: 1663‒2893). Persons < 65 years with chronic medical conditions were 1.2−28 times more likely to be hospitalized for RSV depending on risk condition.ConclusionThe true burden of RSV has been underestimated and is significant among older adults and individuals with chronic medical conditions. A highly effective adult RSV vaccine would have substantial public-health impact.Disclosures John M. McLaughlin, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds Farid L. Khan, MPH, Pfizer: Employee|Pfizer: Stocks/Bonds Elizabeth Begier, M.D., M.P.H., Pfizer: Employee|Pfizer: Stocks/Bonds David Swerdlow, MD, Pfizer: Advisor/Consultant|Pfizer: Stocks/Bonds Luis Jodar, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds Ann R. Falsey, MD, BioFire Diagnostics: Grant/Research Support|Janssen: Grant/Research Support|Merck, Sharp and Dohme: Grant/Research Support|Novavax: Advisor/Consultant|Pfizer: Grant/Research Support.
Virus SARS-CoV MERS-CoV Type of coronavirus Lineage b betacoronavirus Lineage c betacoronavirus H... more Virus SARS-CoV MERS-CoV Type of coronavirus Lineage b betacoronavirus Lineage c betacoronavirus Host cell receptor Angiotensin converting enzyme 2 Dipeptidyl peptidase 4 Animal hosts Chinese horseshoe bats, palm civets Not yet confirmed, but camel is likely host Incubation period Mean (95% CI; days) 4.6 (3.8-5.8) 5.2 (1.9-14.7) Range (days) 2-14 2-13 Serial interval (days) 8.4 7.6 Basic reproduction number 2-3 <1 Patient characteristics Adults 93% 98% Children 5-7% 2% Age range (years) 1-91 1-94 Average age (years) Mean 39.9 Median 50 Sex ratio (M:F) 43%:57% 64.5%:35.5% Mortality Case fatality rate overall 9.6% 40% Case fatality rate with comorbidities 46% 60% Time (days) from symptom onset to hospitalization 2-8 0-16 Time (days) from symptom onset to death 21 12 TABLE 2 Chronology of key events a,b Date Key events April 2012 Cluster of 13 patients in a hospital in Jordan with acute respiratory illness; two deceased patients of this cluster were retrospectively diagnosed (in September 2012) through study of stored specimens with MERS-CoV (5, 90)
Abstract Background A significant burden of disease exists for adults infected with influenza (fl... more Abstract Background A significant burden of disease exists for adults infected with influenza (flu) and SARS-CoV-2, which causes COVID-19. However, data are limited comparing outcomes between hospitalized adults infected with these viruses. Methods Over the course of 3 consecutive winter respiratory viral seasons, adults ≥ 50 years of age admitted with acute respiratory tract infections (ARI) and adults of any age with COPD or CHF-related admissions were enrolled from 2 Atlanta area hospitals. For the 2018-19 and 2019-20 seasons, participants were approached in the hospital. If the participant enrolled, nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected and tested using BioFire® FilmArray® respiratory panel. Due to the COVID-19 pandemic in 2020-21 and limitations involving participant contact, only NP standard of care (SOC) swabs were collected. A comprehensive medical chart review was completed for each subject which encompassed data on their hospitalization, past medical history, and vaccination history. Co-infected patients were excluded from the analyses. Results Of the eligible participants, 118 were flu positive (three RSV-influenza co-infections were excluded) and 527 were COVID-19 positive. Median age was lower for the flu cohort at 62 (IQR 56-71) than those with COVID-19 (67, IQR 59-77) (p < 0.0001). Length of stay (LOS) was shorter in flu-infected patients (median 3 d, IQR 2-6), but was longer for COVID-19 patients (median 5 d, IQR 3-10). ICU admission occurred in 20% of those with flu, and among those admitted to the ICU mechanical ventilation (MV) occurred in 12.5%. ICU admission and MV was significantly higher for those with COVID-19, with 28% of patients admitted to the ICU and 47% of those requiring MV. Among patients with COVID-19, 8.9% died. This was significantly higher than that of flu (3.4%) (p=0.008). Hospital discharge occurred more frequently to a nursing home or LTCF with COVID-19 (10.3%) than with flu (0%) (p< 0.0001). Table 1. Breakdown of age, hospitalization course, and discharge disposition for participants diagnosed with influenza or COVID-19 during hospitalization. Conclusion COVID-19 resulted in a longer hospital admission, a greater chance of ICU admission and MV as compared to flu. Additionally, COVID-19 participants had a high rate of discharge to a nursing home/LTCF and a significantly higher risk of death. While the clinical course was not as severe as COVID-19, influenza contributed a significant burden. Disclosures David L. Swerdlow, MD, Pfizer Vaccines (Employee) Robin Hubler, MS, Pfizer Inc. (Employee) Christina A. Rostad, MD, BioFire Inc, GSK, MedImmune, Micron, Janssen, Merck, Moderna, Novavax, PaxVax, Pfizer, Regeneron, Sanofi-Pasteur. (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support)Meissa Vaccines (Other Financial or Material Support, Co-inventor of patented RSV vaccine technology unrelated to this manuscript, which has been licensed to Meissa Vaccines, Inc.) Larry Anderson, MD, ADVI (Consultant)Bavarian Nordic (Consultant)Novavax (Consultant)Phizer (Grant/Research Support, Scientific Research Study Investigator)Sciogen (Research Grant or Support) Nadine Rouphael, MD, pfizer, sanofi, lily, quidel, merck (Grant/Research Support) Nadine Rouphael, MD, Lilly (Individual(s) Involved: Self): Emory Study PI, Grant/Research Support; Merck (Individual(s) Involved: Self): Emory study PI, Grant/Research Support; Pfizer: I conduct as co-PI the RSV PFIZER study at Emory, Research Grant; Pfizer (Individual(s) Involved: Self): Grant/Research Support, I conduct as co-PI the RSV PFIZER study at Emory; Quidel (Individual(s) Involved: Self): Emory Study PI, Grant/Research Support; Sanofi Pasteur (Individual(s) Involved: Self): Chair phase 3 COVID vaccine, Grant/Research Support Evan J. Anderson, MD, GSK (Scientific Research Study Investigator)Janssen (Consultant, Scientific Research Study Investigator, Advisor or Review Panel member)Kentucky Bioprocessing, Inc (Advisor or Review Panel member)MedImmune (Scientific Research Study Investigator)Medscape (Consultant)Merck (Scientific Research Study Investigator)Micron (Scientific Research Study Investigator)PaxVax (Scientific Research Study Investigator)Pfizer (Consultant, Grant/Research Support, Scientific Research Study Investigator)Regeneron (Scientific Research Study Investigator)Sanofi Pasteur (Consultant, Scientific Research Study Investigator)
medRxiv (Cold Spring Harbor Laboratory), Feb 25, 2021
Nearly one year into the COVID-19 pandemic, the first SARS-COV-2 vaccines received emergency use ... more Nearly one year into the COVID-19 pandemic, the first SARS-COV-2 vaccines received emergency use authorization and vaccination campaigns began. A number of factors can reduce the averted burden of cases and deaths due to vaccination. Here, we use a dynamic model, parametrized with Bayesian inference methods, to assess the effects of non-pharmaceutical interventions, and vaccine administration and uptake rates on infections and deaths averted in the United States. We estimate that high compliance with non-pharmaceutical interventions could avert more than 60% of infections and 70% of deaths during the period of vaccine administration, and that increasing the vaccination rate from 5 to 11 million people per week could increase the averted burden by more than one third. These findings underscore the importance of maintaining non-pharmaceutical interventions and increasing vaccine administration rates.
While some studies have previously estimated lives saved by COVID-19 vaccination, we estimate how... more While some studies have previously estimated lives saved by COVID-19 vaccination, we estimate how many deaths could have been averted by vaccination in the US but were not because of a failure to vaccinate. We used a simple method based on a nationally representative dataset to estimate the preventable deaths among unvaccinated individuals in the US from May 30, 2021 to September 3, 2022 adjusted for the effects of age and time. We estimated that at least 232,000 deaths could have been prevented among unvaccinated adults during the 15 months had they been vaccinated with at least a primary series. While uncertainties exist regarding the exact number of preventable deaths and more granular data are needed on other factors causing differences in death rates between the vaccinated and unvaccinated groups to inform these estimates, this method is a rapid assessment on vaccine-preventable deaths due to SARS-CoV-2 that has crucial public health implications. The same rapid method can be used for future public health emergencies.
Background. The Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD (PAIVED) is a ... more Background. The Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD (PAIVED) is a multicenter study assessing influenza vaccine effectiveness in active duty service members, retirees, and dependents. PAIVED recently completed its third year and offers a unique opportunity to examine influenza-like illness (ILI) trends prior to and during the COVID-19 pandemic in a prospective, well-defined cohort. Methods. During the 2018-19, 2019-20, and 2020-21 influenza seasons, PAIVED enrolled DoD beneficiaries presenting for annual influenza vaccination. After collecting baseline demographic data, participants were randomized to receive egg-based, cell-based, or recombinant-derived influenza vaccine. Weekly throughout the influenza season of enrollment, participants were surveyed electronically for ILI, defined as (1) having cough or sore throat, plus (2) feeling feverish/having chills or having body aches/fatigue. Participants with ILI completed a daily symptom diary for seven days and submitted a nasal swab for pathogen detection.
Between 23 August and 15 December 1990 an epidemic of cholera affected Mozambican refugees in Mal... more Between 23 August and 15 December 1990 an epidemic of cholera affected Mozambican refugees in Malawi causing 1931 cases (attack rate = 2.4%); 86% of patients had arrived in Malawi < 3 months before illness onset. There were 68 deaths (case-fatality rate = 3.5%); most deaths (63%) occurred within 24 h of hospital admission which may have indicated delayed presentation to health facilities and inadequate early rehydration. Mortality was higher in children < 4 years old and febrile deaths may have been associated with prolonged i.v. use. Significant risk factors for illness (P < 0.05) in two case-control studies included drinking river water (odds ratio [OR] = 3.0); placing hands into stored household drinking water (OR = 6.0); and among those without adequate firewood to reheat food, eating leftover cooked peas (OR = 8.0). Toxigenic V. cholerae O1, serotype Inaba, was isolated from patients and stored household water. The rapidity with which newly arrived refugees became infected precluded effective use of a cholera vaccine to prevent cases unless vaccination had occurred immediately upon camp arrival. Improved access to treatment and care of paediatric patients, and increased use of oral rehydration therapy, could decrease mortality. Preventing future cholera outbreaks in Africa will depend on interrupting both waterborne and foodborne transmission of this pathogen.
Risk Control Strategy/Key Issues: To provide early detection and response to biological or chemic... more Risk Control Strategy/Key Issues: To provide early detection and response to biological or chemical terrorism Suggested Program Elements: 1. Include terrorism in your crisis management plan with a subsection that addresses biological and chemical attacks 2. Provide training for all personnel 3. Provide specialized training for first responders 4. Practice response to emergencies 5. Document activities and follow up on noted deficiencies 6. Review the recommendations of the Center for Disease Control Strategic Planning Workgroup, provide on the following pages. Calendar of Events: • Develop procedures and policies • Provide Training • In the event of an attack: Call 911 and alert the crisis management team Activate the crisis management plan Secure and isolate exposed persons Isolate the affected area and close it off Implement media-handling protocols Secure important documentation such as rosters Provide regular communication updates Keep records of activity when possible • Conduct a comprehensive annual program review
Efforts to enhance preparedness and response capacity against terrorist attacks with biological a... more Efforts to enhance preparedness and response capacity against terrorist attacks with biological agents frequently centre on microorganisms or chemicals that are airborne and target the respiratory system. These agents and dissemination modalities were developed in military biowarfare programmes with the objective to produce the greatest number of battlefield casualties as rapidly as possible by the most efficient delivery method. 1 Biological attack on the food supply was not regarded as a primary strategy in military biowarfare programmes. The objectives of terrorists, however, can differ from those of military strategists. Terrorists might target the civilian population to create panic and threaten civil order. As mailings of envelopes containing Bacillus anthracis in the USA have shown, limited dissemination of biological agents by simple means, causing few illnesses, can produce considerable public anxiety and challenge the public-health system. 2 Intentional contamination of food has already happened in the USA. In September, 1984, members of a religious cult contaminated salad bars in The Dalles, Oregon, with Salmonella typhimurium; 751 people developed salmonellosis. This attack was reportedly a trial run for a more extensive attack that was planned to disrupt local elections later that year. 3 The cult was also in possession of strains of Salmonella typhi, the causative organism of typhoid fever, which is a more severe and invasive illness than non-typhoidal salmonellosis. Had the cult used S typhi in a larger subsequent attack, morbidity might have been higher. In 1996, a reference strain of Shigella dysenteriae type 2 was used by a laboratory worker to deliberately infect colleagues with contaminated food. 4 In 1970, a postgraduate student in parasitology at an agricultural institute near Montreal, Canada, deliberately PUBLIC HEALTH 874
American Journal of Tropical Medicine and Hygiene, Jul 1, 2010
Rocky Mountain spotted fever (RMSF), a potentially fatal tick-borne infection caused by Rickettsi... more Rocky Mountain spotted fever (RMSF), a potentially fatal tick-borne infection caused by Rickettsia rickettsii , is considered a notifiable condition in the United States. During 2000 to 2007, the annual reported incidence of RMSF increased from 1.7 to 7 cases per million persons from 2000 to 2007, the highest rate ever recorded. American Indians had a significantly higher incidence than other race groups. Children 5-9 years of age appeared at highest risk for fatal outcome. Enzyme-linked immunosorbent assays became more widely available beginning in 2004 and were used to diagnose 38% of cases during 2005-2007. The proportion of cases classified as confirmed RMSF decreased from 15% in 2000 to 4% in 2007. Concomitantly, case fatality decreased from 2.2% to 0.3%. The decreasing proportion of confirmed cases and cases with fatal outcome suggests that changes in diagnostic and surveillance practices may be influencing the observed increase in reported incidence rates.
Background The burden of Respiratory Syncytial Virus (RSV)-associated hospitalization in adults i... more Background The burden of Respiratory Syncytial Virus (RSV)-associated hospitalization in adults is incompletely understood. The COVID-19 pandemic has resulted in multiple public health measures (e.g., social distancing, handwashing, masking) to decrease SARS-CoV-2 transmission, which could impact RSV-associated hospitalizations. We sought to compare RSV-associated hospitalizations from 2 pre- and one mid-COVID-19 winter viral respiratory seasons. Methods We conducted an IRB-approved prospective surveillance at two Atlanta-area hospitals during the winter respiratory viral seasons from Oct 2018–Apr 2021 for adults ≥ 50 years of age admitted with acute respiratory infections (ARI) and adults of any age with COPD or CHF-related admissions. Adults were eligible if they were residents of an 8 county region surrounding Atlanta, Georgia. Those with symptoms > 14 days were excluded. Standard of care test results were included. Asymptomatic adults ≥ 50 years of age were enrolled as contro...
Novel data streams (NDS), such as web search data or social media updates, hold promise for enhan... more Novel data streams (NDS), such as web search data or social media updates, hold promise for enhancing the capabilities of public health surveillance. In this paper, we outline a conceptual framework for integrating NDS into current public health surveillance. Our approach focuses on two key questions: What are the opportunities for using NDS and what are the minimal tests of validity and utility that must be applied when using NDS? Identifying these opportunities will necessitate the involvement of public health authorities and an appreciation of the diversity of objectives and scales across agencies at different levels (local, state, national, international). We present the case that clearly articulating surveillance objectives and systematically evaluating NDS and comparing the performance of NDS to existing surveillance data and alternative NDS data is critical and has not sufficiently been addressed in many applications of NDS currently in the literature.
medRxiv (Cold Spring Harbor Laboratory), Jan 6, 2021
Long-term care facilities (LTCFs) bear disproportionate burden of COVID-19 and are prioritized fo... more Long-term care facilities (LTCFs) bear disproportionate burden of COVID-19 and are prioritized for vaccine deployment. LTCF outbreaks could continue occurring during vaccine rollout due to incomplete population coverage, and the effect of vaccines on viral transmission are currently unknown. Declining adherence to non-pharmaceutical interventions (NPIs) against withinfacility transmission could therefore limit the effectiveness of vaccination. We built a stochastic model to simulate outbreaks in LTCF populations with differing vaccination coverage and NPI adherence to evaluate their interacting effects. Vaccination combined with strong NPI adherence produced the least morbidity and mortality. Healthcare worker vaccination improved outcomes in unvaccinated LTCF residents but was less impactful with declining NPI adherence. To prevent further illness and deaths, there is a continued need for NPIs in LTCFs during vaccine rollout. MAIN The COVID-19 pandemic has been particularly devastating for residents of LTCFs (skilled nursing homes and assisted living facilities). While there has been a shift of disease burden to. CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity.
The first ever case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported in Se... more The first ever case of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) was reported in September 2012. This report describes the approaches taken by CDC, in collaboration with the World Health Organization (WHO) and other partners, to respond to this novel virus, and outlines the agency responses prior to the first case appearing in the United States in May 2014. During this time, CDC's response integrated multiple disciplines and was divided into three distinct phases: before, during, and after the initial activation of its Emergency Operations Center. CDC's response to MERS-CoV required a large effort, deploying at least 353 staff members who worked in the areas of surveillance, laboratory capacity, infection control guidance, and travelers' health. This response built on CDC's experience with previous outbreaks of other pathogens and provided useful lessons for future emerging threats.
The findings and conclusions in this report are those of the authors and do not necessarily repre... more The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention.
BackgroundAdult respiratory syncytial virus (RSV) vaccines are in late stages of development. A c... more BackgroundAdult respiratory syncytial virus (RSV) vaccines are in late stages of development. A comprehensive synthesis of adult RSV burden is needed to inform public health decision-making.MethodsWe performed a systematic review and meta-analysis of studies describing the incidence of medically-attended RSV (MA-RSV) among US adults. We also identified studies reporting nasopharyngeal (NP) or nasal swab RT-PCR results with paired serology (four-fold-rise) or sputum (RT-PCR) to calculate RSV detection ratios quantifying improved diagnostic yield after adding a second specimen type (ie, serology or sputum).ResultsWe identified 14 studies with 15 unique MA-RSV incidence estimates, all based on NP or nasal swab RT-PCR testing alone. Pooled annual RSV-associated incidence per 100,000 adults ≥65 years of age was 178 (95%CI: 152‒204; n=8 estimates) hospitalizations (4 prospective studies: 189; 4 model-based studies: 157), 133 (95%CI: 0‒319, n=2) emergency department (ED) admissions, and 1519 (95%CI: 1109‒1929, n=3) outpatient visits. Based on 6 studies, RSV detection was ∼1.5 times higher when adding paired serology or sputum. After adjustment for this increased yield, annual RSV-associated rates per 100,000 adults ≥65 years were 267 hospitalizations (UI: 228‒306) (prospective: 282; model-based: 236), 200 ED admissions (UI: 0‒478), and 2278 outpatient visits (UI: 1663‒2893). Persons < 65 years with chronic medical conditions were 1.2−28 times more likely to be hospitalized for RSV depending on risk condition.ConclusionThe true burden of RSV has been underestimated and is significant among older adults and individuals with chronic medical conditions. A highly effective adult RSV vaccine would have substantial public-health impact.Disclosures John M. McLaughlin, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds Farid L. Khan, MPH, Pfizer: Employee|Pfizer: Stocks/Bonds Elizabeth Begier, M.D., M.P.H., Pfizer: Employee|Pfizer: Stocks/Bonds David Swerdlow, MD, Pfizer: Advisor/Consultant|Pfizer: Stocks/Bonds Luis Jodar, PhD, Pfizer: Employee|Pfizer: Stocks/Bonds Ann R. Falsey, MD, BioFire Diagnostics: Grant/Research Support|Janssen: Grant/Research Support|Merck, Sharp and Dohme: Grant/Research Support|Novavax: Advisor/Consultant|Pfizer: Grant/Research Support.
Virus SARS-CoV MERS-CoV Type of coronavirus Lineage b betacoronavirus Lineage c betacoronavirus H... more Virus SARS-CoV MERS-CoV Type of coronavirus Lineage b betacoronavirus Lineage c betacoronavirus Host cell receptor Angiotensin converting enzyme 2 Dipeptidyl peptidase 4 Animal hosts Chinese horseshoe bats, palm civets Not yet confirmed, but camel is likely host Incubation period Mean (95% CI; days) 4.6 (3.8-5.8) 5.2 (1.9-14.7) Range (days) 2-14 2-13 Serial interval (days) 8.4 7.6 Basic reproduction number 2-3 <1 Patient characteristics Adults 93% 98% Children 5-7% 2% Age range (years) 1-91 1-94 Average age (years) Mean 39.9 Median 50 Sex ratio (M:F) 43%:57% 64.5%:35.5% Mortality Case fatality rate overall 9.6% 40% Case fatality rate with comorbidities 46% 60% Time (days) from symptom onset to hospitalization 2-8 0-16 Time (days) from symptom onset to death 21 12 TABLE 2 Chronology of key events a,b Date Key events April 2012 Cluster of 13 patients in a hospital in Jordan with acute respiratory illness; two deceased patients of this cluster were retrospectively diagnosed (in September 2012) through study of stored specimens with MERS-CoV (5, 90)
Abstract Background A significant burden of disease exists for adults infected with influenza (fl... more Abstract Background A significant burden of disease exists for adults infected with influenza (flu) and SARS-CoV-2, which causes COVID-19. However, data are limited comparing outcomes between hospitalized adults infected with these viruses. Methods Over the course of 3 consecutive winter respiratory viral seasons, adults ≥ 50 years of age admitted with acute respiratory tract infections (ARI) and adults of any age with COPD or CHF-related admissions were enrolled from 2 Atlanta area hospitals. For the 2018-19 and 2019-20 seasons, participants were approached in the hospital. If the participant enrolled, nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected and tested using BioFire® FilmArray® respiratory panel. Due to the COVID-19 pandemic in 2020-21 and limitations involving participant contact, only NP standard of care (SOC) swabs were collected. A comprehensive medical chart review was completed for each subject which encompassed data on their hospitalization, past medical history, and vaccination history. Co-infected patients were excluded from the analyses. Results Of the eligible participants, 118 were flu positive (three RSV-influenza co-infections were excluded) and 527 were COVID-19 positive. Median age was lower for the flu cohort at 62 (IQR 56-71) than those with COVID-19 (67, IQR 59-77) (p < 0.0001). Length of stay (LOS) was shorter in flu-infected patients (median 3 d, IQR 2-6), but was longer for COVID-19 patients (median 5 d, IQR 3-10). ICU admission occurred in 20% of those with flu, and among those admitted to the ICU mechanical ventilation (MV) occurred in 12.5%. ICU admission and MV was significantly higher for those with COVID-19, with 28% of patients admitted to the ICU and 47% of those requiring MV. Among patients with COVID-19, 8.9% died. This was significantly higher than that of flu (3.4%) (p=0.008). Hospital discharge occurred more frequently to a nursing home or LTCF with COVID-19 (10.3%) than with flu (0%) (p< 0.0001). Table 1. Breakdown of age, hospitalization course, and discharge disposition for participants diagnosed with influenza or COVID-19 during hospitalization. Conclusion COVID-19 resulted in a longer hospital admission, a greater chance of ICU admission and MV as compared to flu. Additionally, COVID-19 participants had a high rate of discharge to a nursing home/LTCF and a significantly higher risk of death. While the clinical course was not as severe as COVID-19, influenza contributed a significant burden. Disclosures David L. Swerdlow, MD, Pfizer Vaccines (Employee) Robin Hubler, MS, Pfizer Inc. (Employee) Christina A. Rostad, MD, BioFire Inc, GSK, MedImmune, Micron, Janssen, Merck, Moderna, Novavax, PaxVax, Pfizer, Regeneron, Sanofi-Pasteur. (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support)Meissa Vaccines (Other Financial or Material Support, Co-inventor of patented RSV vaccine technology unrelated to this manuscript, which has been licensed to Meissa Vaccines, Inc.) Larry Anderson, MD, ADVI (Consultant)Bavarian Nordic (Consultant)Novavax (Consultant)Phizer (Grant/Research Support, Scientific Research Study Investigator)Sciogen (Research Grant or Support) Nadine Rouphael, MD, pfizer, sanofi, lily, quidel, merck (Grant/Research Support) Nadine Rouphael, MD, Lilly (Individual(s) Involved: Self): Emory Study PI, Grant/Research Support; Merck (Individual(s) Involved: Self): Emory study PI, Grant/Research Support; Pfizer: I conduct as co-PI the RSV PFIZER study at Emory, Research Grant; Pfizer (Individual(s) Involved: Self): Grant/Research Support, I conduct as co-PI the RSV PFIZER study at Emory; Quidel (Individual(s) Involved: Self): Emory Study PI, Grant/Research Support; Sanofi Pasteur (Individual(s) Involved: Self): Chair phase 3 COVID vaccine, Grant/Research Support Evan J. Anderson, MD, GSK (Scientific Research Study Investigator)Janssen (Consultant, Scientific Research Study Investigator, Advisor or Review Panel member)Kentucky Bioprocessing, Inc (Advisor or Review Panel member)MedImmune (Scientific Research Study Investigator)Medscape (Consultant)Merck (Scientific Research Study Investigator)Micron (Scientific Research Study Investigator)PaxVax (Scientific Research Study Investigator)Pfizer (Consultant, Grant/Research Support, Scientific Research Study Investigator)Regeneron (Scientific Research Study Investigator)Sanofi Pasteur (Consultant, Scientific Research Study Investigator)
medRxiv (Cold Spring Harbor Laboratory), Feb 25, 2021
Nearly one year into the COVID-19 pandemic, the first SARS-COV-2 vaccines received emergency use ... more Nearly one year into the COVID-19 pandemic, the first SARS-COV-2 vaccines received emergency use authorization and vaccination campaigns began. A number of factors can reduce the averted burden of cases and deaths due to vaccination. Here, we use a dynamic model, parametrized with Bayesian inference methods, to assess the effects of non-pharmaceutical interventions, and vaccine administration and uptake rates on infections and deaths averted in the United States. We estimate that high compliance with non-pharmaceutical interventions could avert more than 60% of infections and 70% of deaths during the period of vaccine administration, and that increasing the vaccination rate from 5 to 11 million people per week could increase the averted burden by more than one third. These findings underscore the importance of maintaining non-pharmaceutical interventions and increasing vaccine administration rates.
While some studies have previously estimated lives saved by COVID-19 vaccination, we estimate how... more While some studies have previously estimated lives saved by COVID-19 vaccination, we estimate how many deaths could have been averted by vaccination in the US but were not because of a failure to vaccinate. We used a simple method based on a nationally representative dataset to estimate the preventable deaths among unvaccinated individuals in the US from May 30, 2021 to September 3, 2022 adjusted for the effects of age and time. We estimated that at least 232,000 deaths could have been prevented among unvaccinated adults during the 15 months had they been vaccinated with at least a primary series. While uncertainties exist regarding the exact number of preventable deaths and more granular data are needed on other factors causing differences in death rates between the vaccinated and unvaccinated groups to inform these estimates, this method is a rapid assessment on vaccine-preventable deaths due to SARS-CoV-2 that has crucial public health implications. The same rapid method can be used for future public health emergencies.
Background. The Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD (PAIVED) is a ... more Background. The Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD (PAIVED) is a multicenter study assessing influenza vaccine effectiveness in active duty service members, retirees, and dependents. PAIVED recently completed its third year and offers a unique opportunity to examine influenza-like illness (ILI) trends prior to and during the COVID-19 pandemic in a prospective, well-defined cohort. Methods. During the 2018-19, 2019-20, and 2020-21 influenza seasons, PAIVED enrolled DoD beneficiaries presenting for annual influenza vaccination. After collecting baseline demographic data, participants were randomized to receive egg-based, cell-based, or recombinant-derived influenza vaccine. Weekly throughout the influenza season of enrollment, participants were surveyed electronically for ILI, defined as (1) having cough or sore throat, plus (2) feeling feverish/having chills or having body aches/fatigue. Participants with ILI completed a daily symptom diary for seven days and submitted a nasal swab for pathogen detection.
Between 23 August and 15 December 1990 an epidemic of cholera affected Mozambican refugees in Mal... more Between 23 August and 15 December 1990 an epidemic of cholera affected Mozambican refugees in Malawi causing 1931 cases (attack rate = 2.4%); 86% of patients had arrived in Malawi < 3 months before illness onset. There were 68 deaths (case-fatality rate = 3.5%); most deaths (63%) occurred within 24 h of hospital admission which may have indicated delayed presentation to health facilities and inadequate early rehydration. Mortality was higher in children < 4 years old and febrile deaths may have been associated with prolonged i.v. use. Significant risk factors for illness (P < 0.05) in two case-control studies included drinking river water (odds ratio [OR] = 3.0); placing hands into stored household drinking water (OR = 6.0); and among those without adequate firewood to reheat food, eating leftover cooked peas (OR = 8.0). Toxigenic V. cholerae O1, serotype Inaba, was isolated from patients and stored household water. The rapidity with which newly arrived refugees became infected precluded effective use of a cholera vaccine to prevent cases unless vaccination had occurred immediately upon camp arrival. Improved access to treatment and care of paediatric patients, and increased use of oral rehydration therapy, could decrease mortality. Preventing future cholera outbreaks in Africa will depend on interrupting both waterborne and foodborne transmission of this pathogen.
Risk Control Strategy/Key Issues: To provide early detection and response to biological or chemic... more Risk Control Strategy/Key Issues: To provide early detection and response to biological or chemical terrorism Suggested Program Elements: 1. Include terrorism in your crisis management plan with a subsection that addresses biological and chemical attacks 2. Provide training for all personnel 3. Provide specialized training for first responders 4. Practice response to emergencies 5. Document activities and follow up on noted deficiencies 6. Review the recommendations of the Center for Disease Control Strategic Planning Workgroup, provide on the following pages. Calendar of Events: • Develop procedures and policies • Provide Training • In the event of an attack: Call 911 and alert the crisis management team Activate the crisis management plan Secure and isolate exposed persons Isolate the affected area and close it off Implement media-handling protocols Secure important documentation such as rosters Provide regular communication updates Keep records of activity when possible • Conduct a comprehensive annual program review
Efforts to enhance preparedness and response capacity against terrorist attacks with biological a... more Efforts to enhance preparedness and response capacity against terrorist attacks with biological agents frequently centre on microorganisms or chemicals that are airborne and target the respiratory system. These agents and dissemination modalities were developed in military biowarfare programmes with the objective to produce the greatest number of battlefield casualties as rapidly as possible by the most efficient delivery method. 1 Biological attack on the food supply was not regarded as a primary strategy in military biowarfare programmes. The objectives of terrorists, however, can differ from those of military strategists. Terrorists might target the civilian population to create panic and threaten civil order. As mailings of envelopes containing Bacillus anthracis in the USA have shown, limited dissemination of biological agents by simple means, causing few illnesses, can produce considerable public anxiety and challenge the public-health system. 2 Intentional contamination of food has already happened in the USA. In September, 1984, members of a religious cult contaminated salad bars in The Dalles, Oregon, with Salmonella typhimurium; 751 people developed salmonellosis. This attack was reportedly a trial run for a more extensive attack that was planned to disrupt local elections later that year. 3 The cult was also in possession of strains of Salmonella typhi, the causative organism of typhoid fever, which is a more severe and invasive illness than non-typhoidal salmonellosis. Had the cult used S typhi in a larger subsequent attack, morbidity might have been higher. In 1996, a reference strain of Shigella dysenteriae type 2 was used by a laboratory worker to deliberately infect colleagues with contaminated food. 4 In 1970, a postgraduate student in parasitology at an agricultural institute near Montreal, Canada, deliberately PUBLIC HEALTH 874
American Journal of Tropical Medicine and Hygiene, Jul 1, 2010
Rocky Mountain spotted fever (RMSF), a potentially fatal tick-borne infection caused by Rickettsi... more Rocky Mountain spotted fever (RMSF), a potentially fatal tick-borne infection caused by Rickettsia rickettsii , is considered a notifiable condition in the United States. During 2000 to 2007, the annual reported incidence of RMSF increased from 1.7 to 7 cases per million persons from 2000 to 2007, the highest rate ever recorded. American Indians had a significantly higher incidence than other race groups. Children 5-9 years of age appeared at highest risk for fatal outcome. Enzyme-linked immunosorbent assays became more widely available beginning in 2004 and were used to diagnose 38% of cases during 2005-2007. The proportion of cases classified as confirmed RMSF decreased from 15% in 2000 to 4% in 2007. Concomitantly, case fatality decreased from 2.2% to 0.3%. The decreasing proportion of confirmed cases and cases with fatal outcome suggests that changes in diagnostic and surveillance practices may be influencing the observed increase in reported incidence rates.
Background The burden of Respiratory Syncytial Virus (RSV)-associated hospitalization in adults i... more Background The burden of Respiratory Syncytial Virus (RSV)-associated hospitalization in adults is incompletely understood. The COVID-19 pandemic has resulted in multiple public health measures (e.g., social distancing, handwashing, masking) to decrease SARS-CoV-2 transmission, which could impact RSV-associated hospitalizations. We sought to compare RSV-associated hospitalizations from 2 pre- and one mid-COVID-19 winter viral respiratory seasons. Methods We conducted an IRB-approved prospective surveillance at two Atlanta-area hospitals during the winter respiratory viral seasons from Oct 2018–Apr 2021 for adults ≥ 50 years of age admitted with acute respiratory infections (ARI) and adults of any age with COPD or CHF-related admissions. Adults were eligible if they were residents of an 8 county region surrounding Atlanta, Georgia. Those with symptoms > 14 days were excluded. Standard of care test results were included. Asymptomatic adults ≥ 50 years of age were enrolled as contro...
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Papers by David Swerdlow