Benjamin J. Silk

Centers for Disease Control and Prevention

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Heather M. Scobie

Centers for Disease Control and Prevention

Aron J. Hall

Centers for Disease Control and Prevention

Kelly A. Jackson

Centers for Disease Control and Prevention

Ruth L. Berkelman

Emory University

Amber Winn

Centers for Disease Control and Prevention

Heather E. Reese

National Center for Emerging and Zoonotic Infectious Diseases

Sarah Talarico

National Center for HIV/AIDS Viral Hepatitis STD and TB Prevention

Aaron T. Fleischauer

Centers for Disease Control and Prevention

J. Steve Kammerer

Centers for Disease Control and Prevention

Clinton R. Paden

Centers for Disease Control and Prevention

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National Center for Emerging and Zoonotic Infectious Diseases

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Minnesota Department of Health

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Center for Surveillance, Epidemiology, and Laboratory Services

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Epidemic Intelligence Service

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Utah Department of Health

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COVID-19 Incidence and Death Rates Among Unvaccinated and Fully Vaccinated Adults with and Without Booster Doses During Periods of Delta and Omicron Variant Emergence — 25 U.S. Jurisdictions, April 4–December 25, 2021

MMWR Morbidity and Mortality Weekly Report (2022)

Amelia G. Johnson Avnika B. Amin Akilah R. Ali Brooke Hoots Betsy L. Cadwell

Previous reports of COVID-19 case, hospitalization, and death rates by vaccination status

Booster (rocketry)

2019-20 coronavirus outbreak

10.15585/mmwr.mm7104e2

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Citations (311)

Application of a life table approach to assess duration of BNT162b2 vaccine-derived immunity by age using COVID-19 case surveillance data during the Omicron variant period

PLoS ONE (2023)

Maya Sternberg Amelia G. Johnson Justice King Akilah R. Ali Lauren Linde

Background SARS-CoV-2 Omicron variants have the potential to impact vaccine effectiveness and duration of vaccine-derived immunity. We analyzed U.S. multi-jurisdictional COVID-19 vaccine breakthrough surveillance data to examine potential waning of protection against SARS-CoV-2 infection for the Pfizer-BioNTech (BNT162b) primary vaccination series by age. Methods Weekly numbers of SARS-CoV-2 infections during January 16, 2022–May 28, 2022 were analyzed by age group from 22 U.S. jurisdictions that routinely linked COVID-19 case surveillance and immunization data. A life table approach incorporating line-listed and aggregated COVID-19 case datasets with vaccine administration and U.S. Census data was used to estimate hazard rates of SARS-CoV-2 infections, hazard rate ratios (HRR) and percent reductions in hazard rate comparing unvaccinated people to people vaccinated with a Pfizer-BioNTech primary series only, by age group and time since vaccination. Results The percent reduction in hazard rates for persons 2 weeks after vaccination with a Pfizer-BioNTech primary series compared with unvaccinated persons was lowest among children aged 5–11 years at 35.5% (95% CI: 33.3%, 37.6%) compared to the older age groups, which ranged from 68.7%–89.6%. By 19 weeks after vaccination, all age groups showed decreases in the percent reduction in the hazard rates compared with unvaccinated people; with the largest declines observed among those aged 5–11 and 12–17 years and more modest declines observed among those 18 years and older. Conclusions The decline in vaccine protection against SARS-CoV-2 infection observed in this study is consistent with other studies and demonstrates that national case surveillance data were useful for assessing early signals in age-specific waning of vaccine protection during the initial period of SARS-CoV-2 Omicron variant predominance. The potential for waning immunity during the Omicron period emphasizes the importance of continued monitoring and consideration of optimal timing and provision of booster doses in the future.

Age groups

10.1371/journal.pone.0291678

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Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021

MMWR Morbidity and Mortality Weekly Report (2021)

Summer E. Galloway Prabasaj Paul Duncan MacCannell Michael A. Johansson John T. Brooks

On December 14, 2020, the United Kingdom reported a SARS-CoV-2 variant of concern (VOC), lineage B.1.1.7, also referred to as VOC 202012/01 or 20I/501Y.V1.* The B.1.1.7 variant is estimated to have emerged in September 2020 and has quickly become the dominant circulating SARS-CoV-2 variant in England (1). B.1.1.7 has been detected in over 30 countries, including the United States. As of January 13, 2021, approximately 76 cases of B.1.1.7 have been detected in 12 U.S. states.† Multiple lines of evidence indicate that B.1.1.7 is more efficiently transmitted than are other SARS-CoV-2 variants (1-3). The modeled trajectory of this variant in the U.S. exhibits rapid growth in early 2021, becoming the predominant variant in March. Increased SARS-CoV-2 transmission might threaten strained health care resources, require extended and more rigorous implementation of public health strategies (4), and increase the percentage of population immunity required for pandemic control. Taking measures to reduce transmission now can lessen the potential impact of B.1.1.7 and allow critical time to increase vaccination coverage. Collectively, enhanced genomic surveillance combined with continued compliance with effective public health measures, including vaccination, physical distancing, use of masks, hand hygiene, and isolation and quarantine, will be essential to limiting the spread of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19). Strategic testing of persons without symptoms but at higher risk of infection, such as those exposed to SARS-CoV-2 or who have frequent unavoidable contact with the public, provides another opportunity to limit ongoing spread.

Pandemic

Isolation

Herd Immunity

Limiting

10.15585/mmwr.mm7003e2

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Citations (687)

Seasonality of Common Human Coronaviruses, United States, 2014–20211

Emerging infectious diseases (2022)

Melisa M. Shah Amber Winn Rebecca M. Dahl Krista Kniss Benjamin J. Silk

The 4 common types of human coronaviruses (HCoVs)-2 alpha (HCoV-NL63 and HCoV-229E) and 2 beta (HCoV-HKU1 and HCoV-OC43)-generally cause mild upper respiratory illness. Seasonal patterns and annual variation in predominant types of HCoVs are known, but parameters of expected seasonality have not been defined. We defined seasonality of HCoVs during July 2014-November 2021 in the United States by using a retrospective method applied to National Respiratory and Enteric Virus Surveillance System data. In the 6 HCoV seasons before 2020-21, season onsets occurred October 21-November 12, peaks January 6-February 13, and offsets April 18-June 27; most (>93%) HCoV detection was within the defined seasonal onsets and offsets. The 2020-21 HCoV season onset was 11 weeks later than in prior seasons, probably associated with COVID-19 mitigation efforts. Better definitions of HCoV seasonality can be used for clinical preparedness and for determining expected patterns of emerging coronaviruses.

2019-20 coronavirus outbreak

Betacoronavirus

Coronavirus

Coronavirus Infections

Seasonality

10.3201/eid2810.220396

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Citations (41)

COVID-19 Surveillance After Expiration of the Public Health Emergency Declaration ― United States, May 11, 2023

MMWR Morbidity and Mortality Weekly Report (2023)

Benjamin J. Silk Heather M. Scobie William M. Duck Tess Palmer Farida B. Ahmad

On January 31, 2020, the U.S. Department of Health and Human Services (HHS) declared, under Section 319 of the Public Health Service Act, a U.S. public health emergency because of the emergence of a novel virus, SARS-CoV-2.* After 13 renewals, the public health emergency will expire on May 11, 2023. Authorizations to collect certain public health data will expire on that date as well. Monitoring the impact of COVID-19 and the effectiveness of prevention and control strategies remains a public health priority, and a number of surveillance indicators have been identified to facilitate ongoing monitoring. After expiration of the public health emergency, COVID-19-associated hospital admission levels will be the primary indicator of COVID-19 trends to help guide community and personal decisions related to risk and prevention behaviors; the percentage of COVID-19-associated deaths among all reported deaths, based on provisional death certificate data, will be the primary indicator used to monitor COVID-19 mortality. Emergency department (ED) visits with a COVID-19 diagnosis and the percentage of positive SARS-CoV-2 test results, derived from an established sentinel network, will help detect early changes in trends. National genomic surveillance will continue to be used to estimate SARS-CoV-2 variant proportions; wastewater surveillance and traveler-based genomic surveillance will also continue to be used to monitor SARS-CoV-2 variants. Disease severity and hospitalization-related outcomes are monitored via sentinel surveillance and large health care databases. Monitoring of COVID-19 vaccination coverage, vaccine effectiveness (VE), and vaccine safety will also continue. Integrated strategies for surveillance of COVID-19 and other respiratory viruses can further guide prevention efforts. COVID-19-associated hospitalizations and deaths are largely preventable through receipt of updated vaccines and timely administration of therapeutics (1-4).

Public health surveillance

Declaration

10.15585/mmwr.mm7219e1

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Citations (64)

Tuberculosis Outbreaks in State Prisons, United States, 2011–2019

American Journal of Public Health (2022)

Rebekah J. Stewart Kala M. Raz Scott Burns J. Steve Kammerer Maryam B. Haddad

Objectives. To understand the frequency, magnitude, geography, and characteristics of tuberculosis outbreaks in US state prisons. Methods. Using data from the National Tuberculosis Surveillance System, we identified all cases of tuberculosis during 2011 to 2019 that were reported as occurring among individuals incarcerated in a state prison at the time of diagnosis. We used whole-genome sequencing to define 3 or more cases within 2 single nucleotide polymorphisms within 3 years as clustered; we classified clusters with 6 or more cases during a 3-year period as tuberculosis outbreaks. Results. During 2011 to 2019, 566 tuberculosis cases occurred in 41 state prison systems (a median of 3 cases per state). A total of 19 tuberculosis genotype clusters comprising 134 cases were identified in 6 state prison systems; these clusters included a subset of 5 outbreaks in 2 states. Two Alabama outbreaks during 2011 to 2017 totaled 20 cases; 3 Texas outbreaks during 2014 to 2019 totaled 51 cases. Conclusions. Only Alabama and Texas reported outbreaks during the 9-year period; only Texas state prisons had ongoing transmission in 2019. Effective interventions are needed to stop tuberculosis outbreaks in Texas state prisons. (Am J Public Health. 2022;112(8):1170-1179. https://doi.org/10.2105/AJPH.2022.306864).

10.2105/ajph.2022.306864

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Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing

Applied and Environmental Microbiology (2015)

Teresa M. Bergholz Henk C. den Bakker Lee S. Katz Benjamin J. Silk Kelly A. Jackson

We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or "epidemic clones" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.

Subtyping

Horizontal Gene Transfer

10.1128/aem.02440-15

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West Nile Virus among Hospitalized, Febrile Patients: A Case for Expanding Diagnostic Testing

Vector-Borne and Zoonotic Diseases (2006)

Ellen A. Spotts Whitney Katherine L. Heilpern Christopher W. Woods C. Christina Bahn Elizabeth Franko

In Georgia, most individuals reported with West Nile virus (WNV) disease have been diagnosed with West Nile neuroinvasive disease (WNND). Relatively few cases of West Nile Fever (WNF) are reported, and the burden of illness due to WNV is likely underestimated. From July through October 2003, WNV serologic testing was performed on enrolled patients ≥18 years of age with fever admitted to a large, urban hospital in Atlanta, Georgia through the emergency department (ED). Patients' history, clinical, and laboratory data were recorded. Residual blood drawn in the ED was tested to determine the presence of WNV IgG and IgM antibodies. Of 254 patients tested for WNV, four (1.6%) patients were positive for WNV IgM and IgG antibodies, and had a clinical illness compatible with WNV. None of the four positive patients were clinically suspected of having WNV infection; discharge diagnoses included pneumonia, migraine, stroke, and gout. These four patients accounted for 80% of all WNV diagnosed in this hospital, 44% of all cases in Fulton County, and 7% of all cases reported in Georgia in 2003. The occurrence of WNV disease may be substantially greater than currently reflected in disease statistics in Georgia and many other states. When indicators of WNV activity are present and patients are likely to have had intensive mosquito exposure, WNV should be considered in the differential diagnosis of seriously ill, febrile patients.

West Nile virus

10.1089/vbz.2006.6.42

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Citations (7)

Monitoring Incidence of COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Status — 13 U.S. Jurisdictions, April 4–July 17, 2021

MMWR Morbidity and Mortality Weekly Report (2021)

Heather M. Scobie Amelia G. Johnson Amitabh B. Suthar Rachel Severson Nisha B. Alden

Portions of the population in Colorado (49%), Minnesota (55%), New Mexico (61%), and Utah (35%) and the whole population of Maryland are included as part of the COVID-19-Associated Hospitalization Surveillance Network (COVID-NET).https:

2019-20 coronavirus outbreak

10.15585/mmwr.mm7037e1

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Citations (288)

Investigating 2009 Pandemic Influenza A (H1N1) in US Schools: What Have We Learned?

Clinical Infectious Diseases (2010)

A. Danielle Iuliano Fatimah S. Dawood Benjamin J. Silk Achuyt Bhattarai Daphne Copeland

US investigations of school-based outbreaks of 2009 pandemic influenza A (H1N1) virus infection characterized influenza-like illness (ILI) attack rates, transmission risk factors, and adherence to nonpharmaceutical interventions. We summarize seven school-based investigations conducted during April-June 2009 to determine what questions might be answered by future investigations. Surveys were administered 5-28 days after identification of the outbreaks, and participation rates varied among households (39-86%) and individuals (24-49%). Compared with adults (4%-10%) and children aged <4 years (2%-7%), elementary through university students had higher ILI attack rates (4%-32%). Large gatherings or close contact with sick persons were identified as transmission risk factors. More participants reported adherence to hygiene measures, but fewer reported adherence to isolation measures. Challenges included low participation and delays in survey initiation that potentially introduced bias. Although school-based investigations can increase our understanding of epidemiology and prevention strategy effectiveness, investigators should decide which objectives are most feasible, given timing and design constraints.

Pandemic

Isolation

Attack rate

10.1093/cid/ciq032

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Citations (19)