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Article ; Online: Direct observation of repeated infections with endemic coronaviruses

Galanti, M. / Shaman, J.

Abstract: Background: While the mechanisms of adaptive immunity to pandemic coronavirus SARS-CoV-2 are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63 and OC43 provide a useful reference for understanding repeat ... ...

Abstract	Background: While the mechanisms of adaptive immunity to pandemic coronavirus SARS-CoV-2 are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63 and OC43 provide a useful reference for understanding repeat infection risk. Methods: Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses. Results: During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the beta-coronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity but strong association between symptom severity and belonging to the same family. Conclusion: This study provides evidence that re-infections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection.
Keywords	covid19
Publisher	MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.04.27.20082032
Database	COVID19

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Article ; Online: Direct Observation of Repeated Infections With Endemic Coronaviruses.

Galanti, Marta / Shaman, Jeffrey

The Journal of infectious diseases

2020 Volume 223, Issue 3, Page(s) 409–415

Abstract: Background: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful ... ...

Abstract	Background: Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. Methods: Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses. Results: During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the betacoronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity, but found strong association between symptom severity and belonging to the same family. Conclusions: This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection.
MeSH term(s)	Adult ; Betacoronavirus ; COVID-19/epidemiology ; COVID-19/immunology ; Coronavirus/genetics ; Coronavirus/isolation & purification ; Coronavirus Infections/diagnostic imaging ; Coronavirus Infections/epidemiology ; Coronavirus Infections/virology ; Endemic Diseases ; Humans ; Immunity, Innate ; New York City/epidemiology ; Respiratory Tract Infections/diagnostic imaging ; Respiratory Tract Infections/epidemiology ; Respiratory Tract Infections/virology ; SARS-CoV-2 ; Survival Analysis
Keywords	covid19
Language	English
Publishing date	2020-07-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiaa392
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.MO 445: Show issues

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Article ; Online: Will SARS-CoV-2 become endemic?

Shaman, Jeffrey / Galanti, Marta

Science (New York, N.Y.)

2020 Volume 370, Issue 6516, Page(s) 527–529

MeSH term(s)	Adaptive Immunity ; Antigens, Viral/genetics ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/immunology ; Endemic Diseases ; Humans ; Immune Evasion ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/immunology ; SARS-CoV-2
Chemical Substances	Antigens, Viral
Keywords	covid19
Language	English
Publishing date	2020-10-14
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.abe5960
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Socioeconomic Disparities in Severe Acute Respiratory Syndrome Coronavirus 2 Serological Testing and Positivity in New York City.

Lieberman-Cribbin, Wil / Galanti, Marta / Shaman, Jeffrey

Open forum infectious diseases

2021 Volume 8, Issue 12, Page(s) ofab534

Abstract: Background: We characterized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody test prevalence and positive test prevalence across New York City (NYC) in order to investigate disparities in testing outcomes by race and socioeconomic ... ...

Abstract	Background: We characterized severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody test prevalence and positive test prevalence across New York City (NYC) in order to investigate disparities in testing outcomes by race and socioeconomic status (SES). Methods: Serologic data were downloaded from the NYC Coronavirus data repository (August 2020-December 2020). Area-level characteristics for NYC neighborhoods were downloaded from United States census data and a socioeconomic vulnerability index was created. Spatial generalized linear mixed models were performed to examine the association between SES and antibody testing and positivity. Results: The proportion of Hispanic population (posterior median, 0.001 [95% credible interval, 0.0003-0.002]), healthcare workers (0.003 [0.0001-0.006]), essential workers (0.003 [0.001-0.005]), age ≥65 years (0.003 [0.00002-0.006]), and high SES (SES quartile 3 vs 1: 0.034 [0.003-0.062]) were positively associated with antibody tests per 100000 residents. The White proportion (-0.002 [-0.003 to -0.001]), SES index (quartile 3 vs 1, -0.068 [-0.115 to -0.017]; quartile 4 vs 1, -0.077 [-0.134 to -0.018]) and age ≥65 years (-0.005 [-0.009 to -0.002]) were inversely associated with positive test prevalence (%), whereas the Hispanic (0.004 [0.002-0.006]) and essential worker (0.008 [0.003-0.012]) proportions had positive coefficients. Conclusions: Disparities in serologic testing and seropositivity exist on SES and race/ethnicity across NYC, indicative of excess coronavirus disease burden in vulnerable and marginalized populations.
Language	English
Publishing date	2021-10-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2757767-3
ISSN	2328-8957
ISSN	2328-8957
DOI	10.1093/ofid/ofab534
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease.

Cascante-Vega, Jaime / Galanti, Marta / Schley, Katharina / Pei, Sen / Shaman, Jeffrey

PLoS computational biology

2023 Volume 19, Issue 10, Page(s) e1011564

Abstract: The pathogenic bacteria Neisseria meningitidis, which causes invasive meningococcal disease (IMD), predominantly colonizes humans asymptomatically; however, invasive disease occurs in a small proportion of the population. Here, we explore the seasonality ...

Abstract	The pathogenic bacteria Neisseria meningitidis, which causes invasive meningococcal disease (IMD), predominantly colonizes humans asymptomatically; however, invasive disease occurs in a small proportion of the population. Here, we explore the seasonality of IMD and develop and validate a suite of models for simulating and forecasting disease outcomes in the United States. We combine the models into multi-model ensembles (MME) based on the past performance of the individual models, as well as a naive equally weighted aggregation, and compare the retrospective forecast performance over a six-month forecast horizon. Deployment of the complete vaccination regimen, introduced in 2011, coincided with a change in the periodicity of IMD, suggesting altered transmission dynamics. We found that a model forced with the period obtained by local power wavelet decomposition best fit and forecast observations. In addition, the MME performed the best across the entire study period. Finally, our study included US-level data until 2022, allowing study of a possible IMD rebound after relaxation of non-pharmaceutical interventions imposed in response to the COVID-19 pandemic; however, no evidence of a rebound was found. Our findings demonstrate the ability of process-based models to retrospectively forecast IMD and provide a first analysis of the seasonality of IMD before and after the complete vaccination regimen.
MeSH term(s)	Humans ; Retrospective Studies ; Pandemics ; Meningococcal Infections/epidemiology ; Meningococcal Infections/microbiology ; Neisseria meningitidis
Chemical Substances	MME (78185-58-7)
Language	English
Publishing date	2023-10-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011564
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Direct Measurement of Rates of Asymptomatic Infection and Clinical Care-Seeking for Seasonal Coronavirus

Shaman, Jeffrey / Galanti, Marta

Abstract: The pandemic potential of the novel coronavirus (nCoV) that emerged in Wuhan, China, during December 2019 is strongly tied to the number and contagiousness of undocumented human infections. Here we present findings from a proactive longitudinal sampling ... ...

Abstract	The pandemic potential of the novel coronavirus (nCoV) that emerged in Wuhan, China, during December 2019 is strongly tied to the number and contagiousness of undocumented human infections. Here we present findings from a proactive longitudinal sampling study of acute viral respiratory infections that documents rates of asymptomatic infection and clinical care seeking for seasonal coronavirus. We find that the majority of infections are asymptomatic by most symptom definitions and that only 4% of individuals experiencing a seasonal coronavirus infection episode sought medical care for their symptoms. These numbers indicate that a very high percentage of seasonal coronavirus infections are undocumented and provide a reference for understanding the spread of the emergent nCoV.
Keywords	covid19
Publisher	MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.01.30.20019612
Database	COVID19

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Article: Will SARS-CoV-2 become endemic?

Shaman, Jeffrey / Galanti, Marta

Science

Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #873449
Database	COVID19

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Article ; Online: Direct observation of repeated infections with endemic coronaviruses

Galanti, Marta / Shaman, Jeffrey

medRxiv

Abstract	Background: While the mechanisms of adaptive immunity to pandemic coronavirus SARS-CoV-2 are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63 and OC43 provide a useful reference for understanding repeat infection risk. Methods: Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses. Results: During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the beta-coronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity but strong association between symptom severity and belonging to the same family. Conclusion: This study provides evidence that re-infections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection.
Keywords	covid19
Language	English
Publishing date	2020-05-03
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.04.27.20082032
Database	COVID19

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Article ; Online: Direct Measurement of Rates of Asymptomatic Infection and Clinical Care-Seeking for Seasonal Coronavirus

Shaman, Jeffrey / Galanti, Marta

medRxiv

Abstract	The pandemic potential of the novel coronavirus (nCoV) that emerged in Wuhan, China, during December 2019 is strongly tied to the number and contagiousness of undocumented human infections. Here we present findings from a proactive longitudinal sampling study of acute viral respiratory infections that documents rates of asymptomatic infection and clinical care seeking for seasonal coronavirus. We find that the majority of infections are asymptomatic by most symptom definitions and that only 4% of individuals experiencing a seasonal coronavirus infection episode sought medical care for their symptoms. These numbers indicate that a very high percentage of seasonal coronavirus infections are undocumented and provide a reference for understanding the spread of the emergent nCoV.
Keywords	covid19
Language	English
Publishing date	2020-02-03
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.01.30.20019612
Database	COVID19

Full text online

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Article ; Online: Direct Observation of Repeated Infections With Endemic Coronaviruses

Galanti, Marta / Shaman, Jeffrey

The Journal of Infectious Diseases ; ISSN 0022-1899 1537-6613

2020

Abstract: Abstract Background Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a ... ...

Abstract	Abstract Background Although the mechanisms of adaptive immunity to pandemic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are still unknown, the immune response to the widespread endemic coronaviruses HKU1, 229E, NL63, and OC43 provide a useful reference for understanding repeat infection risk. Methods Here we used data from proactive sampling carried out in New York City from fall 2016 to spring 2018. We combined weekly nasal swab collection with self-reports of respiratory symptoms from 191 participants to investigate the profile of recurring infections with endemic coronaviruses. Results During the study, 12 individuals tested positive multiple times for the same coronavirus. We found no significant difference between the probability of testing positive at least once and the probability of a recurrence for the betacoronaviruses HKU1 and OC43 at 34 weeks after enrollment/first infection. We also found no significant association between repeat infections and symptom severity, but found strong association between symptom severity and belonging to the same family. Conclusions This study provides evidence that reinfections with the same endemic coronavirus are not atypical in a time window shorter than 1 year and that the genetic basis of innate immune response may be a greater determinant of infection severity than immune memory acquired after a previous infection.
Keywords	Immunology and Allergy ; Infectious Diseases ; covid19
Language	English
Publisher	Oxford University Press (OUP)
Publishing country	uk
Document type	Article ; Online
DOI	10.1093/infdis/jiaa392
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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