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Article ; Online: Prevention of host-to-host transmission by SARS-CoV-2 vaccines.

Mostaghimi, Darius / Valdez, Caroline N / Larson, Haleigh T / Kalinich, Chaney C / Iwasaki, Akiko

2021 Volume 22, Issue 2, Page(s) e52–e58

Abstract: As the number of individuals vaccinated against SARS-CoV-2 rises worldwide, population-level data regarding the vaccines' ability to reduce infection are being generated. Randomised trials have shown that these vaccines dramatically reduce symptomatic ... ...

Abstract	As the number of individuals vaccinated against SARS-CoV-2 rises worldwide, population-level data regarding the vaccines' ability to reduce infection are being generated. Randomised trials have shown that these vaccines dramatically reduce symptomatic COVID-19; however, less is known about their effects on transmission between individuals. The natural course of infection with SARS-CoV-2 involves infection of the respiratory epithelia and replication within the mucosa to sufficient viral titres for transmission via aerosol particles and droplets. Here we discuss the available data on the existing, approved SARS-CoV-2 vaccines' capacity to reduce transmissibility by reducing primary infection, viral replication, capacity for transmission, and symptomaticity. The potential for mucosal-targeted SARS-CoV-2 vaccine strategies to more effectively limit transmission than intramuscular vaccines is considered with regard to known immunological mechanisms. Finally, we enumerate the population-level effects of approved vaccines on transmission through observational studies following clinical trials and vaccine distribution in real-world settings.
MeSH term(s)	Antibodies, Viral/biosynthesis ; Antibodies, Viral/immunology ; COVID-19/prevention & control ; COVID-19/transmission ; COVID-19 Vaccines/adverse effects ; COVID-19 Vaccines/immunology ; Humans ; Immunoglobulin A/biosynthesis ; Immunoglobulin A/immunology ; Immunoglobulin G/biosynthesis ; Immunoglobulin G/immunology ; Virus Replication/immunology
Chemical Substances	Antibodies, Viral ; COVID-19 Vaccines ; Immunoglobulin A ; Immunoglobulin G
Language	English
Publishing date	2021-09-14
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2061641-7
ISSN	1474-4457 ; 1473-3099
ISSN (online)	1474-4457
ISSN	1473-3099
DOI	10.1016/S1473-3099(21)00472-2
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Article ; Online: Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US Adolescents.

Oliveira, Carlos R / Niccolai, Linda M / Sheikha, Hassan / Elmansy, Lina / Kalinich, Chaney C / Grubaugh, Nathan D / Shapiro, Eugene D

JAMA network open

2022 Volume 5, Issue 3, Page(s) e220935

Abstract: Importance: The emergence of the B.1.617.2 (Delta) variant of SARS-CoV-2 has led to increases in both infections and hospitalizations among adolescents. Little is known about the effectiveness of the BNT162b2 vaccine in adolescents in the general ... ...

Abstract	Importance: The emergence of the B.1.617.2 (Delta) variant of SARS-CoV-2 has led to increases in both infections and hospitalizations among adolescents. Little is known about the effectiveness of the BNT162b2 vaccine in adolescents in the general population, as opposed to a clinical trial population. Objective: To estimate the effectiveness of the BNT162b2 vaccine in adolescents aged 12 to 18 years. Design, setting, and participants: This was a matched case-control study among adolescents (aged 12-18 years) who had results from a SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) test. Immunization histories, relevant clinical data, and RT-PCR test results were obtained from the Yale New Haven Health System's medical records between June 1, 2021, and August 15, 2021, when the Delta variant caused 92% of infections in Connecticut. Case participants were defined as adolescents who had a positive test result and an associated medical encounter. Control participants were defined as those who had a negative test result and were matched to a case participant by age, county of residence, and date of testing. Exposures: Adolescents were defined as fully immunized if they had received 2 doses of vaccine at least 14 days before focal time. Main outcomes and measures: The primary outcome measured was SARS-CoV-2 infection confirmed by RT-PCR. The vaccine's effectiveness (VE) was estimated using matched odds ratios from conditional logistic regression models. Secondary measures included estimated VE by clinical symptoms, number of vaccine doses received, and elapsed time from immunization. Results: A total of 6901 adolescents were tested for SARS-CoV-2. The final sample comprised 186 case participants and 356 matched control participants. The median age was 14 (IQR, 13-16) years, 262 (48%) identified as female, 81 (15%) as Black, 82 (15%) as Hispanic, and 297 (55%) as White. Overall, 134 (25%) were fully immunized (case participants, 10 [5%]; control participants, 124 [35%]). The median time between immunization and the SARS-CoV-2 test was 62 days (range, 17-129 days). Within 4 months of receiving 2 doses, VE against any infection was estimated to be 91% (95% CI, 80%-96%); against asymptomatic infection, 85% (95% CI, 57%-95%). Effectiveness after a single dose was estimated to be 74% (95% CI, 18%-92%). Conclusions and relevance: In this retrospective case-control study of US adolescents, 2 doses of BNT162b2 vaccine appeared to provide excellent protection for at least 4 months after immunization against both symptomatic and asymptomatic SARS-CoV-2 infections.
MeSH term(s)	Adolescent ; BNT162 Vaccine/administration & dosage ; COVID-19/diagnosis ; COVID-19/prevention & control ; COVID-19 Nucleic Acid Testing ; Case-Control Studies ; Connecticut ; Female ; Humans ; Male ; Retrospective Studies ; SARS-CoV-2/immunology ; United States/epidemiology ; Vaccine Efficacy
Chemical Substances	BNT162 Vaccine (N38TVC63NU)
Language	English
Publishing date	2022-03-01
Publishing country	United States
Document type	Journal Article
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2022.0935
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Article: The sensitivity of respiratory tract specimens for the detection of SARS-CoV-2: A protocol for a living systematic review and meta-analysis.

Moore, Adam J / Nakahata, Maura I / Kalinich, Chaney C / Nyhan, Kate / Bromberg, Daniel J / Shi, Xiaoting / Ko, Albert I / Grubaugh, Nathan D / Casanovas-Massana, Arnau / Wyllie, Anne L

medRxiv : the preprint server for health sciences

2020

Abstract: Background: Highly sensitive, non-invasive, and easily accessible diagnostics for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are essential for the control of the Coronavirus Disease 2019 (COVID-19) pandemic. There is a clear need to ... ...

Abstract	Background: Highly sensitive, non-invasive, and easily accessible diagnostics for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are essential for the control of the Coronavirus Disease 2019 (COVID-19) pandemic. There is a clear need to establish a gold standard diagnostic for SARS-CoV-2 infection in humans using respiratory tract specimens. Methods: Searches will be conducted in the bibliographic databases Medline, Embase, bioRxiv, medRxiv, F1000, ChemRxiv, PeerJ Preprints, Preprints.org, Beilstein Archive, and Research Square. Relevant government documents and grey literature will be sought on the FDA's Emergency Use Authorizations website, the ECDC's website, and the website of the Foundation for Innovative New Diagnostics. Finally, papers categorized as diagnosis papers by the EPPI Centre's COVID-19 living systematic map will be added to our screening process; those papers are tagged with the diagnosis topic based on human review, rather than database searches, and thus this set of papers might include ones that have not been captured by our search strategy.
Keywords	covid19
Language	English
Publishing date	2020-07-04
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.07.02.20144543
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Article ; Online: Real-time public health communication of local SARS-CoV-2 genomic epidemiology.

Kalinich, Chaney C / Jensen, Cole G / Neugebauer, Peter / Petrone, Mary E / Peña-Hernández, Mario / Ott, Isabel M / Wyllie, Anne L / Alpert, Tara / Vogels, Chantal B F / Fauver, Joseph R / Grubaugh, Nathan D / Brito, Anderson F

PLoS biology

2020 Volume 18, Issue 8, Page(s) e3000869

Abstract: Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented ... ...

Abstract	Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented towards specially trained scientists and conducted on a national or global scale. Here, we propose a new paradigm: Phylogenetic analyses performed on a local level (municipal, county, or state), with results communicated in a clear, timely, and actionable manner to strengthen public health responses. We believe that presenting results rapidly, and tailored to a non-expert audience, can serve as a template for effective public health response to COVID-19 and other emerging viral diseases.
MeSH term(s)	Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/epidemiology ; Genomics ; Humans ; Information Dissemination ; Pandemics ; Phylogeny ; Pneumonia, Viral/epidemiology ; Public Health ; SARS-CoV-2
Keywords	covid19
Language	English
Publishing date	2020-08-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3000869
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Zs.A 6193: Show issues

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Article ; Online: Comparison of infectious SARS-CoV-2 from the nasopharynx of vaccinated and unvaccinated individuals

Pena-Hernandez, Mario A. / Klein, Jon / Malik, Amyn / Coppi, Andreas / Kalinich, Chaney C / Vogels, Chantal B.F. / Silva, Julio / Yale SARS-CoV-2 Genomic Surveillance Initiative / Peaper, David R. / Landry, Marie / Wilen, Craig / Grubaugh, Nathan D / Schulz, Wade L / Omer, Saad B. / Iwasaki, Akiko

medRxiv

Abstract: The frequency of SARS-CoV-2 breakthrough infections in fully vaccinated individuals increased with the emergence of the Delta variant, particularly with longer time from vaccine completion. However, whether breakthrough infections lead to onward ... ...

Abstract	The frequency of SARS-CoV-2 breakthrough infections in fully vaccinated individuals increased with the emergence of the Delta variant, particularly with longer time from vaccine completion. However, whether breakthrough infections lead to onward transmission remains unclear. Here, we conducted a study involving 125 patients comprised of 72 vaccinated and 53 unvaccinated individuals, to assess the levels of infectious virus in in vaccinated and unvaccinated individuals. Quantitative plaque assays showed no significant differences in the titers of virus between these cohorts. However, the proportion of nasopharyngeal samples with culturable virus was lower in the vaccinated patients relative to unvaccinated patients (21% vs. 40%). Finally, time-to-event analysis with Kaplan-Myer curves revealed that protection from culturable infectious virus waned significantly starting at 5 months after completing a 2-dose regimen of mRNA vaccines. These results have important implications in timing of booster dose to prevent onward transmission from breakthrough cases.
Keywords	covid19
Language	English
Publishing date	2022-01-04
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.12.28.21268460
Database	COVID19

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Article ; Online: Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies.

Kissler, Stephen M / Fauver, Joseph R / Mack, Christina / Olesen, Scott W / Tai, Caroline / Shiue, Kristin Y / Kalinich, Chaney C / Jednak, Sarah / Ott, Isabel M / Vogels, Chantal B F / Wohlgemuth, Jay / Weisberger, James / DiFiori, John / Anderson, Deverick J / Mancell, Jimmie / Ho, David D / Grubaugh, Nathan D / Grad, Yonatan H

PLoS biology

2021 Volume 19, Issue 7, Page(s) e3001333

Abstract: SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform ... ...

Abstract	SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019-2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient's infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient's progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.
MeSH term(s)	Adult ; Athletes ; Basketball ; COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/pathology ; COVID-19/virology ; COVID-19 Nucleic Acid Testing/statistics & numerical data ; Convalescence ; Humans ; Male ; Prospective Studies ; Public Health/methods ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; SARS-CoV-2/growth & development ; Severity of Illness Index ; United States/epidemiology ; Virus Replication/genetics ; Virus Shedding/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001333
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Article ; Online: Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016-2017.

Santiago, Gilberto A / Kalinich, Chaney C / Cruz-López, Fabiola / González, Glenda L / Flores, Betzabel / Hentoff, Aaron / Charriez, Keyla N / Fauver, Joseph R / Adams, Laura E / Sharp, Tyler M / Black, Allison / Bedford, Trevor / Ellis, Esther / Ellis, Brett / Waterman, Steve H / Paz-Bailey, Gabriela / Grubaugh, Nathan D / Muñoz-Jordán, Jorge L

Emerging infectious diseases

2021 Volume 27, Issue 11, Page(s) 2971–2973

Abstract: We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread ... ...

Abstract	We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.
MeSH term(s)	Epidemics ; Evolution, Molecular ; Humans ; Puerto Rico/epidemiology ; Zika Virus/genetics ; Zika Virus Infection/epidemiology
Language	English
Publishing date	2021-10-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2711.211575
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Zs.A 4778: Show issues

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Article ; Online: The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis

Moore, Adam J / Nakahata, Maura I / Kalinich, Chaney C / Nyhan, Kate / Bromberg, Daniel J / Shi, Xiaoting / Ko, Albert I / Grubaugh, Nathan D / Casanovas-Massana, Arnau / Wyllie, Anne L

medRxiv

Abstract: BACKGROUND: Highly sensitive, non-invasive, and easily accessible diagnostics for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are essential for the control of the Coronavirus Disease 2019 (COVID-19) pandemic. There is a clear need to ... ...

Abstract	BACKGROUND: Highly sensitive, non-invasive, and easily accessible diagnostics for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are essential for the control of the Coronavirus Disease 2019 (COVID-19) pandemic. There is a clear need to establish a gold standard diagnostic for SARS-CoV-2 infection in humans using respiratory tract specimens. METHODS: Searches will be conducted in the bibliographic databases Medline, Embase, bioRxiv, medRxiv, F1000, ChemRxiv, PeerJ Preprints, Preprints.org, Beilstein Archive, and Research Square. Relevant government documents and grey literature will be sought on the FDA9s Emergency Use Authorizations website, the ECDC9s website, and the website of the Foundation for Innovative New Diagnostics. Finally, papers categorized as diagnosis papers by the EPPI Centre9s COVID-19 living systematic map will be added to our screening process; those papers are tagged with the diagnosis topic based on human review, rather than database searches, and thus this set of papers might include ones that have not been captured by our search strategy.
Keywords	covid19
Language	English
Publishing date	2020-07-05
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.07.02.20144543
Database	COVID19

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Article ; Online: Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays

Vogels, Chantal B.F. / Brito, Anderson F. / Wyllie, Anne Louise / Fauver, Joseph R / Ott, Isabel M. / Kalinich, Chaney C. / Petrone, Mary E. / Landry, Marie-Louise / Foxman, Ellen F. / Grubaugh, Nathan D.

medRxiv

Abstract: The recent spread of severe acute respiratory syndrome coronavirus (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt public health actions. Currently, several quantitative reverse-transcription polymerase chain ...

Abstract	The recent spread of severe acute respiratory syndrome coronavirus (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt public health actions. Currently, several quantitative reverse-transcription polymerase chain reaction (qRT-PCR) assays are being used by clinical, research, and public health laboratories for rapid detection of the virus. However, it is currently unclear if results from different tests are comparable. Our goal was to evaluate the primer-probe sets used in four common diagnostic assays available on the World Health Organization (WHO) website. To facilitate this effort, we generated RNA transcripts to create standards and distributed them to other laboratories for internal validation. We then used these RNA transcript standards, full-length SARS-CoV-2 RNA, and RNA-spiked mock samples to determine analytical efficiency and sensitivity of nine primer-probe sets. We show that all primer-probe sets can be used to detect SARS-CoV-2, but there are clear differences in the ability to differentiate between true negatives and positives with low amounts of virus. Adding to this, many primer-probe sets, including the "N2" and "N3" sets issued by the US Centers for Disease Control and Prevention, have background amplification with SARS-CoV-2-negative nasopharyngeal swabs, which may lead to inconclusive results. Our findings characterize the limitations of commonly used primer-probe sets and can assist other laboratories in selecting appropriate assays for the detection of SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-04-01
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.03.30.20048108
Database	COVID19

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Article: The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis

Moore, Adam J. / Nakahata, Maura I. / Kalinich, Chaney C. / Nyhan, Kate / Bromberg, Daniel J. / Shi, Xiaoting / Ko, Albert I. / Grubaugh, Nathan D. / Casanovas-Massana, Arnau / Wyllie, Anne L.

Abstract	BACKGROUND: Highly sensitive, non-invasive, and easily accessible diagnostics for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) are essential for the control of the Coronavirus Disease 2019 (COVID-19) pandemic There is a clear need to establish a gold standard diagnostic for SARS-CoV-2 infection in humans using respiratory tract specimens METHODS: Searches will be conducted in the bibliographic databases Medline, Embase, bioRxiv, medRxiv, F1000, ChemRxiv, PeerJ Preprints, Preprints org, Beilstein Archive, and Research Square Relevant government documents and grey literature will be sought on the FDA's Emergency Use Authorizations website, the ECDC's website, and the website of the Foundation for Innovative New Diagnostics Finally, papers categorized as diagnosis papers by the EPPI Centre's COVID-19 living systematic map will be added to our screening process;those papers are tagged with the diagnosis topic based on human review, rather than database searches, and thus this set of papers might include ones that have not been captured by our search strategy
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #637873
Database	COVID19

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