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1.
medrxiv; 2023.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2023.02.02.23285391

ABSTRACT

Wastewater-based epidemiology (WBE) emerged during the COVID-19 pandemic as a scalable and broadly applicable method for community-level monitoring of infectious disease burden, though the lack of high-quality, longitudinal fecal shedding data of SARS-CoV-2 and other viruses limits the interpretation and applicability of wastewater measurements. In this study, we present longitudinal, quantitative fecal shedding data for SARS-CoV-2 RNA, as well as the commonly used fecal indicators Pepper Mild Mottle Virus (PMMoV) RNA and crAss-like phage (crAssphage) DNA. The shedding trajectories from 48 SARS-CoV-2 infected individuals suggest a highly individualized, dynamic course of SARS-CoV-2 RNA fecal shedding, with individual measurements varying from below limit of detection to 2.79x10^6 gene copies/mg - dry mass of stool (gc/mg-dw). Of individuals that contributed at least 3 samples covering a range of at least 15 of the first 30 days after initial acute symptom onset, 77.4% had at least one positive SARS-CoV-2 RNA stool sample measurement. We detected PMMoV RNA in at least one sample from all individuals and in 96% (352/367) of samples overall; and measured crAssphage DNA above detection limits in 80% (38/48) of individuals and 48% (179/371) of samples. Median shedding values for PMMoV and crAssphage nucleic acids were 1x10^5 gc/mg-dw and 1.86x10^3 gc/mg-dw, respectively. These results can be used to inform and build mechanistic models to significantly broaden the potential of WBE modeling and to provide more accurate insight into SARS-CoV-2 prevalence estimates.


Subject(s)
COVID-19 , Severe Acute Respiratory Syndrome
2.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.05.15.22275051

ABSTRACT

The impact of vaccination on SARS-CoV-2 infectiousness is not well understood. We compared longitudinal viral shedding dynamics in unvaccinated and fully vaccinated adults. SARS-CoV-2-infected adults were enrolled within 5 days of symptom onset and nasal specimens were self-collected daily for two weeks and intermittently for an additional two weeks. SARS-CoV-2 RNA load and infectious virus were analyzed relative to symptom onset stratified by vaccination status. We tested 1080 nasal specimens from 52 unvaccinated adults enrolled in the pre-Delta period and 32 fully vaccinated adults with predominantly Delta infections. While we observed no differences by vaccination status in maximum RNA levels, maximum infectious titers and the median duration of viral RNA shedding, the rate of decay from the maximum RNA load was faster among vaccinated; maximum infectious titers and maximum RNA levels were highly correlated. Furthermore, amongst participants with infectious virus, median duration of infectious virus detection was reduced from 7.5 days (IQR: 6.0-9.0) in unvaccinated participants to 6 days (IQR: 5.0-8.0) in those vaccinated (P=0.02). Accordingly, the odds of shedding infectious virus from days 6 to 12 post-onset were lower among vaccinated participants than unvaccinated participants (OR 0.42 95% CI 0.19-0.89). These results indicate that vaccination had reduced the probability of shedding infectious virus after 5 days from symptom onset.


Subject(s)
Hepatitis D , Severe Acute Respiratory Syndrome
3.
medrxiv; 2022.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2022.01.14.22269235

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection elicits an antibody response that targets several viral proteins including spike (S) and nucleocapsid (N); S is the major target of neutralizing antibodies. Here, we assess levels of anti-N binding antibodies and anti-S neutralizing antibodies in unvaccinated children compared with unvaccinated older adults following infection. Specifically, we examine neutralization and anti-N binding by sera collected up to 52 weeks following SARS-CoV-2 infection in children and compare these to a cohort of adults, including older adults, most of whom had mild infections that did not require hospitalization. Neutralizing antibody titers were lower in children than adults early after infection, but by 6 months titers were similar between age groups. The neutralizing activity of the children's sera decreased modestly from one to six months; a pattern that was not significantly different from that observed in adults. However, infection of children induced much lower levels of anti-N antibodies than in adults, and levels of these anti-N antibodies decreased more rapidly in children than in adults, including older adults. These results highlight age-related differences in the antibody responses to SARS-CoV-2 proteins and, as vaccines for children are introduced, may provide comparator data for the longevity of infection-elicited and vaccination-induced neutralizing antibody responses.


Subject(s)
Coronavirus Infections , Severe Acute Respiratory Syndrome , COVID-19
4.
MMWR Morb Mortal Wkly Rep ; 69(early release), 2020.
Article | Centers for Disease Control and Prevention | ID: covidwho-619839

ABSTRACT

This report describes exposures to SARS-CoV-2 of persons in Colorado before implementation of stay-at-home orders.

5.
Rachel M Burke; Sharon Balter; Emily Barnes; Vaughn Barry; Karri Bartlett; Karlyn D Beer; Isaac Benowitz; Holly M Biggs; Hollianne Bruce; Jonathan Bryant-Genevier; Jordan Cates; Kevin Chatham-Stephens; Nora Chea; Howard Chiou; Demian Christiansen; Victoria Chu; Shauna Clark; Sara H. Cody; Max Cohen; Erin E Conners; Vishal Dasari; Patrick Dawson; Traci DeSalvo; Matthew Donahue; Alissa Dratch; Lindsey Duca; Jeffrey Duchin; Jonathan W Dyal; Leora R Feldstein; Marty Fenstersheib; Marc Fischer; Rebecca Fisher; Chelsea Foo; Brandi Freeman-Ponder; Alicia M Fry; Jessica Gant; Romesh Gautom; Isaac Ghinai; Prabhu Gounder; Cheri T Grigg; Jeffrey Gunzenhauser; Aron J Hall; George S Han; Thomas Haupt; Michelle Holshue; Jennifer Hunter; Mireille B Ibrahim; Max W Jacobs; M. Claire Jarashow; Kiran Joshi; Talar Kamali; Vance Kawakami; Moon Kim; Hannah Kirking; Amanda Kita-Yarbro; Rachel Klos; Miwako Kobayashi; Anna Kocharian; Misty Lang; Jennifer Layden; Eva Leidman; Scott Lindquist; Stephen Lindstrom; Ruth Link-Gelles; Mariel Marlow; Claire P Mattison; Nancy McClung; Tristan McPherson; Lynn Mello; Claire M Midgley; Shannon Novosad; Megan T Patel; Kristen Pettrone; Satish K Pillai; Ian W Pray; Heather E Reese; Heather Rhodes; Susan Robinson; Melissa Rolfes; Janell Routh; Rachel Rubin; Sarah L Rudman; Denny Russell; Sarah Scott; Varun Shetty; Sarah E Smith-Jeffcoat; Elizabeth A Soda; Chris Spitters; Bryan Stierman; Rebecca Sunenshine; Dawn Terashita; Elizabeth Traub; Grace E Vahey; Jennifer R Verani; Megan Wallace; Matthew Westercamp; Jonathan Wortham; Amy Xie; Anna Yousaf; Matthew Zahn.
medrxiv; 2020.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2020.04.27.20081901

ABSTRACT

Background Coronavirus disease 2019 (COVID-19), the respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first identified in Wuhan, China and has since become pandemic. As part of initial response activities in the United States, enhanced contact investigations were conducted to enable early identification and isolation of additional cases and to learn more about risk factors for transmission. Methods Close contacts of nine early travel-related cases in the United States were identified. Close contacts meeting criteria for active monitoring were followed, and selected individuals were targeted for collection of additional exposure details and respiratory samples. Respiratory samples were tested for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (RT-PCR) at the Centers for Disease Control and Prevention. Results There were 404 close contacts who underwent active monitoring in the response jurisdictions; 338 had at least basic exposure data, of whom 159 had at least 1 set of respiratory samples collected and tested. Across all known close contacts under monitoring, two additional cases were identified; both secondary cases were in spouses of travel-associated case patients. The secondary attack rate among household members, all of whom had at least 1 respiratory sample tested, was 13% (95% CI: 4 - 38%). Conclusions The enhanced contact tracing investigations undertaken around nine early travel-related cases of COVID-19 in the United States identified two cases of secondary transmission, both spouses. Rapid detection and isolation of the travel-associated case patients, enabled by public awareness of COVID-19 among travelers from China, may have mitigated transmission risk among close contacts of these cases.


Subject(s)
COVID-19 , Respiratory Tract Diseases
6.
Stephanie A. Kujawski; Karen K Wong; Jennifer P. Collins; Lauren Epstein; Marie E. Killerby; Claire M. Midgley; Glen R. Abedi; N. Seema Ahmed; Olivia Almendares; Francisco N. Alvarez; Kayla N. Anderson; Sharon Balter; Vaughn Barry; Karri Bartlett; Karlyn Beer; Michael A. Ben-Aderet; Isaac Benowitz; Holly Biggs; Alison M. Binder; Stephanie R. Black; Brandon Bonin; Catherine M. Brown; Hollianne Bruce; Jonathan Bryant-Genevier; Alicia Budd; Diane Buell; Rachel Bystritsky; Jordan Cates; E. Matt Charles; Kevin Chatham-Stephens; Nora Chea; Howard Chiou; Demian Christiansen; Victoria Chu; Sara Cody; Max Cohen; Erin Conners; Aaron Curns; Vishal Dasari; Patrick Dawson; Traci DeSalvo; George Diaz; Matthew Donahue; Suzanne Donovan; Lindsey M. Duca; Keith Erickson; Mathew D. Esona; Suzanne Evans; Jeremy Falk; Leora R. Feldstein; Martin Fenstersheib; Marc Fischer; Rebecca Fisher; Chelsea Foo; Marielle J. Fricchione; Oren Friedman; Alicia M. Fry; Romeo R. Galang; Melissa M. Garcia; Susa I. Gerber; Graham Gerrard; Isaac Ghinai; Prabhu Gounder; Jonathan Grein; Cheri Grigg; Jeffrey D. Gunzenhauser; Gary I. Gutkin; Meredith Haddix; Aron J. Hall; George Han; Jennifer Harcourt; Kathleen Harriman; Thomas Haupt; Amber Haynes; Michelle Holshue; Cora Hoover; Jennifer C. Hunter; Max W. Jacobs; Claire Jarashow; Michael A. Jhung; Kiran Joshi; Talar Kamali; Shifaq Kamili; Lindsay Kim; Moon Kim; Jan King; Hannah L. Kirking; Amanda Kita-Yarbro; Rachel Klos; Miwako Kobayashi; Anna Kocharian; Kenneth K. Komatsu; Ram Koppaka; Jennifer E. Layden; Yan Li; Scott Lindquist; Stephen Lindstrom; Ruth Link-Gelles; Joana Lively; Michelle Livingston; Kelly Lo; Jennifer Lo; Xiaoyan Lu; Brian Lynch; Larry Madoff; Lakshmi Malapati; Gregory Marks; Mariel Marlow; Glenn E. Mathisen; Nancy McClung; Olivia McGovern; Tristan D. McPherson; Mitali Mehta; Audrey Meier; Lynn Mello; Sung-sil Moon; Margie Morgan; Ruth N. Moro; Janna' Murray; Rekha Murthy; Shannon Novosad; Sara E. Oliver; Jennifer O'Shea; Massimo Pacilli; Clinton R. Paden; Mark A. Pallansch; Manisha Patel; Sajan Patel; Isabel Pedraza; Satish K. Pillai; Talia Pindyck; Ian Pray; Krista Queen; Nichole Quick; Heather Reese; Brian Rha; Heather Rhodes; Susan Robinson; Philip Robinson; Melissa Rolfes; Janell Routh; Rachel Rubin; Sarah L. Rudman; Senthilkumar K. Sakthivel; Sarah Scott; Christopher Shepherd; Varun Shetty; Ethan A. Smith; Shanon Smith; Bryan Stierman; William Stoecker; Rebecca Sunenshine; Regina Sy-Santos; Azaibi Tamin; Ying Tao; Dawn Terashita; Natalie J. Thornburg; Suxiang Tong; Elizabeth Traub; Ahmet Tural; Anna Uehara; Timothy M. Uyeki; Grace Vahey; Jennifer R. Verani; Elsa Villarino; Megan Wallace; Lijuan Wang; John T. Watson; Matthew Westercamp; Brett Whitaker; Sarah Wilkerson; Rebecca C. Woodruff; Jonathan M. Wortham; Tiffany Wu; Amy Xie; Anna Yousaf; Matthew Zahn; Jing Zhang.
medrxiv; 2020.
Preprint in English | medRxiv | ID: ppzbmed-10.1101.2020.03.09.20032896

ABSTRACT

Introduction: More than 93,000 cases of coronavirus disease (COVID-19) have been reported worldwide. We describe the epidemiology, clinical course, and virologic characteristics of the first 12 U.S. patients with COVID-19. Methods: We collected demographic, exposure, and clinical information from 12 patients confirmed by CDC during January 20-February 5, 2020 to have COVID-19. Respiratory, stool, serum, and urine specimens were submitted for SARS-CoV-2 rRT-PCR testing, virus culture, and whole genome sequencing. Results: Among the 12 patients, median age was 53 years (range: 21-68); 8 were male, 10 had traveled to China, and two were contacts of patients in this series. Commonly reported signs and symptoms at illness onset were fever (n=7) and cough (n=8). Seven patients were hospitalized with radiographic evidence of pneumonia and demonstrated clinical or laboratory signs of worsening during the second week of illness. Three were treated with the investigational antiviral remdesivir. All patients had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2-3 weeks after illness onset, with lowest rRT-PCR Ct values often detected in the first week. SARS-CoV-2 RNA was detected after reported symptom resolution in seven patients. SARS-CoV-2 was cultured from respiratory specimens, and SARS-CoV-2 RNA was detected in stool from 7/10 patients. Conclusions: In 12 patients with mild to moderately severe illness, SARS-CoV-2 RNA and viable virus were detected early, and prolonged RNA detection suggests the window for diagnosis is long. Hospitalized patients showed signs of worsening in the second week after illness onset.


Subject(s)
COVID-19 , Coronavirus Infections , Fever , Pneumonia
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