Effects of weather-related social distancing on city-scale transmission of respiratory viruses: a retrospective cohort study

Background

Unusually high snowfall in western Washington State in February 2019 led to widespread school and workplace closures. We assessed the impact of social distancing caused by this extreme weather event on the transmission of respiratory viruses.

Methods

Residual specimens from patients evaluated for acute respiratory illness at hospitals in the Seattle metropolitan area were screened for a panel of respiratory viruses. Transmission models were fit to each virus to estimate the magnitude reduction in transmission due to weather-related disruptions. Changes in contact rates and care-seeking were informed by data on local traffic volumes and hospital visits.

Results

Disruption in contact patterns reduced effective contact rates during the intervention period by 16 to 95%, and cumulative disease incidence through the remainder of the season by 3 to 9%. Incidence reductions were greatest for viruses that were peaking when the disruption occurred and least for viruses in an early epidemic phase.

Conclusion

High-intensity, short-duration social distancing measures may substantially reduce total incidence in a respiratory virus epidemic if implemented near the epidemic peak. For SARS-CoV-2, this suggests that, even when SARS-CoV-2 spread is out of control, implementing short-term disruptions can prevent COVID-19 deaths.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06028-4.

Transplacental Respiratory Syncytial Virus and Influenza Virus Antibody Transfer in Alaska Native and Seattle Mother-Infant Pairs

BACKGROUND

Alaska Native (AN) infants are at risk for severe disease due to respiratory syncytial virus (RSV) and influenza. Maternal immunization protects young infants through transplacental antibody transfer. RSV- and influenza-specific transplacental antibody transfer in mother-infant pairs has not previously been evaluated in the AN population.

METHODS

Serum samples collected during pregnancy and at birth from AN mother-infant pairs in the Yukon-Kuskokwim Delta region (YKD) of Alaska (2000-2011; n = 75) and predominantly white pairs in Seattle, Washington (2014-2016; n = 57), were tested for RSV and influenza antibody using a microneutralization and hemagglutination inhibition assay, respectively, and compared between sites.

RESULTS

Mean RSV antibody concentrations in pregnant women in YKD and Seattle were similar (log2 RSV antibody 10.6 vs 10.7, P = .86), but cord blood RSV antibody concentrations were significantly lower in infants born to mothers in YKD compared with Seattle (log2 RSV antibody 11.0 vs 12.2, P < .001). Maternal and cord blood influenza antibody concentrations were lower for women and infants in YKD compared with Seattle for all 4 influenza antigens tested (all P < .05). The mean cord to maternal RSV antibody transfer ratio was 1.15 (standard deviation [SD], 0.13) in mother-infant pairs in Seattle compared with 1.04 (SD, 0.08) in YKD. Mean cord blood to maternal antibody transfer ratios for influenza antigens ranged from 1.22 to 1.42 in Seattle and from 1.05 to 1.59 in YKD.

CONCLUSIONS

Though the transplacental antibody transfer ratio was high (>1.0) for both groups, transfer ratios for RSV antibody were significantly lower in AN mother-infant pairs. Further studies are needed to elucidate the impact of lower transplacental antibody transfer on infant disease risk in rural Alaska.Alaska Native and continental US mother-infant pairs have high transplacental antibody transfer ratios (>1.0) for influenza and respiratory syncytial virus, but anti-respiratory syncytial virus antibody levels are significantly lower in Alaska Native pairs than in those from the continental US.

Rotavirus Genotype Trends and Gastrointestinal Pathogen Detection in the United States, 2014-16: Results from the New Vaccine Surveillance Network

BACKGROUND

Following the implementation of rotavirus vaccination in 2006, severe acute gastroenteritis (AGE) due to group A rotavirus (RVA) has substantially declined in USA (US) children. We report the RVA genotype prevalence as well as co-infection data from seven US New Vaccine Surveillance Network (NVSN) sites during three consecutive RVA seasons, 2014-2016.

METHODS

A total of 1041 stool samples that tested positive for RVA by Rotaclone enzyme immunoassay (EIA) were submitted to the Centers for Disease Control and Prevention (CDC) for RVA genotyping and multipathogen testing.

RESULTS

A total of 795 (76%) contained detectable RVA at CDC. Rotavirus disease was highest in children < 3 years of age. Four G types (G1, G2, G9, and G12) accounted for 94.6% of strains while two P types (P[4] and P[8]) accounted 94.7% of the strains. Overall, G12P[8] was the most common genotype detected in all three seasons. Stepwise conditional logistic analysis found year and study site were significant predictors of genotype. Twenty four percent (24%) of RVA-positive specimens contained other AGE pathogens.

CONCLUSIONS

G12P[8] predominated over three seasons, but strain predominance varied by year and study site. Ongoing surveillance provides continuous tracking and monitoring of US genotypes during the post vaccine era.

A human coronavirus evolves antigenically to escape antibody immunity

There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these "future" viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8-17 years later. The decreased neutralization of "future" viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.

Vaccine Effectiveness Against Influenza Hospitalization Among Children in the United States, 2015-2016

BACKGROUND

Annual United States (US) estimates of influenza vaccine effectiveness (VE) in children typically measure protection against outpatient medically attended influenza illness, with limited data evaluating VE against influenza hospitalizations. We estimated VE for preventing laboratory-confirmed influenza hospitalization among US children.

METHODS

We included children aged 6 months-17 years with acute respiratory illness enrolled in the New Vaccine Surveillance Network during the 2015-2016 influenza season. Documented influenza vaccination status was obtained from state immunization information systems, the electronic medical record, and/or provider records. Midturbinate nasal and throat swabs were tested for influenza using molecular assays. We estimated VE as 100% × (1 - odds ratio), comparing the odds of vaccination among subjects testing influenza positive with subjects testing negative, using multivariable logistic regression.

RESULTS

Of 1653 participants, 36 of 707 (5%) of those fully vaccinated, 18 of 226 (8%) of those partially vaccinated, and 85 of 720 (12%) of unvaccinated children tested positive for influenza. Of those vaccinated, almost 90% were documented to have received inactivated vaccine. The majority (81%) of influenza cases were in children ≤ 8 years of age. Of the 139 influenza-positive cases, 42% were A(H1N1)pdm09, 42% were B viruses, and 14% were A(H3N2). Overall, adjusted VE for fully vaccinated children was 56% (95% confidence interval [CI], 34%-71%) against any influenza-associated hospitalization, 68% (95% CI, 36%-84%) for A(H1N1)pdm09, and 44% (95% CI, -1% to 69%) for B viruses.

CONCLUSIONS

These findings demonstrate the importance of annual influenza vaccination in prevention of severe influenza disease and of reducing the number of children who remain unvaccinated or partially vaccinated against influenza.

Isolation and Characterization of Cross-Neutralizing Coronavirus Antibodies from COVID-19+ Subjects

SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterized 198 antibodies isolated from four COVID19+ subjects and identified 14 SARS-CoV-2 neutralizing antibodies. One targeted the NTD, one recognized an epitope in S2 and twelve bound the RBD. Three anti-RBD neutralizing antibodies cross-neutralized SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency rather than the antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. The anti-S2 antibody also neutralized SARS-CoV-1 and all four cross-neutralizing antibodies neutralized the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.

The Infectious Diseases Society of America Guidelines on the Diagnosis of COVID-19: Molecular Diagnostic Testing

BACKGROUND

Accurate molecular diagnostic tests are necessary for confirming a diagnosis of coronavirus disease 2019 (COVID-19). Direct detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acids in respiratory tract specimens informs patient, healthcare institution and public health level decision-making. The numbers of available SARS-CoV-2 nucleic acid detection tests are rapidly increasing, as is the COVID-19 diagnostic literature. Thus, the Infectious Diseases Society of America (IDSA) recognized a significant need for frequently updated systematic reviews of the literature to inform evidence-based best practice guidance.

OBJECTIVE

The IDSA's goal was to develop an evidence-based diagnostic guideline to assist clinicians, clinical laboratorians, patients and policymakers in decisions related to the optimal use of SARS-CoV-2 nucleic acid amplification tests. In addition, we provide a conceptual framework for understanding molecular diagnostic test performance, discuss the nuance of test result interpretation in a variety of practice settings and highlight important unmet research needs in the COVID-19 diagnostic testing space.

METHODS

IDSA convened a multidisciplinary panel of infectious diseases clinicians, clinical microbiologists, and experts in systematic literature review to identify and prioritize clinical questions and outcomes related to the use of SARS-CoV-2 molecular diagnostics. Grading of Recommendations Assessment, Development and Evaluation (GRADE) methodology was used to assess the certainty of evidence and make testing recommendations.

RESULTS

The panel agreed on 17 diagnostic recommendations.

CONCLUSIONS

Universal access to accurate SARS-CoV-2 nucleic acid testing is critical for patient care, hospital infection prevention and the public response to the COVID-19 pandemic. Information on the clinical performance of available tests is rapidly emerging, but the quality of evidence of the current literature is considered moderate to very low. Recognizing these limitations, the IDSA panel weighed available diagnostic evidence and recommends nucleic acid testing for all symptomatic individuals suspected of having COVID-19. In addition, testing is recommended for asymptomatic individuals with known or suspected contact with a COVID-19 case. Testing asymptomatic individuals without known exposure is suggested when the results will impact isolation/quarantine/personal protective equipment (PPE) usage decisions, dictate eligibility for surgery, or inform solid organ or hematopoietic stem cell transplantation timing. Ultimately, prioritization of testing will depend on institutional-specific resources and the needs of different patient populations.

Respiratory viruses

Respiratory viruses are commonly detected in both healthy and immunocompromised children. In most healthy children, respiratory viruses are associated with self-limited upper respiratory tract infections and are not accompanied by significant morbidity. In immunocompromised hosts, including hematopoietic cell transplant recipients, solid organ transplant recipients, and oncology patients, respiratory viruses can be associated with significant clinical manifestations, including prolonged viral shedding, lower respiratory tract disease, the need for supplemental oxygen, late airflow obstruction, and even death. This chapter reviews the major respiratory viruses, including respiratory syncytial virus, human metapneumovirus, influenza, parainfluenza viruses, human rhinoviruses, and human coronaviruses. Other viruses can manifest as pulmonary infection; however, these viruses are discussed elsewhere (see Chapter 17 for discussion of cytomegalovirus and Chapter 22 for discussion of adenoviruses).

Characteristics of COVID-19 in Homeless Shelters : A Community-Based Surveillance Study

BACKGROUND

Homeless shelters are a high-risk setting for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission because of crowding and shared hygiene facilities.

OBJECTIVE

To investigate SARS-CoV-2 case counts across several adult and family homeless shelters in a major metropolitan area.

DESIGN

Cross-sectional, community-based surveillance study. (ClinicalTrials.gov: NCT04141917).

SETTING

14 homeless shelters in King County, Washington.

PARTICIPANTS

A total of 1434 study encounters were done in shelter residents and staff, regardless of symptoms.

INTERVENTION

2 strategies were used for SARS-CoV-2 testing: routine surveillance and contact tracing ("surge testing") events.

MEASUREMENTS

The primary outcome measure was test positivity rate of SARS-CoV-2 infection at shelters, determined by dividing the number of positive cases by the total number of participant encounters, regardless of symptoms. Sociodemographic, clinical, and virologic variables were assessed as correlates of viral positivity.

RESULTS

Among 1434 encounters, 29 (2% [95% CI, 1.4% to 2.9%]) cases of SARS-CoV-2 infection were detected across 5 shelters. Most (n = 21 [72.4%]) were detected during surge testing events rather than routine surveillance, and most (n = 21 [72.4% {CI, 52.8% to 87.3%}]) were asymptomatic at the time of sample collection. Persons who were positive for SARS-CoV-2 were more frequently aged 60 years or older than those without SARS-CoV-2 (44.8% vs. 15.9%). Eighty-six percent of persons with positive test results slept in a communal space rather than in a private or shared room.

LIMITATION

Selection bias due to voluntary participation and a relatively small case count.

CONCLUSION

Active surveillance and surge testing were used to detect multiple cases of asymptomatic and symptomatic SARS-CoV-2 infection in homeless shelters. The findings suggest an unmet need for routine viral testing outside of clinical settings for homeless populations.

PRIMARY FUNDING SOURCE

Gates Ventures.

School-Based Surveillance of Respiratory Pathogens on "High-Touch" Surfaces

In order to assess the presence of respiratory pathogens on "high-touch" surfaces and inform sanitation practices at schools, pre-selected surfaces in elementary schools in Seattle, WA, USA were sampled weekly and tested by RT-PCR for 25 viral respiratory pathogens (including SARS-CoV-2 retrospectively) and S. pneumoniae during 2019-2020 winter respiratory illness season. Viral pathogens (rhinovirus, adenovirus, influenza) known to cause respiratory illness were detected on commonly touched surfaces, especially wooden surfaces, and matched the patterns of circulating virus in the community.

78. Acute Respiratory Illnesses in Children During the sars-cov-2 Pandemic: A Prospective Multicenter Surveillance Study

Background

A state of emergency was declared in the United States (US) on March 13, 2020 in response to the SARS-CoV-2 pandemic. Healthcare providers had to alter practice patterns and research priorities. We assessed the frequency of acute respiratory illnesses (ARI) in children, notably those due to respiratory syncytial virus (RSV) and influenza, before and during the pandemic.

Methods

We conducted multi-center active prospective ARI surveillance in children as part of the New Vaccine Surveillance Network. Children < 18 years with fever and/or respiratory symptoms were enrolled in emergency department and inpatient settings at seven US medical centers over four respiratory seasons during 2016–2020 (Fig 1). Pandemic-related restrictions to patient access limited enrollment in some sites beginning March 2020. Respiratory specimens were collected and tested at each site for RSV and influenza by qRT-PCR. Data were analyzed by calendar weeks. We compared the cumulative proportions of RSV and influenza detection after week 13 in 2020 to the previous seasons using Fisher’s exact test.

Figure 1. Numbers of Eligible and Enrolled Acute Respiratory Illness Cases, and Proportions of RSV and Influenza Detection by Week, Stratified by Study Season

Results

Of 44,247 eligible children, 25,375 (57%) were enrolled and tested for RSV and/or influenza. A total of 6351/25375 (25%) and 3446/25372 (14%) children were RSV and influenza-positive over the four seasons, respectively. In 2020, we noted a rapid drop in eligible and enrolled ARI subjects after weeks 11–13 (Fig 1). During weeks 13–18 in 2016–2019, the three-year average of eligible and enrolled subjects was 1802 and 978, respectively. However, over the same period in 2020, there were 675 eligible and 278 enrolled subjects, representing declines of 62.5% and 71.6% respectively (Fig 1). In 2020, there were no RSV or influenza cases detected in weeks 15–18, and the cumulative proportions of RSV and influenza detection after week 13 were lower compared to previous seasons (p< 0.001) (Figs 1 and 2).

Figure 2. Cumulative Proportions of Weekly RSV and Influenza Detection by Study Season

Conclusion

There was a considerable decline in ARI visits and the proportion of RSV and influenza detection across seven distinct geographic sites during the pandemic compared with previous seasons. These findings might be attributable to social distancing measures to lessen the spread of SARS-CoV-2, changes in healthcare-seeking behaviors, and limited access to medical care.

Disclosures

Zaid Haddadin, MD, CDC (Grant/Research Support, Research Grant or Support)Quidel Corporation (Grant/Research Support, Research Grant or Support)sanofi pasteur (Grant/Research Support, Research Grant or Support) John V. Williams, MD, GlaxoSmithKline (Advisor or Review Panel member)IDConnect (Advisor or Review Panel member)Quidel (Advisor or Review Panel member) Christopher J. Harrison, MD, GSK (Grant/Research Support, Infant menigiciccal B conjugate vaccine trial)Merck (Research Grant or Support, Infant pneumococcal conjugate vaccine trial) Janet A. Englund, MD, AstraZeneca (Scientific Research Study Investigator)GSK group of companies (Scientific Research Study Investigator)Meissa vaccines (Consultant)Merck (Scientific Research Study Investigator)Sanofi Pasteur (Consultant) Natasha B. Halasa, MD, MPH, Genentech (Other Financial or Material Support, I receive an honorarium for lectures - it’s a education grant, supported by genetech)Karius (Consultant)Moderna (Consultant)Quidel (Grant/Research Support, Research Grant or Support)Sanofi (Grant/Research Support, Research Grant or Support)

1523. Seasonal Human Coronavirus Infections Following Allogeneic Hematopoietic Cell Transplantation: Factors Associated With Lower Respiratory Tract Infection

Background

Proven/probable lower respiratory tract infection (LRTI) caused by seasonal human coronaviruses (HCoVs) is associated with mortality after hematopoietic cell transplantation (HCT). However, risk factors for LRTI and the significance of virologic documentation of lower respiratory tract involvement by bronchoalveolar lavage (BAL) on outcome are not well characterized.

Methods

Patients receiving allogeneic HCT between 4/2008 and 9/2018 with HCoV (OC43/NL63/HKU1/229E) detected in nasopharyngeal or BAL samples by PCR were retrospectively analyzed. Proven/probable LRTI was defined as having virus detected from a BAL sample with or without new pulmonary infiltrates by chest radiography, respectively. Possible LRTI was defined as having virus detected from an upper respiratory tract sample with new pulmonary infiltrates. We used logistic regression models to evaluate risk factors for LRTI in patients with first documented HCoV infection during pretransplant conditioning or post-HCT. Overall mortality following proven/probable and possible LRTI was compared by the log-rank test.

Results

A total of 297 patients (61 children and 236 adults) developed HCoV infection as follows: 254 had upper respiratory tract infection (URTI) alone, 18 presented with LRTI, and 25 progressed from URTI to LRTI [median 16 days (range, 2–62 days)]. Multivariable analyses showed that male gender, higher immunodeficiency scoring index, albumin < 3 g/dl, glucose > 150 mg/dl and presence of respiratory copathogen at HCoV diagnosis were associated with the occurrence of LRTI (Figure 1). Patients with proven/probable LRTI (N=16) had significantly worse survival than those with possible LRTI (N=37) (p=0.006, Figure 2).

Figure 1.

Figure 2.

Conclusion

Our analyses identified risk factors (hypoalbuminemia, male gender, high glucose and presence of respiratory copathogen) uncommonly appreciated for LRTI due to other respiratory viruses in HCT recipients. Whether these factors are also relevant to LRTI due to SARS-CoV-2 after HCT requires further studies. The association of hyperglycemia with LRTI might provide an opportunity to reduce the risk of LRTI.

Disclosures

Alpana Waghmare, MD, Amazon (Grant/Research Support)Amazon (Employee, Shareholder)Ansun Biopharma (Scientific Research Study Investigator)Kyorin Pharmaceuticals (Advisor or Review Panel member) Janet A. Englund, MD, AstraZeneca (Scientific Research Study Investigator)GSK group of companies (Scientific Research Study Investigator)Meissa vaccines (Consultant)Merck (Scientific Research Study Investigator)Sanofi Pasteur (Consultant) Michael Boeckh, MD PhD, AlloVir (Consultant)EvrysBio (Advisor or Review Panel member, Other Financial or Material Support, share options)Gilead (Consultant, Grant/Research Support)GSK (Consultant)Helocyte (Advisor or Review Panel member, Shareholder)Lophius (Grant/Research Support)Merck (Consultant, Grant/Research Support)SymBio (Consultant)VirBio (Consultant, Grant/Research Support)

178. Vaccine Effectiveness Against Influenza-associated Hospitalizations and Emergency Department (ED) Visits Among Children in the United States in the 2019–2020 Season

Background

The 2019–20 influenza season was predominated by early onset B/Victoria viruses followed by A(H1N1)pdm09 virus circulation. Over 95% of circulating B/Victoria viruses were subclade V1A.3, different from the Northern Hemisphere vaccine strain. Annual estimates of influenza vaccine effectiveness (VE) are important because of frequent changes in circulating and vaccine viruses.

Methods

We assessed VE among children 6 months–17 years old with acute respiratory illness and <10 days of symptoms enrolled during the 2019–20 influenza season at 7 pediatric hospitals (ED patients < 5 years at 3 sites) in the New Vaccine Surveillance Network. Combined mid-turbinate/throat swabs were tested for influenza virus using molecular assays. We estimated age-stratified VE from a test-negative design using logistic regression to compare odds of vaccination among children testing positive versus negative for influenza, adjusting for age in years, enrollment month, and site. For these preliminary analyses, vaccination status was by parental report.

Results

Among 2022 inpatients, 324 (16%) were influenza positive: 38% with influenza B/Victoria alone and 44% with influenza A(H1N1)pdm09 alone (Table). Among 2066 ED children, 653 (32%) were influenza positive: 45% with influenza B/Victoria alone and 43% with influenza A(H1N1)pdm09 alone. VE was 62% (95% confidence interval [CI], 51%–70%) against any influenza-related hospitalizations, 68% (95% CI, 55%–78%) for A(H1N1)pdm09 and 55% (95% CI, 35%–69%) for B/Victoria. VE by age group for any influenza-related hospitalizations was 57% (95% CI, 40%–69%) among children 6 months to < 5 years and 66% (95% CI, 49%–77%) among children 5–17 years. VE was 53% (95% CI, 42%–62%) against any influenza-related ED visits, 46% (95% CI, 28%–60%) for A(H1N1)pdm09 and 54% (95% CI, 39%–66%) for B/Victoria. VE by age group was 52% (95% CI, 37%–63%) among children 6 months to < 5 years and 42% (95% CI, 16%–60%) among children 5–17 years.

Conclusion

Influenza vaccination in the 2019–20 season provided substantial protection against laboratory-confirmed influenza-associated hospitalizations and ED visits associated with the two predominantly circulating influenza viruses among children, including against the emerging B/Victoria virus V1A.3 subclade.

Disclosures

Janet A. Englund, MD, AstraZeneca (Scientific Research Study Investigator)GSK group of companies (Scientific Research Study Investigator)Meissa vaccines (Consultant)Merck (Scientific Research Study Investigator)Sanofi Pasteur (Consultant) John V. Williams, MD, GlaxoSmithKline (Advisor or Review Panel member)IDConnect (Advisor or Review Panel member)Quidel (Advisor or Review Panel member) Natasha B. Halasa, MD, MPH, Genentech (Other Financial or Material Support, I receive an honorarium for lectures - it’s a education grant, supported by genetech)Karius (Consultant)Moderna (Consultant)Quidel (Grant/Research Support, Research Grant or Support)Sanofi (Grant/Research Support, Research Grant or Support) Christopher J. Harrison, MD, GSK (Grant/Research Support, Infant menigiciccal B conjugate vaccine trial)Merck (Research Grant or Support, Infant pneumococcal conjugate vaccine trial)

1506. Burden of Respiratory Syncytial Virus (RSV) and Other Lower Respiratory Tract Viral Infections During the First Two Years of Life: a Prospective Study

Background

Lower respiratory tract infections (LRTIs) are a leading cause of pediatric morbidity and mortality worldwide, with ~650,000 deaths recorded in < 5-year-olds in 2016. Cross-sectional studies on hospitalized LRTIs are available, but longitudinal studies on the total burden of viral LRTIs are scarce. This study (NCT01995175) prospectively collected incident RSV and other viral LRTIs in a multinational cohort.

Methods

From 2013 to 2017, infants in 8 countries were enrolled at birth and followed for LRTIs up to 2 years of age. Infants with suspected LRTIs were clinically examined and swabbed. Nasal swab samples were tested using quantitative real-time PCR for RSV and multiplex PCR panel for 16 other respiratory viruses/subtypes; bacterial culture was not performed. LRTI and severe LRTI episodes were defined per 2015 WHO LRTI case definitions. Viruses detected from nasal swabs collected from participants with WHO-defined LRTI and severe LRTI episodes are reported.

Results

The 2401 infants followed experienced 1012 LRTI episodes; 259 of these were severe LRTIs. At least 1 virus was detected from 909 (90%) and 235 (91%) LRTI and severe LRTI episodes, respectively. Enteroviruses/Rhinoviruses (EV/RV, 49%) were detected most frequently in samples collected from LRTI episodes, followed by RSV (22%), parainfluenza (PIV, 14%), human metapneumovirus (hMPV, 8%) and seasonal coronavirus (CoV, 6%). RSV was detected in 39% of samples from LRTI episodes in < 3-month-olds and in 18% of 1-year-olds (Table 1). In a similar trend, RSV was detected in 47% of samples from severe LRTI episodes in < 3-month-olds and in 21% of 1-year-olds (Table 2). Co-infection with another virus was common in CoV-positive samples (67%), while most samples positive for RSV (71%), hMPV (70%), EV/RV (67%) and PIV (58%) had no other virus detected.

Table 1. Occurrence of laboratory confirmed respiratory viral infections by viral pathogens identified in nasal swab samples from WHO-defined LRTI episodes

Table 2. Occurrence of laboratory confirmed respiratory viral infections by viral pathogens identified in nasal swab samples from WHO-defined severe LRTI episodes

Conclusion

Respiratory viruses are detected in the majority of LRTIs during the first 2 years of life. RSV likely accounts for much of this overall LRTI burden. Our results suggest that RSV most strongly impacted the very young; it was the most commonly detected virus in severe LRTIs in infants aged < 3 months. RSV was also persistently detected at high levels in samples from LRTIs (22%) and severe LRTIs (28%) in children up to 2 years old.

Funding

GlaxoSmithKline Biologicals SA

Disclosures

Ana Ceballos, MD, GSK group of companies (Scientific Research Study Investigator) Jo Ann Colas, MSc, GSK group of companies (Consultant) Luis Cousin, MD, Tecnología en Investigación (Scientific Research Study Investigator) Ilse Dieussaert, IR, GSK group of companies (Employee, Shareholder) Joseph B. Domachowske, MD, Astra Zeneca (Other Financial or Material Support, Grant/Research Support paid to my Institution on my behalf for sponsored human clinical trial activities)GSK group of companies (Other Financial or Material Support, Grant/Research Support paid to my Institution on my behalf for sponsored human clinical trial activities)Merck (Other Financial or Material Support, Grant/Research Support paid to my Institution on my behalf for sponsored human clinical trial activities) Janet A. Englund, MD, AstraZeneca (Scientific Research Study Investigator)GSK group of companies (Scientific Research Study Investigator)Meissa vaccines (Consultant)Merck (Scientific Research Study Investigator)Sanofi Pasteur (Consultant) Sanjay Gandhi, MD, GSK group of companies (Employee) Mélanie Hercor, PhD, GSK group of companies (Employee) Magali de Heusch, PhD, GSK group of companies (Employee) Joanne M. Langley, MD, GSK group of companies (Research Grant or Support)Immunivaccines Inc (Scientific Research Study Investigator, Research Grant or Support)Janssen (Research Grant or Support)Pfizer (Research Grant or Support)Symvivo (Scientific Research Study Investigator, Research Grant or Support)VBI Vaccines (Research Grant or Support) Amanda Leach, MRCPCH, GSK group of companies (Employee) Timo Vesikari, MD, PhD, Denka (Consultant) Sonia K. Stoszek, PhD, GSK group of companies (Employee, Shareholder)

Prevalence of Health Care and Hospital Worker SARS-CoV-2 IgG Antibody in a Pediatric Hospital

OBJECTIVES

Asymptomatic transmission of coronavirus disease 2019 (COVID-19) in health care settings is not well understood. In this study, we aimed to determine the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G (IgG) antibodies in health care and hospital workers (HCHWs) and assess how antibody levels change over time.

METHODS

Cross-sectional study of employed HCHWs at a freestanding, urban pediatric tertiary care hospital. Employed HCHWs ≥18 years old who were asymptomatic and worked in clinical hospital locations were eligible to participate. Participants completed blood draws and surveys at baseline (between May 4, 2020, and June 2, 2020) and 2 months later (between July 6, 2020, and August 7, 2020). Surveys collected demographic information, SARS-CoV-2 exposures, and previous COVID-19 diagnosis.

RESULTS

In total, 530 participants enrolled in and completed baseline study activities. The median age was 37 years (range 19-67 years); 86% identified as female, and 80% identified as white. Two months later, 481 (91%) HCHWs completed another survey and blood draw. Four of 5 (0.9%) seropositive subjects at baseline remained seropositive at 2 months, although 3 had decreasing IgG indices. Five (1.0%) seropositive individuals, including 4 who were previously seropositive and 1 newly seropositive, were detected 2 months later. History of positive SARS-CoV-2 polymerase chain reaction testing results (P < .001) and history of COVID-19 exposure (P < .001) were associated with presence of SARS-CoV-2 antibodies.

CONCLUSIONS

SARS-CoV-2 antibodies were detected in 1% of HCHWs in an urban pediatric hospital in a city with moderate SARS-CoV-2 prevalence. Participants with a known previous COVID-19 diagnosis showed a decline or loss of IgG antibodies over 2 months. These results have implications for identifying those with previous exposure and for ongoing public health recommendations for ensuring workplace safety.

Comparable specimen collection from both ends of at-home mid-turbinate swabs

Unsupervised upper respiratory specimen collection is a key factor in the ability to massively scale SARS-CoV-2 testing. But there is concern that unsupervised specimen collection may produce inferior samples. Across two studies that included unsupervised at-home mid-turbinate specimen collection, ~1% of participants used the wrong end of the swab. We found that molecular detection of respiratory pathogens and a human biomarker were comparable between specimens collected from the handle of the swab and those collected correctly. Older participants were more likely to use the swab backwards. Our results suggest that errors made during home-collection of nasal specimens do not preclude molecular detection of pathogens and specialized swabs may be an unnecessary luxury during a pandemic.

Respiratory syncytial virus immunisation overview

Respiratory syncytial virus (RSV) continues to be a significant source of morbidity and mortality in both adults and children. Natural infection confers incomplete protection, permitting recurrent episodes. Treatment remains limited to supportive care. Initial endeavours to develop a vaccine resulted in an unexpected enhancement of RSV disease and increased recipient mortality. Current proposed strategies to prevent RSV infection rely on the principles of active and passive immunisation and utilise the highly conserved RSV F-protein. Maternal vaccines administered in pregnancy may provide protection; trials are ongoing. Palivizumab, a monoclonal antibody, has a moderate preventative efficacy. A similar newer longer lasting formulation appears promising. A number of other novel options are being developed and are undergoing assessment. Progress has been made, with more vaccine candidates under consideration. We are edging closer to an effective solution to prevent RSV infection. If successful, the impact on paediatric morbidity, mortality, workload and cost will be substantial.

Point-of-care molecular testing and antiviral treatment of influenza in residents of homeless shelters in Seattle, WA: study protocol for a stepped-wedge cluster-randomized controlled trial

Introduction

Influenza is an important public health problem, but data on the impact of influenza among homeless shelter residents are limited. The primary aim of this study is to evaluate whether on-site testing and antiviral treatment of influenza in residents of homeless shelters reduces influenza spread in these settings.

Methods and analysis

This study is a stepped-wedge cluster-randomized trial of on-site testing and antiviral treatment for influenza in nine homeless shelter sites within the Seattle metropolitan area. Participants with acute respiratory illness (ARI), defined as two or more respiratory symptoms or new or worsening cough with onset in the prior 7 days, are eligible to enroll. Approximately 3200 individuals are estimated to participate from October to May across two influenza seasons. All sites will start enrollment in the control arm at the beginning of each season, with routine surveillance for ARI. Sites will be randomized at different timepoints to enter the intervention arm, with implementation of a test-and-treat strategy for individuals with two or fewer days of symptoms. Eligible individuals will be tested on-site with a point-of-care influenza test. If the influenza test is positive and symptom onset is within 48 h, participants will be administered antiviral treatment with baloxavir or oseltamivir depending upon age and comorbidities. Participants will complete a questionnaire on demographics and symptom duration and severity. The primary endpoint is the incidence of influenza in the intervention period compared to the control period, after adjusting for time trends.

Trial registration

ClinicalTrials.gov NCT04141917. Registered 28 October 2019. Trial sponsor: University of Washington.

Supplementary information

The online version contains supplementary material available at 10.1186/s13063-020-04871-5.

Vaccine Effectiveness Against Pediatric Influenza Hospitalizations and Emergency Visits

BACKGROUND

Influenza A(H1N1)pdm09 viruses initially predominated during the US 2018-2019 season, with antigenically drifted influenza A(H3N2) viruses peaking later. We estimated vaccine effectiveness (VE) against laboratory-confirmed influenza-associated hospitalizations and emergency department (ED) visits among children in the New Vaccine Surveillance Network.

METHODS

We tested children 6 months to 17 years with acute respiratory illness for influenza using molecular assays at 7 pediatric hospitals (ED patients <5 years at 3 sites). Vaccination status sources were parental report, state immunization information systems and/or provider records for inpatients, and parental report alone for ED patients. We estimated VE using a test-negative design, comparing odds of vaccination among children testing positive versus negative for influenza using multivariable logistic regression.

RESULTS

Of 1792 inpatients, 226 (13%) were influenza-positive: 47% for influenza A(H3N2), 36% for A(H1N1)pdm09, 9% for A (not subtyped), and 7% for B viruses. Among 1944 ED children, 420 (22%) were influenza-positive: 48% for A(H3N2), 35% for A(H1N1)pdm09, 11% for A (not subtyped), and 5% for B viruses. VE was 41% (95% confidence interval [CI], 20% to 56%) against any influenza-related hospitalizations, 41% (95% CI, 11% to 61%) for A(H3N2), and 47% (95% CI, 16% to 67%) for A(H1N1)pdm09. VE was 51% (95% CI, 38% to 62%) against any influenza-related ED visits, 39% (95% CI, 15% to 56%) against A(H3N2), and 61% (95% CI, 44% to 73%) against A(H1N1)pdm09.

CONCLUSIONS

The 2018-2019 influenza vaccine reduced pediatric influenza A-associated hospitalizations and ED visits by 40% to 60%, despite circulation of a drifted A(H3N2) clade.

Respiratory viral coinfection in a birth cohort of infants in rural Nepal

BACKGROUND

Acute respiratory illnesses are a leading cause of global morbidity and mortality in children. Coinfection with multiple respiratory viruses is common. Although the effects of each virus have been studied individually, the impacts of coinfection on disease severity are less understood.

METHODS

A secondary analysis was performed of a maternal influenza vaccine trial conducted between 2011 and 2014 in Nepal. Prospective weekly household-based active surveillance of infants was conducted from birth to 180 days of age. Mid-nasal swabs were collected and tested for respiratory syncytial virus (RSV), rhinovirus, influenza, human metapneumovirus (HMPV), coronavirus, parainfluenza (HPIV), and bocavirus by RT-PCR. Coinfection was defined as the presence of two or more respiratory viruses detected as part of the same illness episode.

RESULTS

Of 1730 infants with a respiratory illness, 327 (19%) had at least two respiratory viruses detected in their primary illness episode. Of 113 infants with influenza, 23 (20%) had coinfection. Of 214 infants with RSV, 87 (41%) had coinfection. The cohort of infants with coinfection had increased occurrence of fever lasting ≥ 4 days (OR 1.4, 95% CI: 1.1, 2.0), and so did the subset of coinfected infants with influenza (OR 5.8, 95% CI: 1.8, 18.7). Coinfection was not associated with seeking further care (OR 1.1, 95% CI: 0.8, 1.5) or pneumonia (OR 1.2, 95% CI: 0.96, 1.6).

CONCLUSION

A high proportion of infants had multiple viruses detected. Coinfection was associated with greater odds of fever lasting for four or more days, but not with increased illness severity by other measures.

Cryptic transmission of SARS-CoV-2 in Washington state

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.

The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology

INTRODUCTION

Influenza epidemics and pandemics cause significant morbidity and mortality. An effective response to a potential pandemic requires the infrastructure to rapidly detect, characterise, and potentially contain new and emerging influenza strains at both an individual and population level. The objective of this study is to use data gathered simultaneously from community and hospital sites to develop a model of how influenza enters and spreads in a population.

METHODS AND ANALYSIS

Starting in the 2018-2019 season, we have been enrolling individuals with acute respiratory illness from community sites throughout the Seattle metropolitan area, including clinics, childcare facilities, Seattle-Tacoma International Airport, workplaces, college campuses and homeless shelters. At these sites, we collect clinical data and mid-nasal swabs from individuals with at least two acute respiratory symptoms. Additionally, we collect residual nasal swabs and data from individuals who seek care for respiratory symptoms at four regional hospitals. Samples are tested using a multiplex molecular assay, and influenza whole genome sequencing is performed for samples with influenza detected. Geospatial mapping and computational modelling platforms are in development to characterise the regional spread of influenza and other respiratory pathogens.

ETHICS AND DISSEMINATION

The study was approved by the University of Washington's Institutional Review Board (STUDY00006181). Results will be disseminated through talks at conferences, peer-reviewed publications and on the study website (www.seattleflu.org).

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.