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

Little 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 1–3 after 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-minutes fine-, 1.2 × 104/30-minutes coarse-aerosol sample, and 8.2 × 108 per NP swab. Fine- and coarse-aerosol viral RNA were positively associated with body mass index and number of coughs and negatively associated with increasing days since symptom onset in adjusted models. Fine-aerosol viral RNA was also positively associated with having influenza vaccination for both the current and prior season. NP swab viral RNA was positively associated with upper respiratory symptoms and negatively associated with age 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.

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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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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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Daily Viral Kinetics and Innate and Adaptive Immune Response Assessment in COVID-19: a Case Series

mSphere ◽

10.1128/msphere.00827-20 ◽

2020 ◽

Vol 5 (6) ◽

Author(s):

Pauline Vetter ◽

Christiane S. Eberhardt ◽

Benjamin Meyer ◽

Paola Andrea Martinez Murillo ◽

Giulia Torriani ◽

...

Keyword(s):

Immune Response ◽

Symptom Onset ◽

Infectious Virus ◽

Case Series ◽

Viral Rna ◽

Adaptive Responses ◽

Innate Response ◽

Viral Control ◽

Virus Shedding ◽

Viral Loads

ABSTRACT Viral shedding patterns and their correlations with immune responses are still poorly characterized in mild coronavirus (CoV) disease 2019 (COVID-19). We monitored shedding of viral RNA and infectious virus and characterized the immune response kinetics of the first five patients quarantined in Geneva, Switzerland. High viral loads and infectious virus shedding were observed from the respiratory tract despite mild symptoms, with isolation of infectious virus and prolonged positivity by reverse transcriptase PCR (RT-PCR) until days 7 and 19 after symptom onset, respectively. Robust innate responses characterized by increases in activated CD14+ CD16+ monocytes and cytokine responses were observed as early as 2 days after symptom onset. Cellular and humoral severe acute respiratory syndrome (SARS)-CoV-2-specific adaptive responses were detectable in all patients. Infectious virus shedding was limited to the first week after symptom onset. A strong innate response, characterized by mobilization of activated monocytes during the first days of infection and SARS-CoV-2-specific antibodies, was detectable even in patients with mild disease. IMPORTANCE This work is particularly important because it simultaneously assessed the virology, immunology, and clinical presentation of the same subjects, whereas other studies assess these separately. We describe the detailed viral and immune profiles of the first five patients infected by SARS-CoV-2 and quarantined in Geneva, Switzerland. Viral loads peaked at the very beginning of the disease, and infectious virus was shed only during the early acute phase of disease. No infectious virus could be isolated by culture 7 days after onset of symptoms, while viral RNA was still detectable for a prolonged period. Importantly, we saw that all patients, even those with mild symptoms, mount an innate response sufficient for viral control (characterized by early activated cytokines and monocyte responses) and develop specific immunity as well as cellular and humoral SARS-CoV-2-specific adaptive responses, which already begin to decline a few months after the resolution of symptoms.

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Recent smell loss is the best predictor of COVID-19 among individuals with recent respiratory symptoms

Chemical Senses ◽

10.1093/chemse/bjaa081 ◽

2020 ◽

Author(s):

Richard C Gerkin ◽

Kathrin Ohla ◽

Maria G Veldhuizen ◽

Paule V Joseph ◽

Christine E Kelly ◽

...

Keyword(s):

Symptom Onset ◽

Respiratory Symptom ◽

Respiratory Illness ◽

Cross Sectional Study ◽

Cross Sectional ◽

Logistic Regression Models ◽

Olfactory Loss ◽

Visual Analog Scales ◽

Cardinal Symptoms ◽

Smell Loss

Abstract In a preregistered, cross-sectional study we investigated whether olfactory loss is a reliable predictor of COVID-19 using a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified univariate and multivariate predictors of COVID-19 status and post-COVID-19 olfactory recovery. Both C19+ and C19- groups exhibited smell loss, but it was significantly larger in C19+ participants (mean±SD, C19+: -82.5±27.2 points; C19-: -59.8±37.7). Smell loss during illness was the best predictor of COVID-19 in both univariate and multivariate models (ROC AUC=0.72). Additional variables provide negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms (e.g., fever). Olfactory recovery within 40 days of respiratory symptom onset was reported for ~50% of participants and was best predicted by time since respiratory symptom onset. We find that quantified smell loss is the best predictor of COVID-19 amongst those with symptoms of respiratory illness. To aid clinicians and contact tracers in identifying individuals with a high likelihood of having COVID-19, we propose a novel 0-10 scale to screen for recent olfactory loss, the ODoR-19. We find that numeric ratings ≤2 indicate high odds of symptomatic COVID-19 (4<OR<10). Once independently validated, this tool could be deployed when viral lab tests are impractical or unavailable.

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Quantitative measurement of infectious virus in SARS-CoV-2 Alpha, Delta and Epsilon variants reveals higher infectivity (viral titer:RNA ratio) in clinical samples containing the Delta and Epsilon variants.

10.1101/2021.09.07.21263229 ◽

2021 ◽

Author(s):

Hannah W Despres ◽

Margaret G Mills ◽

David J Shirley ◽

Madaline M Schmidt ◽

Meei-Li Huang ◽

...

Keyword(s):

Quantitative Measurement ◽

Infectious Virus ◽

Viral Rna ◽

Clinical Samples ◽

Rt Pcr ◽

Genome Copy ◽

Live Virus ◽

High Degree ◽

The Relationship ◽

Rna Levels

ABSTRACT Background Novel SARS-CoV-2 Variants of Concern (VoC) pose a challenge to controlling the COVID-19 pandemic. Previous studies indicate that clinical samples collected from individuals infected with the Delta variant may contain higher levels of RNA than previous variants, but the relationship between viral RNA and infectious virus for individual variants is unknown. Methods We measured infectious viral titer (using a micro-focus forming assay) as well as total and subgenomic viral RNA levels (using RT-PCR) in a set of 165 clinical samples containing SARS-CoV-2 Alpha, Delta and Epsilon variants that were processed within two days of collection from the patient. Results We observed a high degree of variation in the relationship between viral titers and RNA levels. Despite the variability we observed for individual samples the overall infectivity differed among the three variants. Both Delta and Epsilon had significantly higher infectivity than Alpha, as measured by the number of infectious units per quantity of viral E gene RNA (6 and 4 times as much, p=0.0002 and 0.009 respectively) or subgenomic E RNA (11 and 7 times as much, p<0.0001 and 0.006 respectively). Conclusion In addition to higher viral RNA levels reported for the Delta variant, the infectivity (amount of replication competent virus per viral genome copy) may also be increased compared to Alpha. Measuring the relationship between live virus and viral RNA is an important step in assessing the infectivity of novel SARS-CoV-2 variants. An increase in the infectivity of the Delta variant may further explain increased spread and suggests a need for increased measures to prevent viral transmission.

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Duration of Infectious Virus Shedding in Patients With Severe Coronavirus Disease 2019 Who Required Mechanical Ventilation

10.21203/rs.3.rs-395009/v1 ◽

2021 ◽

Author(s):

Toshihito Nomura ◽

Hiroki Kitagawa ◽

Keitaro Omori ◽

Norifumi Shigemoto ◽

Masaki Kakimoto ◽

...

Keyword(s):

Mechanical Ventilation ◽

Symptom Onset ◽

Infectious Virus ◽

Quantitative Polymerase Chain Reaction ◽

University Hospital ◽

Nasopharyngeal Swab ◽

Test Results ◽

Virus Shedding ◽

Viral Culture ◽

Respiratory Management

Abstract Approximately 5% of patients with coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 develop severe COVID-19. Severe COVID-19 requires respiratory management with mechanical ventilation and an extended period of treatment. Prolonged infectious virus shedding is a concern in severe COVID-19 cases, but few reports have examined the duration of infectious virus shedding. Therefore, we investigated the duration of infectious virus shedding in patients transferred to Hiroshima University Hospital with severe COVID-19 requiring mechanical ventilation. Nasopharyngeal swab specimens were collected and analyzed using both viral culture and reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) tests between December 2020 and February 2021. Of the 23 patients tested, the proportions of those with positive test results at first specimen collection on RT-qPCR and viral culture tests were 95·7% and 30·4%, respectively. All six patients with positive viral culture test results who were followed-up tested negative 24 days after symptom onset but remained positive on RT-qPCR. The longest negative conversion time was observed in a dialysis patient on immunosuppressive drugs. This study indicated that patients with severe COVID-19 remain culture positive for ≥ 10 days after symptom onset. Additionally, immunosuppressed patients with severe COVID-19 could consider isolation for ≥ 20 days.

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Ebola Virus Ribonucleic Acid Detection in Semen More Than Two Years After Resolution of Acute Ebola Virus Infection

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx155 ◽

2017 ◽

Vol 4 (3) ◽

Cited By ~ 21

Author(s):

William A Fischer ◽

Jerry Brown ◽

David Alain Wohl ◽

Amy James Loftis ◽

Sam Tozay ◽

...

Keyword(s):

Virus Infection ◽

Ribonucleic Acid ◽

Ebola Virus ◽

Infectious Virus ◽

Virus Disease ◽

Viral Rna ◽

Ebola Virus Disease ◽

Positive Specimen ◽

Ebola Virus Infection

Abstract Among 149 men who survived Ebola virus disease (EVD) and donated semen 260–1016 days after EVD onset, Ebola virus (EBOV) ribonucleic acid (RNA) was detected in 13 (9%). Of 137 men who donated semen 2 years after EVD onset, 11 (8%) had an EBOV RNA-positive specimen. The mechanism underlying the persistence of EBOV RNA in semen is unclear, and it is unclear whether the detection of viral RNA represents the presence of infectious virus.

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Lack of Middle East Respiratory Syndrome Coronavirus Transmission in Rabbits

Viruses ◽

10.3390/v11040381 ◽

2019 ◽

Vol 11 (4) ◽

pp. 381 ◽

Cited By ~ 4

Author(s):

W. Widagdo ◽

Nisreen M. A. Okba ◽

Mathilde Richard ◽

Dennis de Meulder ◽

Theo M. Bestebroer ◽

...

Keyword(s):

Middle East ◽

Animal Species ◽

Infectious Virus ◽

Clinical Manifestations ◽

Middle East Respiratory Syndrome ◽

Viral Rna ◽

Nasal Discharge ◽

Upper Respiratory Tract ◽

Transmission Potential ◽

Livestock Animal

Middle East respiratory syndrome coronavirus (MERS-CoV) transmission from dromedaries to humans has resulted in major outbreaks in the Middle East. Although some other livestock animal species have been shown to be susceptible to MERS-CoV, it is not fully understood why the spread of the virus in these animal species has not been observed in the field. In this study, we used rabbits to further characterize the transmission potential of MERS-CoV. In line with the presence of MERS-CoV receptor in the rabbit nasal epithelium, high levels of viral RNA were shed from the nose following virus inoculation. However, unlike MERS-CoV-infected dromedaries, these rabbits did not develop clinical manifestations including nasal discharge and did shed only limited amounts of infectious virus from the nose. Consistently, no transmission by contact or airborne routes was observed in rabbits. Our data indicate that despite relatively high viral RNA levels produced, low levels of infectious virus are excreted in the upper respiratory tract of rabbits as compared to dromedary camels, thus resulting in a lack of viral transmission.

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Experimental Assessment of Zika Virus Mechanical Transmission by Aedes aegypti

Viruses ◽

10.3390/v11080695 ◽

2019 ◽

Vol 11 (8) ◽

pp. 695 ◽

Cited By ~ 3

Author(s):

Antoine Boullis ◽

Nadège Cordel ◽

Cécile Herrmann-Storck ◽

Anubis Vega-Rúa

Keyword(s):

Experimental Design ◽

Aedes Aegypti ◽

Zika Virus ◽

Infectious Virus ◽

Viral Rna ◽

Mechanical Transmission ◽

Experimental Assessment ◽

Infected Blood ◽

Virus Titration ◽

Blood Meals

The pandemic emergence of several mosquito-borne viruses highlights the need to understand the different ways in which they can be transmitted by vectors to human hosts. In this study, we evaluated the propensity of Aedes aegypti to transmit mechanically Zika virus (ZIKV) using an experimental design. Mosquitoes were allowed to feed on ZIKV-infected blood and were then rapidly transferred to feed on ZIKV-free blood until they finished their meal. The uninfected blood meals, the mosquito abdomens, as well as the mouthparts dissected from fully and partially engorged mosquitoes were analyzed using RT-qPCR and/or virus titration. All the fully engorged mosquito abdomens were ZIKV-infected, whereas their mouthparts were all ZIKV-negative. Nonetheless, one of the partially engorged mosquitoes carried infectious particles on mouthparts. No infectious virus was found in the receiver blood meals, while viral RNA was detected in 9% of the samples (2/22). Thus, mechanical transmission of ZIKV may sporadically occur via Ae. aegypti bite. However, as the number of virions detected on mouthparts (2 particles) is not sufficient to induce infection in a naïve host, our results indicate that mechanical transmission does not impact ZIKV epidemiology.

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Persistent Infection of Human Oligodendrocytic and Neuroglial Cell Lines by Human Coronavirus 229E

Journal of Virology ◽

10.1128/jvi.73.4.3326-3337.1999 ◽

1999 ◽

Vol 73 (4) ◽

pp. 3326-3337 ◽

Cited By ~ 74

Author(s):

Nathalie Arbour ◽

Sophie Ekandé ◽

Geneviève Côté ◽

Claude Lachance ◽

Fanny Chagnon ◽

...

Keyword(s):

Nervous System ◽

Cell Lines ◽

Persistent Infection ◽

Viral Antigen ◽

Infectious Virus ◽

Acute Infection ◽

Viral Rna ◽

Persistent Infections ◽

Virus Progeny

ABSTRACT Human coronaviruses (HuCV) cause common colds. Previous reports suggest that these infectious agents may be neurotropic in humans, as they are for some mammals. With the long-term aim of providing experimental evidence for the neurotropism of HuCV and the establishment of persistent infections in the nervous system, we have evaluated the susceptibility of various human neural cell lines to acute and persistent infection by HuCV-229E. Viral antigen, infectious virus progeny and viral RNA were monitored during both acute and persistent infections. The astrocytoma cell lines U-87 MG, U-373 MG, and GL-15, as well as neuroblastoma SK-N-SH, neuroglioma H4, and oligodendrocytic MO3.13 cell lines, were all susceptible to an acute infection by HuCV-229E. The CHME-5 immortalized fetal microglial cell line was not susceptible to infection by this virus. The MO3.13 and H4 cell lines also sustained a persistent viral infection, as monitored by detection of viral antigen and infectious virus progeny. Sequencing of the S1 gene from viral RNA after ∼130 days of infection showed two point mutations, suggesting amino acid changes during persistent infection of MO3.13 cells but none for H4 cells. Thus, persistent in vitro infection did not generate important changes in the S1 portion of the viral spike protein, which was shown for murine coronaviruses to bear hypervariable domains and to interact with cellular receptor. These results are consistent with the potential persistence of HuCV-229E in cells of the human nervous system, such as oligodendrocytes and possibly neurons, and the virus’s apparent genomic stability.

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