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Article: Determining the source of transmission of SARS-CoV-2 infection in a healthcare worker.

Safdar, Nasia / Moreno, Gage K / Braun, Katarina M / Friedrich, Thomas C / O'Connor, David H

medRxiv : the preprint server for health sciences

2020

Abstract: Healthcare workers (HCWs) are at the frontlines of the COVID-19 pandemic and are at risk of exposure to SARS-CoV-2 infection from their interactions with patients and in the community. Limited availability of recommended personal protective equipment ( ... ...

Abstract	Healthcare workers (HCWs) are at the frontlines of the COVID-19 pandemic and are at risk of exposure to SARS-CoV-2 infection from their interactions with patients and in the community. Limited availability of recommended personal protective equipment (PPE), in particular N95 respirators, has fueled concerns about whether HCWs are adequately protected from exposure while caring for patients. Understanding the source of SARS-CoV-2 infection in a HCW - the community or the healthcare system - is critical for understanding the effectiveness of hospital infection control and PPE practices. In Dane County, Wisconsin, community prevalence of SARS-CoV-2 is relatively low (cumulative prevalence of ~0.06% - positive cases / total population in Dane county as of April 17). Although SARS-CoV-2 infections in HCWs are often presumed to be acquired during the course of patient care, there are few reports unambiguously identifying the source of acquisition. The objective of this brief report was to determine the source of transmission of SARS-CoV-2 in a healthcare worker.
Keywords	covid19
Language	English
Publishing date	2020-05-01
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.04.27.20077016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Using Virus Sequencing to Determine Source of SARS-CoV-2 Transmission for Healthcare Worker.

Safdar, Nasia / Moreno, Gage K / Braun, Katarina M / Friedrich, Thomas C / O'Connor, David H

Emerging infectious diseases

2020 Volume 26, Issue 10, Page(s) 2489–2491

Abstract: Whether a healthcare worker's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is community or hospital acquired affects prevention practices. We used virus sequencing to determine that infection of a healthcare worker who cared for ...

Abstract	Whether a healthcare worker's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is community or hospital acquired affects prevention practices. We used virus sequencing to determine that infection of a healthcare worker who cared for 2 SARS-CoV-2-infected patients was probably community acquired. Appropriate personal protective equipment may have protected against hospital-acquired infection.
MeSH term(s)	Betacoronavirus ; COVID-19 ; Community-Acquired Infections/virology ; Coronavirus Infections/transmission ; Coronavirus Infections/virology ; Health Personnel ; Humans ; Infectious Disease Transmission, Patient-to-Professional/prevention & control ; Occupational Diseases/prevention & control ; Pandemics ; Personal Protective Equipment ; Pneumonia, Viral/transmission ; Pneumonia, Viral/virology ; RNA, Viral/analysis ; SARS-CoV-2 ; Sequence Analysis, RNA
Chemical Substances	RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-08-06
Publishing country	United States
Document type	Case Reports ; Letter
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2610.202322
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission during the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study using Genomic Epidemiology.

medRxiv : the preprint server for health sciences

2024

Abstract: Background: Households are a major setting for SARS-CoV-2 infections, but there remains a lack of knowledge regarding the dynamics of viral transmission, particularly in the setting of widespread pre-existing SARS-CoV-2 immunity and evolving variants.!## ...

Abstract	Background: Households are a major setting for SARS-CoV-2 infections, but there remains a lack of knowledge regarding the dynamics of viral transmission, particularly in the setting of widespread pre-existing SARS-CoV-2 immunity and evolving variants. Methods: We conducted a prospective, case-ascertained household transmission study in the greater Boston area in March-July 2022. Anterior nasal swabs, along with clinical and demographic data, were collected for 14 days. Nasal swabs were tested for SARS-CoV-2 by PCR. Whole genome sequencing was performed on high-titer samples. Results: We enrolled 33 households in a primary analysis set, with a median age of participants of 25 years old (range 2-66); 98% of whom had received at least 2 doses of a COVID-19 vaccine. 58% of households had a secondary case during follow up and the secondary attack rate (SAR) for contacts infected was 39%. We further examined a strict analysis set of 21 households that had only 1 PCR+ case at baseline, finding an SAR of 22.5%. Genomic epidemiology further determined that there were multiple sources of infection for household contacts, including the index case and outside introductions. When limiting estimates to only highly probable transmissions given epidemiologic and genomic data, the SAR was 18.4%. Conclusions: Household contacts of a person newly diagnosed with COVID-19 are at high risk for SARS-CoV-2 infection in the following 2 weeks. This is, however, not only due to infection from the household index case, but also because the presence of an infected household member implies increased SARS-CoV-2 community transmission. Further studies to understand and mitigate household transmission are needed.
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.05.24302348
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Article: Inferring Viral Transmission Pathways from Within-Host Variation.

Specht, Ivan O A / Petros, Brittany A / Moreno, Gage K / Brock-Fisher, Taylor / Krasilnikova, Lydia A / Schifferli, Mark / Yang, Katherine / Cronan, Paul / Glennon, Olivia / Schaffner, Stephen F / Park, Daniel J / MacInnis, Bronwyn L / Ozonoff, Al / Fry, Ben / Mitzenmacher, Michael D / Varilly, Patrick / Sabeti, Pardis C

medRxiv : the preprint server for health sciences

2023

Abstract: Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust ... ...

Abstract	Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust evolutionary model for transmission reconstruction that tracks the genetic composition of within-host viral populations over time and the lineages transmitted between hosts. We confirm that our model reliably describes within-host variant frequencies in a dataset of 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts, USA. We then demonstrate that our reconstruction approach infers transmissions more accurately than two leading methods on synthetic data, as well as in a controlled outbreak of bovine respiratory syncytial virus and an epidemiologically-investigated SARS-CoV-2 outbreak in South Africa. Finally, we apply our transmission reconstruction tool to 5,692 outbreaks among the 134,682 Massachusetts genomes. Our methods and results demonstrate the utility of within-host variation for transmission inference of SARS-CoV-2 and other pathogens, and provide an adaptable mathematical framework for tracking within-host evolution.
Language	English
Publishing date	2023-10-15
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.14.23297039
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Anti-membrane Antibodies Persist at Least One Year and Discriminate Between Past Coronavirus Disease 2019 Infection and Vaccination.

Amjadi, Maya F / Adyniec, Ryan R / Gupta, Srishti / Bashar, S Janna / Mergaert, Aisha M / Braun, Katarina M / Moreno, Gage K / O'Connor, David H / Friedrich, Thomas C / Safdar, Nasia / McCoy, Sara S / Shelef, Miriam A

The Journal of infectious diseases

2022 Volume 226, Issue 11, Page(s) 1897–1902

Abstract: Background: The consequences of past coronavirus disease 2019 (COVID-19) infection for personal and population health are emerging, but accurately identifying distant infection is a challenge. Anti-spike antibodies rise after both vaccination and ... ...

Abstract	Background: The consequences of past coronavirus disease 2019 (COVID-19) infection for personal and population health are emerging, but accurately identifying distant infection is a challenge. Anti-spike antibodies rise after both vaccination and infection and anti-nucleocapsid antibodies rapidly decline. Methods: We evaluated anti-membrane antibodies in COVID-19 naive, vaccinated, and convalescent subjects to determine if they persist and accurately detect distant infection. Results: We found that anti-membrane antibodies persist for at least 1 year and are a sensitive and specific marker of past COVID-19 infection. Conclusions: Thus, anti-membrane and anti-spike antibodies together can differentiate between COVID-19 convalescent, vaccinated, and naive states to advance public health and research.
MeSH term(s)	Humans ; COVID-19/diagnosis ; Vaccination ; Public Health ; Virion ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus
Chemical Substances	Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-06-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiac263
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Zs.MO 445: Show issues

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Article ; Online: Determining the source of transmission of SARS-CoV-2 infection in a healthcare worker

Safdar, Nasia / Moreno, Gage K / Braun, Katarina M / Friedrich, Thomas C / O'Connor, David H

medRxiv

Abstract	Healthcare workers (HCWs) are at the frontlines of the COVID-19 pandemic and are at risk of exposure to SARS-CoV-2 infection from their interactions with patients and in the community. Limited availability of recommended personal protective equipment (PPE), in particular N95 respirators, has fueled concerns about whether HCWs are adequately protected from exposure while caring for patients. Understanding the source of SARS-CoV-2 infection in a HCW - the community or the healthcare system - is critical for understanding the effectiveness of hospital infection control and PPE practices. In Dane County, Wisconsin, community prevalence of SARS-CoV-2 is relatively low (cumulative prevalence of ~0.06% - positive cases / total population in Dane county as of April 17). Although SARS-CoV-2 infections in HCWs are often presumed to be acquired during the course of patient care, there are few reports unambiguously identifying the source of acquisition. The objective of this brief report was to determine the source of transmission of SARS-CoV-2 in a healthcare worker.
Keywords	covid19
Language	English
Publishing date	2020-05-01
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.04.27.20077016
Database	COVID19

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Article: Using Virus Sequencing to Determine Source of SARS-CoV-2 Transmission for Healthcare Worker

Safdar, Nasia / Moreno, Gage K / Braun, Katarina M / Friedrich, Thomas C / O039, / Connor, David H

Emerg Infect Dis

Abstract	Whether a healthcare worker's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is community or hospital acquired affects prevention practices. We used virus sequencing to determine that infection of a healthcare worker who cared for 2 SARS-CoV-2-infected patients was probably community acquired. Appropriate personal protective equipment may have protected against hospital-acquired infection.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #696601
Database	COVID19

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Article: SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing.

Moreno, Gage K / Braun, Katarina M / Pray, Ian W / Segaloff, Hannah E / Lim, Ailam / Poulson, Keith / Meiman, Jonathan / Borcher, James / Westergaard, Ryan P / Moll, Michael K / Friedrich, Thomas C / O'Connor, David H

medRxiv : the preprint server for health sciences

2021

Abstract: Background: High frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, two SARS-CoV-2 outbreaks occurred among intercollegiate university ... ...

Abstract	Background: High frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester despite mandatory directly observed daily antigen testing. Methods: During the fall 2020 semester, athletes and staff in both programs were tested daily using Quidel's Sofia SARS Antigen Fluorescent Immunoassay (FIA), with positive antigen results requiring confirmatory testing with real-time reverse transcription polymerase chain reaction (RT-PCR). We used genomic sequencing to investigate transmission dynamics in these two outbreaks. Results: In Outbreak 1, 32 confirmed cases occurred within a university athletics program after the index patient attended a meeting while infectious despite a negative antigen test on the day of the meeting. Among isolates sequenced from Outbreak 1, 24 (92%) of 26 were closely related, suggesting sustained transmission following an initial introduction event. In Outbreak 2, 12 confirmed cases occurred among athletes from two university programs that faced each other in an athletic competition despite receiving negative antigen test results on the day of the competition. Sequences from both teams were closely related and unique from strains circulating in the community, suggesting transmission during intercollegiate competition. Conclusions: These findings suggest that antigen testing alone, even when mandated and directly observed, may not be sufficient as an intervention to prevent SARS-CoV-2 outbreaks in congregate settings, and highlights the importance of supplementing serial antigen testing with appropriate mitigation strategies to prevent SARS-CoV-2 outbreak in congregate settings. Summary: High frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, here we describe two SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester.
Language	English
Publishing date	2021-03-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.03.03.21252838
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Anti-membrane and anti-spike antibodies are long-lasting and together discriminate between past COVID-19 infection and vaccination.

medRxiv : the preprint server for health sciences

2021

Abstract: The consequences of past COVID-19 infection for personal health and long-term population immunity are only starting to be revealed. Unfortunately, detecting past infection is currently a challenge, limiting clinical and research endeavors. Widely ... ...

Abstract	The consequences of past COVID-19 infection for personal health and long-term population immunity are only starting to be revealed. Unfortunately, detecting past infection is currently a challenge, limiting clinical and research endeavors. Widely available anti-SARS-CoV-2 antibody tests cannot differentiate between past infection and vaccination given vaccine-induced anti-spike antibodies and the rapid loss of infection-induced anti-nucleocapsid antibodies. Anti-membrane antibodies develop after COVID-19, but their long-term persistence is unknown. Here, we demonstrate that anti-membrane IgG is a sensitive and specific marker of past COVID-19 infection and persists at least one year. We also confirm that anti-receptor binding domain (RBD) Ig is a long-lasting, sensitive, and specific marker of past infection and vaccination, while anti-nucleocapsid IgG lacks specificity and quickly declines after COVID-19. Thus, a combination of anti-membrane and anti-RBD antibodies can accurately differentiate between distant COVID-19 infection, vaccination, and naïve states to advance public health, individual healthcare, and research goals.
Language	English
Publishing date	2021-11-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2021.11.02.21265750
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in Intercollegiate Athletics Not Fully Mitigated With Daily Antigen Testing.

Moreno, Gage K / Braun, Katarina M / Pray, Ian W / Segaloff, Hannah E / Lim, Ailam / Poulsen, Keith / Meiman, Jonathan / Borcher, James / Westergaard, Ryan P / Moll, Michael K / Friedrich, Thomas C / O'Connor, David H

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2021 Volume 73, Issue Suppl 1, Page(s) S45–S53

Abstract: Background: High-frequency, rapid-turnaround severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, 2 SARS-CoV-2 ... ...

Abstract	Background: High-frequency, rapid-turnaround severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, 2 SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester, despite mandatory directly observed daily antigen testing. Methods: During the fall 2020 semester, athletes and staff in both programs were tested daily using Quidel's Sofia SARS Antigen Fluorescent Immunoassay, with positive antigen results requiring confirmatory testing with real-time reverse-transcription polymerase chain reaction. We used genomic sequencing to investigate transmission dynamics in these 2 outbreaks. Results: In the first outbreak, 32 confirmed cases occurred within a university athletics program after the index patient attended a meeting while infectious, despite a negative antigen test on the day of the meeting. Among isolates sequenced from that outbreak, 24 (92%) of 26 were closely related, suggesting sustained transmission following an initial introduction event. In the second outbreak, 12 confirmed cases occurred among athletes from 2 university programs that faced each other in an athletic competition, despite receipt of negative antigen test results on the day of the competition. Sequences from both teams were closely related and distinct from viruses circulating in the community for team 1, suggesting transmission during intercollegiate competition in the community for team 2. Conclusions: These findings suggest that antigen testing alone, even when mandated and directly observed, may not be sufficient as an intervention to prevent SARS-CoV-2 outbreaks in congregate settings, and they highlight the importance of vaccination to prevent SARS-CoV-2 outbreak in congregate settings.
MeSH term(s)	COVID-19 ; Humans ; Immunologic Tests ; SARS-CoV-2 ; Sports ; Universities
Language	English
Publishing date	2021-05-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciab343
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