Trajectory of Viral RNA Load Among Persons With Incident SARS-CoV-2 G614 Infection (Wuhan Strain) in Association With COVID-19 Symptom Onset and Severity

ABSTRACTOBJECTIVETo investigate the dynamics of viral RNA, IgM, and IgG and their relationships in patients with SARS-CoV-2 pneumonia over an 8-week period.DESIGNRetrospective, observational case series.SETTINGWenzhou Sixth People’s HospitalPARTICIPANTSThirty-three patients with laboratory confirmed SARS-CoV-2 pneumonia admitted to hospital. Data were collected from January 27 to April 10, 2020.MAIN OUTCOME MEASURESThroat swabs, sputum, stool, and blood samples were collected, and viral load was measured by reverse transcription PCR (RT-PCR). Specific IgM and IgG against spike protein (S), spike protein receptor binding domain (RBD), and nucleocapsid (N) were analyzed.RESULTSAt the early stages of symptom onset, SARS-CoV-2 viral load is higher in throat swabs and sputum, but lower in stool. The median (IQR) time of undetectable viral RNA in throat swab, sputum, and stool was 18.5 (13.25-22) days, 22 (18.5-27.5) days, and 17 (11.5-32) days, respectively. In sputum, 17 patients (51.5%) had undetectable viral RNA within 22 days (short persistence), and 16 (48.5%) had persistent viral RNA more than 22 days (long persistence). Three patients (9.1%) had a detectable relapse of viral RNA in sputum within two weeks of their discharge from the hospital. One patient had persistent viral RNA for 59 days or longer. The median (IQR) seroconversion time of anti-S IgM, anti-RBD IgM, and anti-N IgM was 10.5 (7.75-15.5) days, 14 (9-24) days, and 10 (7-14) days, respectively. The median (IQR) seroconversion time of anti-S IgG, anti-RBD IgG, and anti-N IgG was 10 (7.25-16.5) days, 13 (9-17) days, and 10 (7-14) days, respectively. By week 8 after symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels were 4-times higher in convalescence than in acute phase. SARS-CoV-2 RNA coexisted with antibodies for more than 50 days. Anti-RBD IgM and IgG levels, including anti-RBD IgM levels at presentation and peak time, were significantly higher in viral RNA short persistence patients than in long persistence patients.CONCLUSIONThis study adds important new information about the features of viral load and antibody dynamics of SARS-CoV-2. It is clear from these results that the viral RNA persists in sputum and stool specimens for a relatively long time in many patients. Anti-RBD may also serve as a potential protective antibody against SARS-CoV-2 infection, as viral persistence appears to be related to anti-RBD levels. Earlier treatment intervention also appears to be a factor in viral persistence.WHAT IS ALREADY KNOWN ON THIS TOPICThere are several reports about the serum antibodies against SARS-CoV-2. However, most of them evaluate diagnostic accuracy. Only two articles report dynamics of SARS-CoV-2 viral RNA and antibodies with serial samples, but the observation periods are within 30 days. None of the studies investigate the profiles of SARS-CoV-2 viral load and antibodies in a long period. Three reports investigate profiles in respiratory samples, but there are no reports on the dynamics of the viral load in stool samples.WHAT THIS STUDY ADDSIn both sputum and stool, SARS-CoV-2 RNA persists for a long time. The anti-RBD antibodies may involve in the clearance of SARS-CoV-2 infection. After eight weeks from symptom onset, IgM were negative in many of the previously positive patients, and IgG levels remained less than 50% of the peak levels in more than 20% of the patients. In about 40% of the patients, anti-RBD IgG levels increased 4-time higher in convalescence than in acute phase. Long persistence of SARS-CoV-2 viral RNA in sputum and stool presents challenges for management of the infection. The IgM/IgG comb test is better than single IgM test as a supplement diagnostic tool. Anti-RBD may be a protective antibody, and is valuable for development of vaccines.

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SARS-CoV-2 infectious virus, viral RNA in nasopharyngeal swabs, and serostatus of symptomatic COVID-19 outpatients in the United States

10.1101/2021.05.28.21258011 ◽

2021 ◽

Author(s):

Katie R. Mollan ◽

Joseph J. Eron ◽

Taylor J. Krajewski ◽

Wendy Painter ◽

Elizabeth R. Duke ◽

...

Keyword(s):

United States ◽

Symptom Onset ◽

Infectious Virus ◽

Virus Isolation ◽

Clinical Symptoms ◽

Comprehensive Evaluation ◽

Upper Airway ◽

The United States ◽

Viral Rna ◽

Treatment And Prevention

Background: SARS-CoV-2 infectious virus isolation in the upper airway of COVID-19 patients is associated with higher levels of viral RNA. However, comprehensive evaluation of the relationships between host and disease factors and infectious, replication competent virus is needed. Methods: Symptomatic COVID-19 outpatients were enrolled from the United States. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay. Findings: Among 204 participants within one week of reported symptom onset (median=5, IQR 4-5 days), median age was 40 (min-max: 18-82 years), median nasopharyngeal viral RNA was 6.5 (IQR 4.7-7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies at baseline. Infectious virus was recovered in 7% of participants with antibodies compared to 58% of participants without antibodies (probability ratio (PR)=0.12, 95% CI: 0.04, 0.36; p=0.00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log10, 95% CI: 2.2, 3.0; p<0.0001) and fewer days since symptom onset (PR=0.79, 95% CI: 0.71, 0.88 per day; p<0.0001). Interpretation: The presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus isolation. Seropositivity and viral RNA are likely more reliable markers of infectious virus suppression than subjective measure of COVID-19 symptoms. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion. Funding: Ridgeback Biotherapeutics, LP and NIH ClinicalTrials.gov Identifier: NCT04405570

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Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in a longitudinally sampled cohort of COVID-19 outpatients

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab195 ◽

2021 ◽

Author(s):

Annukka A R Antar ◽

Tong Yu ◽

Nora Pisanic ◽

Razvan Azamfirei ◽

Jeffrey A Tornheim ◽

...

Keyword(s):

Symptom Onset ◽

Oral Fluid ◽

Gingival Crevicular Fluid ◽

Rna Virus ◽

Cox Proportional Hazards ◽

Viral Rna ◽

Antibody Detection ◽

Upper Respiratory Tract ◽

Rt Pcr ◽

Virus Culture

Abstract Background Sustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection. Methods Ninety-five symptomatic outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models. Results Viral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI ≥ 25kg/m2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044). Conclusions We demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.

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Persistent SARS-CoV-2 RNA Shedding Without Evidence of Infectiousness: A Cohort Study of Individuals With COVID-19

The Journal of Infectious Diseases ◽

10.1093/infdis/jiab107 ◽

2021 ◽

Cited By ~ 1

Author(s):

Daniel Owusu ◽

Mary A Pomeroy ◽

Nathaniel M Lewis ◽

Ashutosh Wadhwa ◽

Anna R Yousaf ◽

...

Keyword(s):

Symptom Onset ◽

Proportional Hazards ◽

Cox Proportional Hazards ◽

Viral Rna ◽

Cox Proportional Hazards Regression ◽

Viral Culture ◽

Proportional Hazards Regression ◽

Kaplan Meier ◽

Participant Characteristics ◽

Pcr Test

Abstract Background To better understand severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shedding and infectivity, we estimated SARS-CoV-2 RNA shedding duration, described participant characteristics associated with the first negative rRT-PCR test (resolution), and determined if replication-competent viruses was recoverable ≥10 days after symptom onset. Methods We collected serial nasopharyngeal specimens from 109 individuals with rRT-PCR–confirmed COVID-19 in Utah and Wisconsin. We calculated viral RNA shedding resolution probability using the Kaplan-Meier estimator and evaluated characteristics associated with shedding resolution using Cox proportional hazards regression. We attempted viral culture for 35 rRT-PCR–positive nasopharyngeal specimens collected ≥10 days after symptom onset. Results The likelihood of viral RNA shedding resolution at 10 days after symptom onset was approximately 3%. Time to shedding resolution was shorter among participants aged <18 years (adjusted hazards ratio [aHR], 3.01; 95% confidence interval [CI], 1.6–5.6) and longer among those aged ≥50 years (aHR, 0.50; 95% CI, .3–.9) compared to participants aged 18–49 years. No replication-competent viruses were recovered. Conclusions Although most patients were positive for SARS-CoV-2 for ≥10 days after symptom onset, our findings suggest that individuals with mild to moderate COVID-19 are unlikely to be infectious ≥10 days after symptom onset.

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Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant

10.1101/2022.01.13.22269257 ◽

2022 ◽

Author(s):

James A Hay ◽

Stephen M Kissler ◽

Joseph R Fauver ◽

Christina Mack ◽

Caroline G Tai ◽

...

Keyword(s):

Symptom Onset ◽

Time Course ◽

Infected Individual ◽

Viral Rna ◽

Disease Spread ◽

Infectious Period ◽

Test Results ◽

Frequent Testing ◽

Viral Proliferation ◽

Testing Protocols

Background. The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and escape from prior immunity. Defining the time course of Omicron viral proliferation and clearance is crucial to inform isolation protocols aiming to minimize disease spread. Methods. We obtained longitudinal, quantitative RT-qPCR test results using combined anterior nares and oropharyngeal samples (n = 10,324) collected between July 5th, 2021 and January 10th, 2022 from the National Basketball Association's (NBA) occupational health program. We quantified the fraction of tests with PCR cycle threshold (Ct) values <30, chosen as a proxy for potential infectivity and antigen test positivity, on each day after first detection of suspected and confirmed Omicron infections, stratified by individuals detected under frequent testing protocols and those detected due to symptom onset or concern for contact with an infected individual. We quantified the duration of viral proliferation, clearance rate, and peak viral concentration for individuals with acute Omicron and Delta variant SARS-CoV-2 infections. Results. A total of 97 infections were confirmed or suspected to be from the Omicron variant and 107 from the Delta variant. Of 27 Omicron-infected individuals testing positive ≤1 day after a previous negative or inconclusive test, 52.0% (13/25) were PCR positive with Ct values <30 at day 5, 25.0% (6/24) at day 6, and 13.0% (3/23) on day 7 post detection. Of 70 Omicron-infected individuals detected ≥2 days after a previous negative or inconclusive test, 39.1% (25/64) were PCR positive with Ct values <30 at day 5, 33.3% (21/63) at day 6, and 22.2% (14/63) on day 7 post detection. Overall, Omicron infections featured a mean duration of 9.87 days (95% CI 8.83-10.9) relative to 10.9 days (95% CI 9.41-12.4) for Delta infections. The peak viral RNA based on Ct values was lower for Omicron infections than for Delta infections (Ct 23.3, 95% CI 22.4-24.3 for Omicron; Ct 20.5, 95% CI 19.2-21.8 for Delta) and the clearance phase was shorter for Omicron infections (5.35 days, 95% CI 4.78-6.00 for Omicron; 6.23 days, 95% CI 5.43-7.17 for Delta), though the rate of clearance was similar (3.13 Ct/day, 95% CI 2.75-3.54 for Omicron; 3.15 Ct/day, 95% CI 2.69-3.64 for Delta). Conclusions. While Omicron infections feature lower peak viral RNA and a shorter clearance phase than Delta infections on average, it is unclear to what extent these differences are attributable to more immunity in this largely vaccinated population or intrinsic characteristics of the Omicron variant. Further, these results suggest that Omicron's infectiousness may not be explained by higher viral load measured in the nose and mouth by RT-PCR. The substantial fraction of individuals with Ct values <30 at days 5 of infection, particularly in those detected due to symptom onset or concern for contact with an infected individual, underscores the heterogeneity of the infectious period, with implications for isolation policies.

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Viral Culture in Hospitalized Congregate Care Patients With Prolonged SARS-CoV-2 Viral RNA Detection

Innovation in Aging ◽

10.1093/geroni/igab046.2713 ◽

2021 ◽

Vol 5 (Supplement_1) ◽

pp. 734-735

Author(s):

Thilaka Arunachalam ◽

Amit Singh ◽

Kathleen Stellrecht ◽

Sarah Elmendorf ◽

Tarani K Barman ◽

...

Keyword(s):

Viral Load ◽

Symptom Onset ◽

Clinical Symptoms ◽

Academic Medical Center ◽

Clinical Signs ◽

Viral Rna ◽

Nasopharyngeal Swab ◽

Active Virus ◽

Viral Culture ◽

Congregate Care

Abstract Prolonged detection of SARS-CoV-2 viral RNA has been observed in hospitalized congregate care patients following resolution of clinical symptoms. It is unknown whether patients with persistent PCR positivity pose a risk for COVID-19 transmission. The purpose of this study was to examine the results of serial PCR testing, viral load, and viral culture in patients awaiting discharge prior to a negative PCR test. We sampled 14 patients who were admitted from skilled nursing and/or rehabilitation facilities to a large academic medical center, had clinical signs and symptoms of COVID-19, and had multiple PCR-positive tests separated by at least 14 days. PCR-positive nasopharyngeal swabs were obtained from each patient for viral load quantification and viral culture. The mean age of patients was 72.5 years (55 – 92), with a mean peak SOFA score of 5.6 (1 – 11). Patients were hospitalized for a mean of 37.0 days (25 – 60). RNA was detected by PCR for a mean of 32.9 days (19 – 47). Mean viral load for the first PCR-positive nasopharyngeal swab collected at our hospital was 5.81 genomic copies/mL (2.12 – 9.72). Viral load decreased significantly with days from clinical symptom onset (R = -0.69, 95% CI, -0.80 – -0.55). Four out of 28 samples grew active virus via culture, with no active virus isolates after 2 days of symptom onset. Our viral culture data suggests that persistent PCR positivity may not correlate with infectivity, which has important implications for COVID-19 infection control precautions among older congregate care patients.

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SARS-CoV-2, SARS-CoV-1 and MERS-CoV viral load dynamics, duration of viral shedding and infectiousness: a living systematic review and meta-analysis

10.1101/2020.07.25.20162107 ◽

2020 ◽

Cited By ~ 1

Author(s):

Muge Cevik ◽

Matthew Tate ◽

Oliver Lloyd ◽

Alberto Enrico Maraolo ◽

Jenna Schafers ◽

...

Keyword(s):

Viral Load ◽

Respiratory Tract ◽

Symptom Onset ◽

Grey Literature ◽

Viral Rna ◽

Viral Dynamics ◽

Upper Respiratory Tract ◽

Live Virus ◽

Viral Shedding ◽

Upper Respiratory

Background Viral load kinetics and the duration of viral shedding are important determinants for disease transmission. We aim i) to characterise viral load dynamics, duration of viral RNA, and viable virus shedding of SARS-CoV-2 in various body fluids and ii) to compare SARS-CoV-2 viral dynamics with SARS-CoV-1 and MERS-CoV. Methods: Medline, EMBASE, Europe PMC, preprint servers and grey literature were searched to retrieve all articles reporting viral dynamics and duration of SARS-CoV-2, SARS-CoV-1 and MERS-CoV shedding. We excluded case reports and case series with < 5 patients, or studies that did not report shedding duration from symptom onset. PROSPERO registration: CRD42020181914. Findings: Seventy-nine studies on SARS-CoV-2, 8 on SARS-CoV-1, and 11 on MERS-CoV were included. Mean SARS-CoV-2 RNA shedding duration in upper respiratory tract, lower respiratory tract, stool and serum were 17.0, 14.6, 17.2 and 16.6 days, respectively. Maximum duration of SARS-CoV-2 RNA shedding reported in URT, LRT, stool and serum was 83, 59, 35 and 60 days, respectively. Pooled mean duration of SARS-CoV-2 RNA shedding was positively associated with age (p=0.002), but not gender (p = 0.277). No study to date has detected live virus beyond day nine of illness despite persistently high viral loads. SARS-CoV-2 viral load in the upper respiratory tract appears to peak in the first week of illness, while SARS-CoV-1 and MERS-CoV peak later. Conclusion: Although SARS-CoV-2 RNA shedding in respiratory and stool can be prolonged, duration of viable virus is relatively short-lived. Thus, detection of viral RNA cannot be used to infer infectiousness. High SARS-CoV-2 titres are detectable in the first week of illness with an early peak observed at symptom onset to day 5 of illness. This review underscores the importance of early case finding and isolation, as well as public education on the spectrum of illness. However, given potential delays in the isolation of patients, effective containment of SARS-CoV-2 may be challenging even with an early detection and isolation strategy. Funding: No funding was received.

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Epidemiological Correlates of Polymerase Chain Reaction Cycle Threshold Values in the Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Clinical Infectious Diseases ◽

10.1093/cid/ciaa1469 ◽

2020 ◽

Cited By ~ 2

Author(s):

Phillip P Salvatore ◽

Patrick Dawson ◽

Ashutosh Wadhwa ◽

Elizabeth M Rabold ◽

Sean Buono ◽

...

Keyword(s):

Polymerase Chain Reaction ◽

Severe Acute Respiratory Syndrome ◽

Symptom Onset ◽

Temporal Trends ◽

Viral Rna ◽

Chain Reaction ◽

Cycle Threshold ◽

Ct Value ◽

Polymerase Chain ◽

Epidemiological Characteristics

Abstract Background Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has principally been performed through the use of real-time reverse-transcription polymerase chain reaction testing. Results of such tests can be reported as cycle threshold (Ct) values, which may provide semi-quantitative or indirect measurements of viral load. Previous reports have examined temporal trends in Ct values over the course of a SARS-CoV-2 infection. Methods Using testing data collected during a prospective household transmission investigation of outpatient and mild coronavirus disease 2019 cases, we examined the relationships between Ct values of the viral RNA N1 target and demographic, clinical, and epidemiological characteristics collected through participant interviews and daily symptom diaries. Results We found that Ct values are lowest (corresponding to a higher viral RNA concentration) soon after symptom onset and are significantly correlated with the time elapsed since onset (P < .001); within 7 days after symptom onset, the median Ct value was 26.5, compared with a median Ct value of 35.0 occurring 21 days after onset. Ct values were significantly lower among participants under 18 years of age (P = .01) and those reporting upper respiratory symptoms at the time of sample collection (P = .001), and were higher among participants reporting no symptoms (P = .05). Conclusions These results emphasize the importance of early testing for SARS-CoV-2 among individuals with symptoms of respiratory illness, and allow cases to be identified and isolated when their viral shedding may be highest.

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The Correlation Between Clinical Features and Viral RNA Shedding in Outpatients With COVID-19

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa331 ◽

2020 ◽

Vol 7 (8) ◽

Author(s):

Tingting Liao ◽

Zhengrong Yin ◽

Juanjuan Xu ◽

Zhilei Lv ◽

Sufei Wang ◽

...

Keyword(s):

Logistic Regression ◽

Clinical Features ◽

Symptom Onset ◽

Protective Factor ◽

Multivariate Logistic Regression Analysis ◽

Viral Rna ◽

Severe Illness ◽

Time Interval ◽

Multivariate Logistic Regression ◽

Virus Shedding

Abstract Background Patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can shed virus, thereby causing human-to-human transmission, and the viral RNA shedding is commonly used as a proxy measure for infectivity. Methods We retrospectively reviewed confirmed cases of COVID-19 who attended the fever clinic of Wuhan Union Hospital from January 14 to February 24. In terms of the viral RNA shedding (median values) at first visit, patients were divided into a high–viral RNA shedding group and a low–viral RNA shedding group. Univariate and multivariate logistic regression analysis were performed to investigate the correlation between viral RNA shedding and clinical features. Results A total of 918 consecutive COVID-19 patients were enrolled, and severe patients made up 26.1%. After univariate and multivariate logistic regression, advanced age (odds ratio [OR], 1.02; 95% CI, 1.01–1.03; P = .001), having severe chronic diseases (OR, 1.44; 95% CI, 1.03–2.01; P = .04), and severe illness (OR, 1.60; 95% CI, 1.12–2.28; P = .01) were independent risk factors for high viral RNA shedding. Shorter time interval from symptom onset to viral detection was a protective factor for viral RNA shedding (OR, 0.97; 95% CI, 0.94–0.99; P = .01). Compared with mild patients, severe patients have higher virus shedding over a long period of time after symptom onset (P = .01). Conclusions Outpatients who were old, had severe illness, and had severe underlying diseases had high viral RNA shedding.

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Infectious virus in exhaled breath of symptomatic seasonal influenza cases from a college community

10.1101/194985 ◽

2017 ◽

Author(s):

Jing Yan ◽

Michael Grantham ◽

Jovan Pantelic ◽

P. Jacob Bueno de Mesquita ◽

Barbara Albert ◽

...

Keyword(s):

Influenza Virus ◽

Symptom Onset ◽

Infectious Virus ◽

Influenza Infection ◽

Geometric Mean ◽

Viral Rna ◽

Exhaled Breath ◽

Negatively Associated ◽

Aerosol Generation ◽

Coarse Aerosol

AbstractLittle is known about the amount and infectiousness of influenza virus shed into exhaled breath. This contributes to uncertainty about the importance of airborne influenza transmission. We screened 355 symptomatic volunteers with acute respiratory illness and report 142 cases with confirmed influenza infection who provided 218 paired nasopharyngeal (NP) and 30-minute breath samples (coarse >5 μm and fine <5 μm fractions) on days 1 to 3 post symptom onset. We assessed viral RNA copy number for all samples and cultured NP swabs and fine aerosols. We recovered infectious virus from 52 (39%) of the fine aerosols and 150 (89%) of the NP swabs with valid cultures. The geometric mean RNA copy numbers were 3.8×104/30-min fine, 1.2×104/30-min coarse aerosol sample, and 8.2×108 per NP swab. Fine and coarse aerosol viral RNA was positively associated with body mass index (fine p<0.05, coarse p<0.10) and number of coughs (fine p<0.001, coarse p<0.01) and negatively associated with increasing days since symptom onset (fine p<0.05 to p<0.01, coarse p<0.10) in adjusted models. Fine aerosol viral RNA was also positively associated with having influenza vaccination for both the current and prior season (p<0.01). NP swab viral RNA was positively associated with upper respiratory symptoms (p<0.01) and negatively associated with age (p<0.01) but was not significantly associated with fine or coarse aerosol viral RNA or their predictors. Sneezing was rare, and sneezing and coughing were not necessary for infectious aerosol generation. Our observations suggest that influenza infection in the upper and lower airways are compartmentalized and independent.SignificanceLack of human data on influenza virus aerosol shedding fuels debate over the importance of airborne transmission. We provide overwhelming evidence that humans generate infectious aerosols and quantitative data to improve mathematical models of transmission and public health interventions. We show that sneezing is rare and not important for, and that coughing is not required for influenza virus aerosolization. Our findings, that upper and lower airway infection are independent and that fine particle exhaled aerosols reflect infection in the lung, open a new pathway for understanding the human biology of influenza infection and transmission. Our observation of an association between repeated vaccination and increased viral aerosol generation demonstrated the power of our method, but needs confirmation.

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