Viral Shedding and Transmission Potential of Asymptomatic and Paucisymptomatic Influenza Virus Infections in the Community

Reduction of acute respiratory infections in day-care by non-pharmaceutical interventions: a narrative review

Objective

Children who start in day-care have 2-4 times as many respiratory infections compared to children who are cared for at home, and day-care staff are among the employees with the highest absenteeism. The extensive new knowledge that has been generated in the COVID-19 era should be used in the prevention measures we prioritize. The purpose of this narrative review is to answer the questions: Which respiratory viruses are the most significant in day-care centers and similar indoor environments? What do we know about the transmission route of these viruses? What evidence is there for the effectiveness of different non-pharmaceutical prevention measures?

Design

Literature searches with different terms related to respiratory infections in humans, mitigation strategies, viral transmission mechanisms, and with special focus on day-care, kindergarten or child nurseries, were conducted in PubMed database and Web of Science. Searches with each of the main viruses in combination with transmission, infectivity, and infectious spread were conducted separately supplemented through the references of articles that were retrieved.

Results

Five viruses were found to be responsible for ≈95% of respiratory infections: rhinovirus, (RV), influenza virus (IV), respiratory syncytial virus (RSV), coronavirus (CoV), and adenovirus (AdV). Novel research, emerged during the COVID-19 pandemic, suggests that most respiratory viruses are primarily transmitted in an airborne manner carried by aerosols (microdroplets).

Conclusion

Since airborne transmission is dominant for the most common respiratory viruses, the most important preventive measures consist of better indoor air quality that reduces viral concentrations and viability by appropriate ventilation strategies. Furthermore, control of the relative humidity and temperature, which ensures optimal respiratory functionality and, together with low resident density (or mask use) and increased time outdoors, can reduce the occurrence of respiratory infections.

Treatment of COVID-19 symptoms with over the counter (OTC) medicines used for treatment of common cold and flu

Persons suffering from acute upper respiratory tract viral infections (URTI) commonly use over the counter (OTC) medicines to relieve symptoms such as fever, muscle aches, cough, runny nose, sore throat and nasal congestion. At present OTC medicines are only licensed for treatment of common cold and flu symptoms and not for treatment of the same symptoms associated with COVID-19. The innate immune response responsible for the mechanisms of the symptoms of URTI is the same for all respiratory viruses including SARS-CoV-2 and these symptoms can be relieved by treatment with the same OTC medicines as available for treatment of colds and flu. This review provides scientific information that OTC treatments for common cold and flu-like illness caused by respiratory viruses are safe and effective treatments for the same symptoms associated with COVID-19.

Influenza transmissibility among patients and health-care professionals in a geriatric short-stay unit using individual contact data

Detailed information are lacking on influenza transmissibility in hospital although clusters are regularly reported. In this pilot study, our goal was to estimate the transmission rate of H3N2 2012-influenza, among patients and health care professionals in a short-term Acute Care for the Elderly Unit by using a stochastic approach and a simple susceptible-exposed-infectious-removed model. Transmission parameters were derived from documented individual contact data collected by Radio Frequency IDentification technology at the epidemic peak. From our model, nurses appeared to transmit infection to a patient more frequently with a transmission rate of 1.04 per day on average compared to 0.38 from medical doctors. This transmission rate was 0.34 between nurses. These results, even obtained in this specific context, might give a relevant insight of the influenza dynamics in hospitals and will help to improve and to target control measures for preventing nosocomial transmission of influenza. The investigation of nosocomial transmission of SARS-COV-2 might gain from similar approaches.

Aerosolized nicotine from e-cigarettes alters gene expression, increases lung protein permeability, and impairs viral clearance in murine influenza infection

E-cigarette use has rapidly increased as an alternative means of nicotine delivery by heated aerosolization. Recent studies demonstrate nicotine-containing e-cigarette aerosols can have immunosuppressive and pro-inflammatory effects, but it remains unclear how e-cigarettes and the constituents of e-liquids may impact acute lung injury and the development of acute respiratory distress syndrome caused by viral pneumonia. Therefore, in these studies, mice were exposed one hour per day over nine consecutive days to aerosol generated by the clinically-relevant tank-style Aspire Nautilus aerosolizing e-liquid containing a mixture of vegetable glycerin and propylene glycol (VG/PG) with or without nicotine. Exposure to the nicotine-containing aerosol resulted in clinically-relevant levels of plasma cotinine, a nicotine-derived metabolite, and an increase in the pro-inflammatory cytokines IL-17A, CXCL1, and MCP-1 in the distal airspaces. Following the e-cigarette exposure, mice were intranasally inoculated with influenza A virus (H1N1 PR8 strain). Exposure to aerosols generated from VG/PG with and without nicotine caused greater influenza-induced production in the distal airspaces of the pro-inflammatory cytokines IFN-γ, TNFα, IL-1β, IL-6, IL-17A, and MCP-1 at 7 days post inoculation (dpi). Compared to the aerosolized carrier VG/PG, in mice exposed to aerosolized nicotine there was a significantly lower amount of Mucin 5 subtype AC (MUC5AC) in the distal airspaces and significantly higher lung permeability to protein and viral load in lungs at 7 dpi with influenza. Additionally, nicotine caused relative downregulation of genes associated with ciliary function and fluid clearance and an increased expression of pro-inflammatory pathways at 7 dpi. These results show that (1) the e-liquid carrier VG/PG increases the pro-inflammatory immune responses to viral pneumonia and that (2) nicotine in an e-cigarette aerosol alters the transcriptomic response to pathogens, blunts host defense mechanisms, increases lung barrier permeability, and reduces viral clearance during influenza infection. In conclusion, acute exposure to aerosolized nicotine can impair clearance of viral infection and exacerbate lung injury, findings that have implications for the regulation of e-cigarette products.

SARS-CoV-2 viral load and shedding kinetics

SARS-CoV-2 viral load and detection of infectious virus in the respiratory tract are the two key parameters for estimating infectiousness. As shedding of infectious virus is required for onward transmission, understanding shedding characteristics is relevant for public health interventions. Viral shedding is influenced by biological characteristics of the virus, host factors and pre-existing immunity (previous infection or vaccination) of the infected individual. Although the process of human-to-human transmission is multifactorial, viral load substantially contributed to human-to-human transmission, with higher viral load posing a greater risk for onward transmission. Emerging SARS-CoV-2 variants of concern have further complicated the picture of virus shedding. As underlying immunity in the population through previous infection, vaccination or a combination of both has rapidly increased on a global scale after almost 3 years of the pandemic, viral shedding patterns have become more distinct from those of ancestral SARS-CoV-2. Understanding the factors and mechanisms that influence infectious virus shedding and the period during which individuals infected with SARS-CoV-2 are contagious is crucial to guide public health measures and limit transmission. Furthermore, diagnostic tools to demonstrate the presence of infectious virus from routine diagnostic specimens are needed.

Viral dynamics of the SARS-CoV-2 Omicron Variant among household contacts with 2 or 3 COVID-19 vaccine doses

OBJECTIVES

SARS-CoV-2 shedding has changed as new variants have emerged. It is important to understand the trajectory of PCR positivity due to Omicron in vaccinated populations.

METHODS

Double- or triple-vaccinated adult household contacts of individuals with COVID-19 self-collected oral-nasal swabs for 14 days. A hierarchical linear model estimated viral load trajectories and an exploratory logistic regression model assessed for factors associated with viral detection before symptom onset.

RESULTS

Forty-one participants developed COVID-19 with 37 (90%) symptomatic. Viral load peaked 3 days after symptom onset at a median concentration of 8.83 log₁₀ copies/milliliter (range 5.95-10.32) and the mean difference between participants with two or three COVID-19 vaccine doses was 0.02 log₁₀ copies/milliliter (95% CI -0.13 to 0.16). PCR positivity began with a range of 4 days prior to 3 days after symptom onset and was positive on the day of symptom onset in 76% (28/37). SARS-CoV-2 detection on the day of symptom onset was less likely among those with 2 vaccine doses (OR 0.13, 95%CI 0.02-0.79). 68% (25/37) of infected participants had detectable SARS-CoV-2 with Ct<30 at 7 days after symptom onset.

CONCLUSIONS

Peak viral load and duration of PCR positivity were similar in participants with COVID-19 after two versus three COVID-19 vaccine doses. Onset of viral detection relative to symptom onset was variable.

Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.

Influenza A Virus Exacerbates Group A Streptococcus Infection and Thwarts Anti-Bacterial Inflammatory Responses in Murine Macrophages

Seasonal influenza epidemics pose a considerable hazard for global health. In the past decades, accumulating evidence revealed that influenza A virus (IAV) renders the host vulnerable to bacterial superinfections which in turn are a major cause for morbidity and mortality. However, whether the impact of influenza on anti-bacterial innate immunity is restricted to the vicinity of the lung or systemically extends to remote sites is underexplored. We therefore sought to investigate intranasal infection of adult C57BL/6J mice with IAV H1N1 in combination with bacteremia elicited by intravenous application of Group A Streptococcus (GAS). Co-infection in vivo was supplemented in vitro by challenging murine bone marrow derived macrophages and exploring gene expression and cytokine secretion. Our results show that viral infection of mice caused mild disease and induced the depletion of CCL2 in the periphery. Influenza preceding GAS infection promoted the occurrence of paw edemas and was accompanied by exacerbated disease scores. In vitro co-infection of macrophages led to significantly elevated expression of TLR2 and CD80 compared to bacterial mono-infection, whereas CD163 and CD206 were downregulated. The GAS-inducible upregulation of inflammatory genes, such as Nos2, as well as the secretion of TNFα and IL-1β were notably reduced or even abrogated following co-infection. Our results indicate that IAV primes an innate immune layout that is inadequately equipped for bacterial clearance.

Antigenic characterization of influenza and SARS-CoV-2 viruses

Antigenic characterization of emerging and re-emerging viruses is necessary for the prevention of and response to outbreaks, evaluation of infection mechanisms, understanding of virus evolution, and selection of strains for vaccine development. Primary analytic methods, including enzyme-linked immunosorbent/lectin assays, hemagglutination inhibition, neuraminidase inhibition, micro-neutralization assays, and antigenic cartography, have been widely used in the field of influenza research. These techniques have been improved upon over time for increased analytical capacity, and some have been mobilized for the rapid characterization of the SARS-CoV-2 virus as well as its variants, facilitating the development of highly effective vaccines within 1 year of the initially reported outbreak. While great strides have been made for evaluating the antigenic properties of these viruses, multiple challenges prevent efficient vaccine strain selection and accurate assessment. For influenza, these barriers include the requirement for a large virus quantity to perform the assays, more than what can typically be provided by the clinical samples alone, cell- or egg-adapted mutations that can cause antigenic mismatch between the vaccine strain and circulating viruses, and up to a 6-month duration of vaccine development after vaccine strain selection, which allows viruses to continue evolving with potential for antigenic drift and, thus, antigenic mismatch between the vaccine strain and the emerging epidemic strain. SARS-CoV-2 characterization has faced similar challenges with the additional barrier of the need for facilities with high biosafety levels due to its infectious nature. In this study, we review the primary analytic methods used for antigenic characterization of influenza and SARS-CoV-2 and discuss the barriers of these methods and current developments for addressing these challenges.

Incidence of Influenza Virus Infection among Wroclaw's Healthcare Workers in Pre-COVID-19 2019-2020 Influenza Season Using Novel Flu SensDx Device

Background: Healthcare workers (HCWs) are more exposed to influenza infection, and the influenza vaccination is recommended each year, to reduce the risk of influenza infection and prevent influenza transmission. This study is a cross-sectional study and the objectives were to determine the rate of influenza virus infection among HCWs in the 2019−2020 influenza season. Methods: Between January and March 2020, a survey was carried out in 2 hospitals and 15 primary health-care settings (PHCS) in Wroclaw (Poland). The novel point-of-care testing Flu SensDx device was used, which detects the M1 protein of the influenza virus using electrochemical impedance spectroscopy from biological material (throat/nasal swabs). Results: A total of 150 samples were collected. The majority of participating HCWs by profession were 83 physicians (55.3%) and half (51.3%) of the participating HCWs worked in PHCS. Influenza vaccination coverage was 61.3% in 2019−2020 and 46.0% in the 2018−2019 season for all participants. Of the participating HCWs, 44.0% were positive tested by the Flu SensDx device. There were no statistically significant differences among the positive tested HCWs, their influenza immunization history, and the presence of symptoms of influenza-like illness (p > 0.05). Conclusion: Although the results of the present study suggest that influenza vaccination does not reduce the frequency of influenza virus detection by Flu SensDx testing in the HCWs participants, larger studies are needed to estimate the incidence of influenza virus infection among HCWs to understand the underlying mechanism and fine-tune policies aimed at reducing nosocomial infections.

Using contact tracing from interlocking diaries to map mood contagion along network chains

Both viruses and moods are transmitted through interpersonal contacts, but it has been extremely difficult to track each unique chain of contacts through which particular moods diffuse. By analyzing 56,060 contact records from 113 interlocking, yearlong diaries collected through a web-based platform in Taiwan, we traced mood states before and after each specific contact along a triplet of persons where B contacts C and subsequently contacts A. Multilevel analyses show that both positive and negative emotions are contagious, but the two paths diverge markedly in how the diffusion stops. Positive contact between C and B (which leads to improved mood for B) spreads to A through B’s contact with A, making A feel better afterward, regardless of whether B’s mood deteriorated between the two interactions. Negative contact between C and B (which leads to worsened mood for B) also spreads to A, making A feel worse after the contact with B. However, the spread of a negative mood discontinues if B’s mood improved between the two contacts. The different patterns of diffusion suggest that a negative mood is harder to disperse, probably because people generally make efforts to keep their negative emotions from spreading to others.

Inferring the reproduction number using the renewal equation in heterogeneous epidemics

Real-time estimation of the reproduction number has become the focus of modelling groups around the world as the SARS-CoV-2 pandemic unfolds. One of the most widely adopted means of inference of the reproduction number is via the renewal equation, which uses the incidence of infection and the generation time distribution. In this paper, we derive a multi-type equivalent to the renewal equation to estimate a reproduction number which accounts for heterogeneity in transmissibility including through asymptomatic transmission, symptomatic isolation and vaccination. We demonstrate how use of the renewal equation that misses these heterogeneities can result in biased estimates of the reproduction number. While the bias is small with symptomatic isolation, it can be much larger with asymptomatic transmission or transmission from vaccinated individuals if these groups exhibit substantially different generation time distributions to unvaccinated symptomatic transmitters, whose generation time distribution is often well defined. The bias in estimate becomes larger with greater population size or transmissibility of the poorly characterized group. We apply our methodology to Ebola in West Africa in 2014 and the SARS-CoV-2 in the UK in 2020-2021.

Clinical impact of nosocomial infection with pandemic influenza A (H1N1) 2009 in a respiratory ward in Guangzhou

Background

Nosocomial outbreaks of pandemic influenza A (H1N1) 2009 virus [A(H1N1)pdm09] easily develop due to its high transmissibility. This study aimed to investigate the clinical impacts of a nosocomial outbreak of A(H1N1)pdm09 between 21 January and 17 February 2016.

Methods

Patients who developed influenza-like illness (ILI) more than 48 hours after hospitalization in the index ward were enrolled as suspected patients, defined as group A and quarantined. Patients in other wards were defined as group B. A phylogenetic tree was constructed to determine the origins of the hemagglutinin and neuraminidase genes.

Results

After the implementation of an infection control measure bundle, the outbreak was limited to eight patients with ILIs in group A. Nasal swabs from seven patients were positive for A(H1N1)pdm09. All the patients recovered after treatment. Prolonged viral shedding was observed in a patient with bronchiectasis and Penicillium marneffei infection. Compared to the expected duration of hospitalization in patients without fever, those with fever had a median 7-day delay in discharge and a mean excess cost of 3,358 RMB. The four influenza strains identified were genetically identical to the A/California/115/2015 strain. Six of the 54 patients in group B who underwent bronchoscopy developed transient fever. These patients were hospitalized in various wards of the hospital and recovered after a short-term course of empirical antibiotics.

Conclusions

After the implementation of infection control measures, the nosocomial A(H1N1)pdm09 outbreak was rapidly contained; infected patients had a delay in discharge and excess costs, but no deaths occurred.

Awareness, Attitude, and Current Practices Toward Influenza Vaccination Among Physicians in India: A Multicenter, Cross-Sectional Study

Background: Although annual influenza vaccination is recommended for healthcare providers (HCPs), vaccination rate among HCPs in India is generally low. This cross-sectional survey was conducted to evaluate physicians' awareness, attitude, and current practices toward influenza vaccination in high-risk groups in India.

Methods: The survey was performed in June–July 2020, wherein consulting physicians, pulmonologists, diabetologists, obstetricians/gynecologists, or cardiologists across 14 cities completed a 39-item questionnaire consisting of 3 sections, one each on awareness, attitude, and practice patterns. Descriptive statistics were used to summarize the study results. Statistical analysis was performed for comparison of subgroups by physician specialty, city of practice (metro/non-metro), and zone of practice (north/south/east/west). Level of statistical significance was set at p < 0.05.

Results: In all, 780 physicians completed the survey. Of these, 3.97, 53.08, and 42.95% had high, medium, and low level of awareness about influenza/influenza vaccination, respectively. Statistically significant (p < 0.05) between-group differences were found by physician specialty and zone of practice. In terms of attitude toward vaccination of high-risk group subjects, only 0.9% physicians were “extremely concerned,” while the majority (92.56%) were “quite concerned” and 6.54% were a “little concerned,” with no reported significant differences between different subgroups. With regard to practice patterns, 82.82% of physicians offered influenza vaccines to their patients, 32.69% vaccinated 10–25% of patients per month, and 38.85% required and offered the vaccine to their office staff. Physicians' reasons for not prescribing influenza vaccines to patients included fear of side effects (16.54%), cost (15.64%), lack of awareness about availability (15.38%), absence of belief that it is beneficial (14.36%), history of side effects (13.46%), and patients' fear of needles (11.28%).

Conclusion: These findings suggest the need to implement educational strategies among physicians to enhance their awareness about influenza vaccination and improve their attitudes and current practices toward influenza vaccination especially in high-risk groups in India.

Rationale for Mass Masking in Controlling the COVID-19 Pandemic

The rapid spread of the coronavirus disease 2019 (COVID-19) into a global pandemic caught the world unprepared. Previously effective measures for containing disease outbreaks were overwhelmed, necessitating strict controls such as lockdowns or curfews. Among the disease control interventions, community mass masking was one of the highly controversial issues with differing opinions on its indications or effectiveness from different health authorities around the world. Regions where community mass masking was timely introduced were associated with lower transmission rates, and more effective disease control. In this article, we discuss the evidence on the effectiveness, and rationale for community mass masking to prevent the COVID-19 transmission. Areas for further research to define the role of mass masking in light of the COVID-19 pandemic will be suggested. This would help policy makers in formulating mass masking policies.

Hyperspectral Mapping for the Detection of SARS-CoV-2 Using Nanomolecular Probes with Yoctomole Sensitivity

Efficient monitoring of SARS-CoV-2 outbreak requires the use of a sensitive and rapid diagnostic test. Although SARS-CoV-2 RNA can be detected by RT-qPCR, the molecular-level quantification of the viral load is still challenging, time-consuming, and labor-intensive. Here, we report an ultrasensitive hyperspectral sensor (HyperSENSE) based on hafnium nanoparticles (HfNPs) for specific detection of COVID-19 causative virus, SARS-CoV-2. Density functional theoretical calculations reveal that HfNPs exhibit higher changes in their absorption wavelength and light scattering when bound to their target SARS-CoV-2 RNA sequence relative to the gold nanoparticles. The assay has a turnaround time of a few seconds and has a limit of detection in the yoctomolar range, which is 1 000 000-fold times higher than the currently available COVID-19 tests. We demonstrated in ∼100 COVID-19 clinical samples that the assay is highly sensitive and has a specificity of 100%. We also show that HyperSENSE can rapidly detect other viruses such as influenza A H1N1. The outstanding sensitivity indicates the potential of the current biosensor in detecting the prevailing presymptomatic and asymptomatic COVID-19 cases. Thus, integrating hyperspectral imaging with nanomaterials establishes a diagnostic platform for ultrasensitive detection of COVID-19 that can potentially be applied to any emerging infectious pathogen.

Does vitamin D supplementation prevent SARS-CoV-2 infection in military personnel? Review of the evidence

For most individuals residing in Northwestern Europe, maintaining replete vitamin D status throughout the year is unlikely without vitamin D supplementation and deficiency remains common. Military studies have investigated the association with vitamin D status, and subsequent supplementation, with the risk of stress fractures particularly during recruit training. The expression of nuclear vitamin D receptors and vitamin D metabolic enzymes in immune cells additionally provides a rationale for the potential role of vitamin D in maintaining immune homeostasis. One particular area of interest has been in the prevention of acute respiratory tract infections (ARTIs). The aims of this review were to consider the evidence of vitamin D supplementation in military populations in the prevention of ARTIs, including SARS-CoV-2 infection and consequent COVID-19 illness. The occupational/organisational importance of reducing transmission of SARS-CoV-2, especially where infected young adults may be asymptomatic, presymptomatic or paucisymptomatic, is also discussed.

Multi-agent system collision model to predict the transmission of seasonal influenza in Tokyo from 2014-2015 to 2018-2019 seasons

The objective of this study was to apply the multi-agent system (MAS) collision model to predict seasonal influenza epidemic in Tokyo for 5 seasons (2014-2015 to 2018-2019 seasons). The MAS collision model assumes each individual as a particle inside a square domain. The particles move within the domain and disease transmission occurs in a certain probability when an infected particle collides a susceptible particle. The probability was determined based on the basic reproduction number calculated using the actual data. The simulation started with 1 infected particle and 999 susceptible particles to correspond to the onset of an influenza epidemic. We performed the simulation for 150 days and the calculation was repeated 500 times for each season. To improve the accuracy of the prediction, we selected simulations which have similar incidence number to the actual data in specific weeks. Analysis including all simulations corresponded good to the actual data in 2014-2015 and 2015-2016 seasons. However, the model failed to predict the sharp peak incidence after the New Year Holidays in 2016-2017, 2017-2018, and 2018-2019 seasons. A model which included simulations selected by the week of peak incidence predicted the week and number of peak incidence better than a model including all simulations in all seasons. The reproduction number was also similar to the actual data in this model. In conclusion, the MAS collision model predicted the epidemic curve with good accuracy by selecting the simulations using the actual data without changing the initial parameters such as the basic reproduction number and infection time.

Asymptomatic transmission and high community burden of seasonal influenza in an urban and a rural community in South Africa, 2017-18 (PHIRST): a population cohort study

Background

Data on influenza community burden and transmission are important to plan interventions especially in resource-limited settings. However, data are limited, particularly from low-income and middle-income countries. We aimed to evaluate the community burden and transmission of influenza in a rural and an urban setting in South Africa.

Methods

In this prospective cohort study approximately 50 households were selected sequentially from both a rural setting (Agincourt, Mpumalanga Province, South Africa; with a health and sociodemographic surveillance system) and an urban setting (Klerksdorp, Northwest Province, South Africa; using global positioning system data), enrolled, and followed up for 10 months in 2017 and 2018. Different households were enrolled in each year. Households of more than two individuals in which 80% or more of the occupants agreed to participate were included in the study. Nasopharyngeal swabs were collected twice per week from participating household members irrespective of symptoms and tested for influenza using real-time RT-PCR. The primary outcome was the incidence of influenza infection, defined as the number of real-time RT-PCR-positive episodes divided by the person-time under observation. Household cumulative infection risk (HCIR) was defined as the number of subsequent infections within a household following influenza introduction.

Findings

81 430 nasopharyngeal samples were collected from 1116 participants in 225 households (follow-up rate 88%). 917 (1%) tested positive for influenza; 178 (79%) of 225 households had one or more influenza-positive individual. The incidence of influenza infection was 43·6 (95% CI 39·8–47·7) per 100 person-seasons. 69 (17%) of 408 individuals who had one influenza infection had a repeat influenza infection during the same season. The incidence (67·4 per 100 person-seasons) and proportion with repeat infections (22 [23%] of 97 children) were highest in children younger than 5 years and decreased with increasing age (p<0·0001). Overall, 268 (56%) of 478 infections were symptomatic and 66 (14%) of 478 infections were medically attended. The overall HCIR was 10% (109 of 1088 exposed household members infected [95% CI 9–13%). Transmission (HCIR) from index cases was highest in participants aged 1–4 years (16%; 40 of 252 exposed household members) and individuals with two or more symptoms (17%; 68 of 396 exposed household members). Individuals with asymptomatic influenza transmitted infection to 29 (6%) of 509 household contacts. HIV infection, affecting 167 (16%) of 1075 individuals, was not associated with increased incidence or HCIR.

Interpretation

Approximately half of influenza infections were symptomatic, with asymptomatic individuals transmitting influenza to 6% of household contacts. This suggests that strategies, such as quarantine and isolation, might be ineffective to control influenza. Vaccination of children, with the aim of reducing influenza transmission might be effective in African settings given the young population and high influenza burden.

Droplets and aerosols: An artificial dichotomy in respiratory virus transmission

In the medical literature, three mutually non-exclusive modes of pathogen transmission associated with respiratory droplets are usually identified: contact, droplet, and airborne (or aerosol) transmission. The demarcation between droplet and airborne transmission is often based on a cut-off droplet diameter, most commonly 5 μm. We argue here that the infectivity of a droplet, and consequently the transmissivity of the virus, as a function of droplet size is a continuum, depending on numerous factors (gravitational settling rate, transport, and dispersion in a turbulent air jet, viral load and viral shedding, virus inactivation) that cannot be adequately characterized by a single droplet diameter. We propose instead that droplet and aerosol transmission should be replaced by a unique airborne transmission mode, to be distinguished from contact transmission.

Estimating infectiousness throughout SARS-CoV-2 infection course

The role that individuals with asymptomatic or mildly symptomatic severe acute respiratory syndrome coronavirus 2 have in transmission of the virus is not well understood. Jones et al. investigated viral load in patients, comparing those showing few, if any, symptoms with hospitalized cases. Approximately 400,000 individuals, mostly from Berlin, were tested from February 2020 to March 2021 and about 6% tested positive. Of the 25,381 positive subjects, about 8% showed very high viral loads. People became infectious within 2 days of infection, and in hospitalized individuals, about 4 days elapsed from the start of virus shedding to the time of peak viral load, which occurred 1 to 3 days before the onset of symptoms. Overall, viral load was highly variable, but was about 10-fold higher in persons infected with the B.1.1.7 variant. Children had slightly lower viral loads than adults, although this difference may not be clinically significant.

Science, abi5273, this issue p. eabi5273

INTRODUCTION

Although post facto studies have revealed the importance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission from presymptomatic, asymptomatic, and mildly symptomatic (PAMS) cases, the virological basis of their infectiousness remains largely unquantified. The reasons for the rapid spread of variant lineages of concern, such as B.1.1.7, have yet to be fully determined.

RATIONALE

Viral load (viral RNA concentration) in patient samples and the rate of isolation success of virus from clinical specimens in cell culture are the clinical parameters most directly relevant to infectiousness and hence to transmission. To increase our understanding of the infectiousness of SARS-CoV-2, especially in PAMS cases and those infected with the B.1.1.7 variant, we analyzed viral load data from 25,381 German cases, including 9519 hospitalized patients, 6110 PAMS cases from walk-in test centers, 1533 B.1.1.7 variant infections, and the viral load time series of 4434 (mainly hospitalized) patients. Viral load results were then combined with estimated cell culture isolation probabilities, producing a clinical proxy estimate of infectiousness.

RESULTS

PAMS subjects had, at the first positive test, viral loads and estimated infectiousness only slightly less than hospitalized patients. Similarly, children were found to have mean viral loads only slightly lower (0.5 log₁₀ units or less) than those of adults and ~78% of the adult peak cell culture isolation probability. Eight percent of first-positive viral loads were 10⁹ copies per swab or higher, across a wide age range (mean 37.6 years, standard deviation 13.4 years), representing a likely highly infectious minority, one-third of whom were PAMS. Relative to non-B.1.1.7 cases, patients with the B.1.1.7 variant had viral loads that were higher by a factor of 10 and estimated cell culture infectivity that was higher by a factor of 2.6. Similar ranges of viral loads from B.1.1.7 and B.1.177 samples were shown to be capable of causing infection in Caco-2 cell culture. A time-course analysis estimates that a peak viral load of 10^8.1 copies per swab is reached 4.3 days after onset of shedding and shows that, across the course of infection, hospitalized patients have slightly higher viral loads than nonhospitalized cases, who in turn have viral loads slightly higher than PAMS cases. Higher viral loads are observed in first-positive tests of PAMS subjects, likely as a result of systematic earlier testing. Mean culture isolation probability declines to 0.5 at 5 days after peak viral load and to 0.3 at 10 days after peak viral load. We estimate a rate of viral load decline of 0.17 log₁₀ units per day, which, combined with reported estimates of incubation time and time to loss of successful cell culture isolation, suggests that viral load peaks 1 to 3 days before onset of symptoms (in symptomatic cases).

CONCLUSION

PAMS subjects who test positive at walk-in test centers can be expected to be approximately as infectious as hospitalized patients. The level of expected infectious viral shedding of PAMS people is of high importance because they are circulating in the community at the time of detection of infection. Although viral load and cell culture infectivity cannot be translated directly to transmission probability, it is likely that the rapid spread of the B.1.1.7 variant is partly attributable to higher viral load in these cases. Easily measured virological parameters can be used, for example, to estimate transmission risk from different groups (by age, gender, clinical status, etc.), to quantify variance, to show differences in virus variants, to highlight and quantify overdispersion, and to inform quarantine, containment, and elimination strategies.

Two elementary parameters for quantifying viral infection and shedding are viral load and whether samples yield a replicating virus isolate in cell culture. We examined 25,381 cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Germany, including 6110 from test centers attended by presymptomatic, asymptomatic, and mildly symptomatic (PAMS) subjects, 9519 who were hospitalized, and 1533 B.1.1.7 lineage infections. The viral load of the youngest subjects was lower than that of the older subjects by 0.5 (or fewer) log₁₀ units, and they displayed an estimated ~78% of the peak cell culture replication probability; in part this was due to smaller swab sizes and unlikely to be clinically relevant. Viral loads above 10⁹ copies per swab were found in 8% of subjects, one-third of whom were PAMS, with a mean age of 37.6 years. We estimate 4.3 days from onset of shedding to peak viral load (10^8.1 RNA copies per swab) and peak cell culture isolation probability (0.75). B.1.1.7 subjects had mean log₁₀ viral load 1.05 higher than that of non-B.1.1.7 subjects, and the estimated cell culture replication probability of B.1.1.7 subjects was higher by a factor of 2.6.

Contrasting SARS-CoV-2 RNA copies and clinical symptoms in a large cohort of Colombian patients during the first wave of the COVID-19 pandemic

BACKGROUND

There is limited and controverting evidence looking at possible associations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA copies and patient variables in large cohorts of symptomatic and asymptomatic patients.

METHODS

We studied 2275 symptomatic and asymptomatic patients from Colombia with coronavirus disease 2019 (COVID-19) and analyzed the associations between RT-PCR cycle threshold (Ct) value with gender, age, comorbidities, symptomatology, and disease severity.

RESULTS

15.4 % of the samples (n = 428) reported at least one comorbidity. There were 2011 symptomatic cases (72.4 %), being the most common reported symptom cough (57.2 %, n = 1586). Respiratory distress was present in 21.4 % of patients (n = 595), and 435 patients (15.6 %) required hospital admission. We observed that patients with no prior medical history harbored higher RNA copies than patients with comorbidities (p = 0.02). No significant differences in RNA copies were observed between symptomatic and asymptomatic patients (p = 0.82). Strong correlations were detected between Ct values and the presence of odynophagia (p = 0.03), diarrhea (p = 0.04), and headache (p = 0.0008). An inverse association was found between RNA copy number and markers of disease severity, namely, respiratory distress (P < 0.0001) and hospitalization requirement (P < 0.0001).

CONCLUSIONS

SARS-CoV-2 RT-PCR cycle thresholds reveal strong associations with a prior medical history, specific symptomatology, and disease severity markers. Further research controlling potential confounding variables needs to be conducted to evaluate the nature and usefulness of these associations in managing COVID-19 patients.

Increased risk of respiratory viral infections in elite athletes: A controlled study

BACKGROUND

Respiratory symptoms are commonly recognised in elite athletes. The occurrence, etiology and clinical presentation of the illnesses in athletes is unclear.

METHODS

We performed a prospective controlled study of respiratory viral infections in Team Finland during Nordic World Ski Championships 2019. There were 26 athletes and 36 staff members. Nasal swabs were taken at the onset of a symptom and on days 1, 7, and 13 during the follow-up of 14 days. Respiratory viruses were searched for by 3 different molecular multiplex tests. Fifty-two matched control subjects were studied in Finland during the same period.

RESULTS

Ten out of 26 (38%) athletes, 6 out of 36 (17%) staff, and 3 out of 52 (6%) control subjects experienced symptoms of respiratory infection (p = 0.0013). The relative risks for acquiring symptomatic infection were 6.7 (95% confidence interval [CI], 2.1-21.0) of athletes and 2.9 (95% CI, 0.84-10.0) of the staff as compared to the controls. Asymptomatic infections were identified in 8%, 22%, and 19%, respectively (p = 0.30). The etiology of respiratory infections was detected in 84% of the cases.

CONCLUSION

The athletes had a 7-fold increase in the risk of illness compared to normally exercising control subjects.

Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study

During infectious disease epidemics, an important question is whether cases travelling to new locations will trigger local outbreaks. The risk of this occurring depends on the transmissibility of the pathogen, the susceptibility of the host population and, crucially, the effectiveness of surveillance in detecting cases and preventing onward spread. For many pathogens, transmission from pre-symptomatic and/or asymptomatic (together referred to as non-symptomatic) infectious hosts can occur, making effective surveillance challenging. Here, by using SARS-CoV-2 as a case study, we show how the risk of local outbreaks can be assessed when non-symptomatic transmission can occur. We construct a branching process model that includes non-symptomatic transmission and explore the effects of interventions targeting non-symptomatic or symptomatic hosts when surveillance resources are limited. We consider whether the greatest reductions in local outbreak risks are achieved by increasing surveillance and control targeting non-symptomatic or symptomatic cases, or a combination of both. We find that seeking to increase surveillance of symptomatic hosts alone is typically not the optimal strategy for reducing outbreak risks. Adopting a strategy that combines an enhancement of surveillance of symptomatic cases with efforts to find and isolate non-symptomatic infected hosts leads to the largest reduction in the probability that imported cases will initiate a local outbreak.

Healthcare Resource Use and Burden Associated with Influenza Transmission Among Household Members with a Primary Infection: Commercial Claims Data Analysis

PURPOSE

To assess the burden of influenza transmission and care-seeking patterns over 3 influenza seasons among commercially insured households with a primary influenza infection.

PATIENTS AND METHODS

This retrospective cohort study used commercial claims data from the US MarketScan® Commercial and Medicare Supplemental databases for the 2014, 2015, and 2016 influenza seasons. Patients with a billed diagnosis of influenza and with coverage for at least 1 household member under the same health plan policy were included. A secondary diagnosed case was defined as a diagnosis of influenza in a second household member occurring within 14 days of the index case in a household.

RESULTS

Among 1,224,808 households with ≥2 members and a primary case of influenza, a secondary case of influenza was reported in 119,883 households (9.8%). A secondary diagnosed case of influenza occurred within 4 days of the primary diagnosis in 93,883 (78.3%) of those households. Both primary and secondary diagnosed influenza cases occurred most often among children (~60%). Household size was positively correlated to both the risk of a second case (6.4% of households with 2 or 3 members versus 12.6% of households with ≥4 members, P < 0.001) and the time to diagnosis of a second case (Spearman rank correlation coefficient = 0.09; P < 0.001).

CONCLUSION

Claims data for 3 influenza seasons (2014, 2015, 2016) showed that intrahousehold transmission of influenza occurs in approximately 10% of households with a primary case and poses a higher burden on larger households. Intrahousehold transmission of influenza represents a large healthcare resource use burden, with an unmet need for interventions that limit transmission.

Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols

Background

Which virological factors mediate overdispersion in the transmissibility of emerging viruses remains a long-standing question in infectious disease epidemiology.

Methods

Here, we use systematic review to develop a comprehensive dataset of respiratory viral loads (rVLs) of SARS-CoV-2, SARS-CoV-1 and influenza A(H1N1)pdm09. We then comparatively meta-analyze the data and model individual infectiousness by shedding viable virus via respiratory droplets and aerosols.

Results

The analyses indicate heterogeneity in rVL as an intrinsic virological factor facilitating greater overdispersion for SARS-CoV-2 in the COVID-19 pandemic than A(H1N1)pdm09 in the 2009 influenza pandemic. For COVID-19, case heterogeneity remains broad throughout the infectious period, including for pediatric and asymptomatic infections. Hence, many COVID-19 cases inherently present minimal transmission risk, whereas highly infectious individuals shed tens to thousands of SARS-CoV-2 virions/min via droplets and aerosols while breathing, talking and singing. Coughing increases the contagiousness, especially in close contact, of symptomatic cases relative to asymptomatic ones. Infectiousness tends to be elevated between 1 and 5 days post-symptom onset.

Conclusions

Intrinsic case variation in rVL facilitates overdispersion in the transmissibility of emerging respiratory viruses. Our findings present considerations for disease control in the COVID-19 pandemic as well as future outbreaks of novel viruses.

Funding

Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant program, NSERC Senior Industrial Research Chair program and the Toronto COVID-19 Action Fund.

Influenza A (H1N1) and Respiratory Syncytial Virus (RSV) Coinfection in a Newborn Child: A Case Report

This paper presents a case of coinfection of influenza A virus (H1N1) and respiratory syncytial virus (RSV) in a male newborn. On the first day of life, the newborn required passive oxygen therapy, followed by respiratory support with nasal continuous positive airway pressure (nCPAP) due to respiratory insufficiency. As the newborn's respiratory effort was intensifying, he was intubated. In the second day of life, a nasopharyngeal swab was taken yielding the presence of H1N1 and RSV in the RT-PCR test. The child was isolated and given oseltamivir and empirical antibiotic therapy, which improved his condition. Other newborns who initially stayed with the sick child in the post-delivery room did not obtain oseltamivir prophylactically as their nasopharyngeal swabs were negative. The child's parents denied the occurrence of influenza-like symptoms within 14 days of delivery, which suggests a transplacental transmission of the child's infection or asymptomatic course of infection in the parents. In conclusion, this report confirms the possibility of viral coinfections in newborns, which points attention to considering a panel of respiratory viruses in the diagnostics. Symptoms of influenza in newborns may be atypical, including a fever-free course. Oseltamivir treatment in newborns with influenza seems an effective therapeutic measure.

Symptoms, Infection Duration, and Hemagglutinin Inhibition Antibody Response in Influenza A Infections

BACKGROUND

Many influenza studies assume that symptomatic and asymptomatic cases have equivalent antibody responses.

METHODS

This study examines the relationship between influenza symptoms and serological response. Influenza-positive index cases and household members in Managua, Nicaragua, during 2012-2017 were categorized by symptom status.

RESULTS

Antibody response was assessed using hemagglutination inhibition assays (HAI). Among 510 cases, 74.5% had ≥4-fold increase in HAI antibodies, and 75.3% had febrile illness. In a logistic regression model, febrile cases had 2.17 times higher odds of a ≥4-fold titer rise compared to asymptomatic cases (95% confidence interval, 1.02-4.64).

CONCLUSIONS

Studies relying on serological assays may not generalize to asymptomatic infections.

Using serological measures to estimate influenza incidence in the presence of secular trends in exposure and immuno-modulation of antibody response

BACKGROUND

Influenza infection is often measured by a fourfold antibody titer increase over an influenza season (ie seroconversion). However, this approach may fail when influenza seasons are less distinct as it does not account for transient effects from recent infections. Here, we present a method to determine seroconversion for non-paired sera, adjusting for changes in individuals' antibody titers to influenza due to the transient impact of recent exposures, varied sampling times, and laboratory processes.

METHODS

We applied our method using data for five H3N2 strains collected from 942 individuals, aged 2-90 years, during the first two study visits of the Fluscape cohort study (2009-2012) in Guangzhou, China.

RESULTS

After adjustment, apparent seroconversion rates for non-circulating strains decreased while we observed a 20% increase in seroconversion rates to recently circulating strains. When examining seroconversion to the most recently circulating strain (A/Brisbane/20/2007) in our study, participants aged under 18, and over 64 had the highest seroconversion rates compared to other age groups.

CONCLUSIONS

Our results highlight the need for improved methods when using antibody titers as an endpoint in settings where there is no clear influenza "off" season. Methods, like those presented here, that use titers from circulating and non-circulating strains may be key.

Optimizing antiviral treatment for seasonal influenza in the USA: a mathematical modeling analysis

BACKGROUND

Seasonal influenza remains a major cause of morbidity and mortality in the USA. Despite the US Centers for Disease Control and Prevention recommendation promoting the early antiviral treatment of high-risk patients, treatment coverage remains low.

METHODS

To evaluate the population-level impact of increasing antiviral treatment timeliness and coverage among high-risk patients in the USA, we developed an influenza transmission model that incorporates data on infectious viral load, social contact, and healthcare-seeking behavior. We modeled the reduction in transmissibility in treated individuals based on their reduced daily viral load. The reduction in hospitalizations following treatment was based on estimates from clinical trials. We calibrated the model to weekly influenza data from Texas, California, Connecticut, and Virginia between 2014 and 2019. We considered in the baseline scenario that 2.7-4.8% are treated within 48 h of symptom onset while an additional 7.3-12.8% are treated after 48 h of symptom onset. We evaluated the impact of improving the timeliness and uptake of antiviral treatment on influenza cases and hospitalizations.

RESULTS

Model projections suggest that treating high-risk individuals as early as 48 h after symptom onset while maintaining the current treatment coverage level would avert 2.9-4.5% of all symptomatic cases and 5.5-7.1% of all hospitalizations. Geographic variability in the effectiveness of earlier treatment arises primarily from variabilities in vaccination coverage and population demographics. Regardless of these variabilities, we found that when 20% of the high-risk individuals were treated within 48 h, the reduction in hospitalizations doubled. We found that treatment of the elderly population (> 65 years old) had the highest impact on reducing hospitalizations, whereas treating high-risk individuals aged 5-19 years old had the highest impact on reducing transmission. Furthermore, the population-level benefit per treated individual is enhanced under conditions of high vaccination coverage and a low attack rate during an influenza season.

CONCLUSIONS

Increased timeliness and coverage of antiviral treatment among high-risk patients have the potential to substantially reduce the burden of seasonal influenza in the USA, regardless of influenza vaccination coverage and the severity of the influenza season.

Clinical Endpoints for Evaluating Efficacy in COVID-19 Vaccine Trials

Several vaccine candidates to protect against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19) have entered or will soon enter large-scale, phase 3, placebo-controlled randomized clinical trials. To facilitate harmonized evaluation and comparison of the efficacy of these vaccines, a general set of clinical endpoints is proposed, along with considerations to guide the selection of the primary endpoints on the basis of clinical and statistical reasoning. The plausibility that vaccine protection against symptomatic COVID-19 could be accompanied by a shift toward more SARS-CoV-2 infections that are asymptomatic is highlighted, as well as the potential implications of such a shift.

Why does the spread of COVID-19 vary greatly in different countries? Revealing the efficacy of face masks in epidemic prevention

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is highly contagious, and the coronavirus disease 2019 (COVID-19) pandemic caused by it has forced many countries to adopt 'lockdown' measures to prevent the spread of the epidemic through social isolation of citizens. Some countries proposed universal mask wearing as a protection measure of public health to strengthen national prevention efforts and to limit the wider spread of the epidemic. In order to reveal the epidemic prevention efficacy of masks, this paper systematically evaluates the experimental studies of various masks and filter materials, summarises the general characteristics of the filtration efficiency of isolation masks with particle size, and reveals the actual efficacy of masks by combining the volume distribution characteristics of human exhaled droplets with different particle sizes and the SARS-CoV-2 virus load of nasopharynx and throat swabs from patients. The existing measured data show that the filtration efficiency of all kinds of masks for large particles and extra-large droplets is close to 100%. From the perspective of filtering the total number of pathogens discharged in the environment and protecting vulnerable individuals from breathing live viruses, the mask has a higher protective effect. If considering the weighted average filtration efficiency with different particle sizes, the filtration efficiencies of the N95 mask and the ordinary mask are 99.4% and 98.5%, respectively. The mask can avoid releasing active viruses to the environment from the source of infection, thus maximising the protection of vulnerable individuals by reducing the probability of inhaling a virus. Therefore, if the whole society strictly implements the policy of publicly wearing masks, the risk of large-scale spread of the epidemic can be greatly reduced. Compared with the overall cost of social isolation, limited personal freedoms and forced suspension of economic activities, the inconvenience for citizens caused by wearing masks is perfectly acceptable.

SARS-CoV-2 Transmission Dynamics in Households With Children, Los Angeles, California

Objectives: Studies of household transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) focused on households with children are limited. We investigated household secondary attack rate (SAR), transmission dynamics, and contributing factors in households with children. Materials and Methods: In this prospective case-ascertained study in Los Angeles County, California, all households members were enrolled if ≥1 member tested positive for SARS-CoV-2 by polymerase chain reaction (PCR). Nasopharyngeal PCRs, serology, and symptom data were obtained over multiple visits. Results: A total of 489 individuals in 105 households were enrolled from June to December 2020. The majority (77.3%) reported a household annual income of <$50,000, and most (92.9%) were of Hispanic/Latinx ethnicity. Children <18 years old accounted for 46.9% index cases, of whom 45.3% were asymptomatic. Household index cases were predominantly children during low community transmission and adults during the high community transmission period (χ² = 7.647, p = 0.0036. The mean household SAR was 77.0% (95% CI: 69.4-84.6%). Child and adult index cases both efficiently transmitted SARS-CoV-2 within households [81.9%, (95% CI: 72.1-91.9%) vs. 72.4% (95% CI: 59.8-85.1%), p = 0.23]. Household income and pets were significantly associated with higher SAR in the multivariable analysis of household factors (p = 0.0013 and 0.004, respectively). Conclusions: The SAR in households with children in an urban setting with a large ethnic minority population is much higher than previously described. Children play important roles as index cases. SAR was disproportionately impacted by household income. Vaccination and public health efforts need special focus on children and vulnerable communities to help mitigate SARS-CoV-2 spread.

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

BACKGROUND

Viral load kinetics and duration of viral shedding are important determinants for disease transmission. We aimed to characterise viral load dynamics, duration of viral RNA shedding, and viable virus shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in various body fluids, and to compare SARS-CoV-2, SARS-CoV, and Middle East respiratory syndrome coronavirus (MERS-CoV) viral dynamics.

METHODS

In this systematic review and meta-analysis, we searched databases, including MEDLINE, Embase, Europe PubMed Central, medRxiv, and bioRxiv, and the grey literature, for research articles published between Jan 1, 2003, and June 6, 2020. We included case series (with five or more participants), cohort studies, and randomised controlled trials that reported SARS-CoV-2, SARS-CoV, or MERS-CoV infection, and reported viral load kinetics, duration of viral shedding, or viable virus. Two authors independently extracted data from published studies, or contacted authors to request data, and assessed study quality and risk of bias using the Joanna Briggs Institute Critical Appraisal Checklist tools. We calculated the mean duration of viral shedding and 95% CIs for every study included and applied the random-effects model to estimate a pooled effect size. We used a weighted meta-regression with an unrestricted maximum likelihood model to assess the effect of potential moderators on the pooled effect size. This study is registered with PROSPERO, CRD42020181914.

FINDINGS

79 studies (5340 individuals) on SARS-CoV-2, eight studies (1858 individuals) on SARS-CoV, and 11 studies (799 individuals) on MERS-CoV were included. Mean duration of SARS-CoV-2 RNA shedding was 17·0 days (95% CI 15·5-18·6; 43 studies, 3229 individuals) in upper respiratory tract, 14·6 days (9·3-20·0; seven studies, 260 individuals) in lower respiratory tract, 17·2 days (14·4-20·1; 13 studies, 586 individuals) in stool, and 16·6 days (3·6-29·7; two studies, 108 individuals) in serum samples. Maximum shedding duration was 83 days in the upper respiratory tract, 59 days in the lower respiratory tract, 126 days in stools, and 60 days in serum. Pooled mean SARS-CoV-2 shedding duration was positively associated with age (slope 0·304 [95% CI 0·115-0·493]; p=0·0016). No study detected live virus beyond day 9 of illness, despite persistently high viral loads, which were inferred from cycle threshold values. SARS-CoV-2 viral load in the upper respiratory tract appeared to peak in the first week of illness, whereas that of SARS-CoV peaked at days 10-14 and that of MERS-CoV peaked at days 7-10.

INTERPRETATION

Although SARS-CoV-2 RNA shedding in respiratory and stool samples can be prolonged, duration of viable virus is relatively short-lived. SARS-CoV-2 titres in the upper respiratory tract peak in the first week of illness. Early case finding and isolation, and public education on the spectrum of illness and period of infectiousness are key to the effective containment of SARS-CoV-2.

FUNDING

None.

Studying the progress of COVID-19 outbreak in India using SIRD model

We explore a standard epidemiological model, known as the SIRD model, to study the COVID-19 infection in India, and a few other countries around the world. We use (a) the stable cumulative infection of various countries and (b) the number of infection versus the tests carried out to evaluate the model. The time-dependent infection rate is set in the model to obtain the best fit with the available data. The model is simulated aiming to project the probable features of the infection in India, various Indian states, and other countries. India imposed an early lockdown to contain the infection that can be treated by its healthcare system. We find that with the current infection rate and containment measures, the total active infection in India would be maximum at the end of June or beginning of July 2020. With proper containment measures in the infected zones and social distancing, the infection is expected to fall considerably from August. If the containment measures are relaxed before the arrival of the peak infection, more people from the susceptible population will fall sick as the infection is expected to see a threefold rise at the peak. If the relaxation is given a month after the peak infection, a second peak with a moderate infection will follow. However, a gradual relaxation of the lockdown started well ahead of the peak infection, leads to a nearly twofold increase of the peak infection with no second peak. The model is further extended to incorporate the infection arising from the population showing no symptoms. The preliminary finding suggests that random testing needs to be carried out within the asymptomatic population to contain the spread of the disease. Our model provides a semi-quantitative overview of the progression of COVID-19 in India, with model projections reasonably replicating the current progress. The projection of the model is highly sensitive to the choice of the parameters and the available data.

Predicting the second wave of COVID-19 in Washtenaw County, MI

The COVID-19 pandemic has highlighted the patchwork nature of disease epidemics, with infection spread dynamics varying wildly across countries and across states within the US. To explore this issue, we study and predict the spread of COVID-19 in Washtenaw County, MI, which is home to University of Michigan and Eastern Michigan University, and in close proximity to Detroit, MI, a major epicenter of the epidemic in Michigan. We apply a discrete and stochastic network-based modeling framework allowing us to track every individual in the county. In this framework, we construct contact networks based on synthetic population datasets specific for Washtenaw County that are derived from US Census datasets. We assign individuals to households, workplaces, schools, and group quarters (such as prisons or long term care facilities). In addition, we assign casual contacts to each individual at random. Using this framework, we explicitly simulate Michigan-specific government-mandated workplace and school closures as well as social distancing measures. We perform sensitivity analyses to identify key model parameters and mechanisms contributing to the observed disease burden in the three months following the first observed cases of COVID-19 in Michigan. We then consider several scenarios for relaxing restrictions and reopening workplaces to predict what actions would be most prudent. In particular, we consider the effects of 1) different timings for reopening, and 2) different levels of workplace vs. casual contact re-engagement. We find that delaying reopening does not reduce the magnitude of the second peak of cases, but only delays it. Reducing levels of casual contact, on the other hand, both delays and lowers the second peak. Through simulations and sensitivity analyses, we explore mechanisms driving the magnitude and timing of a second wave of infections upon re-opening. We find that the most significant factors are workplace and casual contacts and protective measures taken by infected individuals who have sought care. This model can be adapted to other US counties using synthetic population databases and data specific to those regions.

COVID-19 Outbreak and Presymptomatic Transmission in Pilgrim Travelers Who Returned to Korea from Israel

BACKGROUND

On February 21, 2020, 2 coronavirus disease 2019 (COVID-19) cases in pilgrim travelers from Korea to Israel were identified. We investigated the source of infection, clinical features of COVID-19, and transmission potential of presymptomatic and asymptomatic cases.

METHODS

All 39 pilgrim travelers were aggressively tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Their clinical features and possible source of infection were investigated by interview and review of their medical records. Ten confirmed cases without symptoms at the first sampling dates were selected for follow-up reverse transcription polymerase chain reaction tests.

RESULTS

Of 39 pilgrim travelers, 30 (77%) were positive for SARS-CoV-2. Among the 30 positive COVID-19 cases, 4 (13%) were asymptomatic. Available follow-up cycle threshold values from 10 cases gradually increased over time and were lower during the presymptomatic period than during the postsymptomatic period. Out of 328 contacts related to the COVID-19 cases in the pilgrim travelers, 22 additional cases (7%) were confirmed with SARS-CoV-2 infections. Three tertiary cases were identified to be transmitted by presymptomatic secondary cases.

CONCLUSION

To prevent transmission of COVID-19, we need to focus on presymptomatic and asymptomatic cases, and massive testing for SARS-CoV-2 is required. More research about the possibility of presymptomatic transmission over 2 days before symptom onset is required.

Decoding Asymptomatic COVID-19 Infection and Transmission

One of the major challenges in controlling the coronavirus disease 2019 (COVID-19) outbreak is its asymptomatic transmission. The pathogenicity and virulence of asymptomatic COVID-19 remain mysterious. On the basis of the genotyping of 75775 SARS-CoV-2 genome isolates, we reveal that asymptomatic infection is linked to SARS-CoV-2 11083G>T mutation (i.e., L37F at nonstructure protein 6 (NSP6)). By analyzing the distribution of 11083G>T in various countries, we unveil that 11083G>T may correlate with the hypotoxicity of SARS-CoV-2. Moreover, we show a global decaying tendency of the 11083G>T mutation ratio indicating that 11083G>T hinders the SARS-CoV-2 transmission capacity. Artificial intelligence, sequence alignment, and network analysis are applied to show that NSP6 mutation L37F may have compromised the virus's ability to undermine the innate cellular defense against viral infection via autophagy regulation. This assessment is in good agreement with our genotyping of the SARS-CoV-2 evolution and transmission across various countries and regions over the past few months.

Early experience with universal preoperative and pre-procedural screening for COVID-19 in low-risk pediatric surgical patients requiring general anesthesia

PURPOSE

The COVID-19 pandemic has placed extraordinary demands on healthcare services worldwide. Some have reported increased viral transmission to healthcare workers during aerosol-generating procedures such as intubation. We report our experience with universal preoperative and preprocedural screening for COVID-19 in children requiring general anaesthesia with low risk of having the infection.

METHODS

This was a data review involving children aged < 18 years undergoing procedures under general anaesthesia in our institution from 18th March to 31st May 2020 and deemed low risk for COVID 19 infection, as defined by our institutional protocol. Confirmation of COVID-19 was by real time reverse-transcription polymerase chain reaction with confirmation by nucleic acid sequencing. All patients were followed up 14 days post-swab.

RESULTS

Of the 66 children (median age 4.5 years, range 0-16.8) eligible for the study, 39 (60%) were male and infants (1-12 months) formed the largest group (n = 24, 36%). None were positive for COVID-19. On 14 day follow-up, none had symptoms related to COVID-19.

CONCLUSION

Our study shows that low risk asymptomatic children with no history of contact with COVID-19 patients test negative on universal screening. Larger studies are required to ascertain the role of screening prior to procedures done under general anaesthesia.

Prolonged presence of viral nucleic acid in clinically recovered COVID-19 patients was not associated with effective infectiousness

Prolonged presence of viral nucleic acid was reported in certain patients with coronavirus disease 2019 (COVID-19), with unclear clinical and epidemiological significance. We here described the clinical and epidemiological characteristics of 37 recovered COVID-19 patients with prolonged presence of viral RNA in Wuhan, China. For those who had been discharged and re-admitted, their close contacts outside the hospital were traced and evaluated. The median age of the 37 patients was 62 years (IQR 50, 68), and 24 (64.9%) were men. They had common or severe COVID-19. With prolonged positive RT-PCR, most patients were clinically stable, 29 (78.4%) denied any symptoms. A total of 431 PCR tests were carried out, with each patient at a median of 8 time points. The median time of PCR positivity to April 18 was 78 days (IQR 67.7, 84.5), and the longest 120 days. 22 of 37 patients had been discharged at a median of 44 days (IQR 22.3, 50) from disease onset, and 9 had lived with their families without personal protections for a total of 258 person-days and no secondary infection was identified through epidemiological investigation, nucleic acid and antibody screening. Infectiousness in COVID-19 patients with prolonged presence of viral nucleic acid should not solely be evaluated by RT-PCR. Those patients who have clinically recovered and whose disease course has exceeded four weeks were associated with very limited infectiousness. Reconsideration of disease control in such patients is needed.

Screening policies, preventive measures and in-hospital infection of COVID-19 in global surgical practices

Background

In a surgical setting, COVID-19 patients may trigger in-hospital outbreaks and have worse postoperative outcomes. Despite these risks, there have been no consistent statements on surgical guidelines regarding the perioperative screening or management of COVID-19 patients, and we do not have objective global data that describe the current conditions surrounding this issue. This study aimed to clarify the current global surgical practice including COVID-19 screening, preventive measures and in-hospital infection under the COVID-19 pandemic, and to clarify the international gaps on infection control policies among countries worldwide.

Methods

During April 2-8, 2020, a cross-sectional online survey on surgical practice was distributed to surgeons worldwide through international surgical societies, social media and personal contacts. Main outcome and measures included preventive measures and screening policies of COVID-19 in surgical practice and centers' experiences of in-hospital COVID-19 infection. Data were analyzed by country's cumulative deaths number by April 8, 2020 (high risk, >5000; intermediate risk, 100-5000; low risk, <100).

Results

A total of 936 centers in 71 countries responded to the survey (high risk, 330 centers; intermediate risk, 242 centers; low risk, 364 centers). In the majority (71.9%) of the centers, local guidelines recommended preoperative testing based on symptoms or suspicious radiologic findings. Universal testing for every surgical patient was recommended in only 18.4% of the centers. In-hospital COVID-19 infection was reported from 31.5% of the centers, with higher rates in higher risk countries (high risk, 53.6%; intermediate risk, 26.4%; low risk, 14.8%; P < 0.001). Of the 295 centers that experienced in-hospital COVID-19 infection, 122 (41.4%) failed to trace it and 58 (19.7%) reported the infection originating from asymptomatic patients/staff members. Higher risk countries adopted more preventive measures including universal testing, routine testing of hospital staff and use of dedicated personal protective equipment in operation theatres, but there were remarkable discrepancies across the countries.

Conclusions

This large international survey captured the global surgical practice under the COVID-19 pandemic and highlighted the insufficient preoperative screening of COVID-19 in the current surgical practice. More intensive screening programs will be necessary particularly in severely affected countries/institutions.

Study registration

Registered in ClinicalTrials.gov: NCT04344197.

Lack of Serologic Evidence of Infection Among Health Care Personnel and Other Contacts of First 2 Confirmed Patients With COVID-19 in Illinois, 2020

OBJECTIVES

Widespread global transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19), continues. Many questions remain about asymptomatic or atypical infections and transmission dynamics. We used comprehensive contact tracing of the first 2 confirmed patients in Illinois with COVID-19 and serologic SARS-CoV-2 antibody testing to determine whether contacts had evidence of undetected COVID-19.

METHODS

Contacts were eligible for serologic follow-up if previously tested for COVID-19 during an initial investigation or had greater-risk exposures. Contacts completed a standardized questionnaire during the initial investigation. We classified exposure risk as high, medium, or low based on interactions with 2 index patients and use of personal protective equipment (PPE). Serologic testing used a SARS-CoV-2 spike enzyme-linked immunosorbent assay on serum specimens collected from participants approximately 6 weeks after initial exposure to either index patient. The 2 index patients provided serum specimens throughout their illness. We collected data on demographic, exposure, and epidemiologic characteristics.

RESULTS

Of 347 contacts, 110 were eligible for serologic follow-up; 59 (17% of all contacts) enrolled. Of these, 53 (90%) were health care personnel and 6 (10%) were community contacts. Seventeen (29%) reported high-risk exposures, 15 (25%) medium-risk, and 27 (46%) low-risk. No participant had evidence of SARS-CoV-2 antibodies. The 2 index patients had antibodies detected at dilutions >1:6400 within 4 weeks after symptom onset.

CONCLUSIONS

In serologic follow-up of the first 2 known patients in Illinois with COVID-19, we found no secondary transmission among tested contacts. Lack of seroconversion among these contacts adds to our understanding of conditions (ie, use of PPE) under which SARS-CoV-2 infections might not result in transmission and demonstrates that SARS-CoV-2 antibody testing is a useful tool to verify epidemiologic findings.

Associations Between Relative Viral Load at Diagnosis and Influenza A Symptoms and Recovery

Background

Rapid point-of-care polymerase chain reaction (PCR) diagnostic tests generally provide a qualitative result of positive or negative only. Additional information about the relative viral load could be calculated. Such quantitative information might be useful for making treatment decisions.

Methods

We enrolled students at a university health center who presented with cough and 1 additional flu-like symptom from December 2016 to February 2017. Data were collected before, during, and 5 days after the clinic visit. All those enrolled in the study received a point-of-care PCR test (cobas Liat). For those patients that tested positive for influenza A, we investigated correlations between the relative viral load and measures of disease severity and recovery.

Results

One hundred thirty-five students tested positive for influenza A. We found a positive correlation between viral load and body temperature. Time since symptom onset seemed to have a negative correlation but was not statistically significant. We did not find any correlations between viral load and overall symptom severity or outcomes related to recovery.

Conclusions

Although we found a correlation between relative viral load and body temperature, for our study population of young, overall healthy adults, we did not find that relative viral load provided additional information that could help in determining treatment and disease outcomes. It could be that viral load does provide useful additional information for other groups of patients, such as young children or older adults. Further studies on those populations are warranted.

A critical review of point-of-care diagnostic technologies to combat viral pandemics

The COVID-19 global pandemic of 2019-2020 pointedly revealed the lack of diagnostic solutions that are able to keep pace with the rapid spread of the virus. Despite the promise of decades of lab-on-a-chip research, no commercial products were available to deliver rapid results or enable testing in the field at the onset of the pandemic. In this critical review, we assess the current state of progress on the development of point-of-care technologies for the diagnosis of viral diseases that cause pandemics. While many previous reviews have reported on progress in various lab-on-a-chip technologies, here we address the literature from the perspective of the testing needs of a rapidly expanding pandemic. First, we recommend a set of requirements to heed when designing point-of-care diagnostic technologies to address the testing needs of a pandemic. We then review the current state of assay technologies with a focus on isothermal amplification and lateral-flow immunoassays. Though there is much progress on assay development, we argue that the largest roadblock to deployment exists in sample preparation. We summarize current approaches to automate sample preparation and discuss both the progress and shortcomings of these developments. Finally, we provide our recommendations to the field of specific challenges to address in order to prepare for the next pandemic.

COVID-19 Related Mortality During Management of a Hepatic Abscess

The coronavirus disease (COVID-19) is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in the capital city of the Hubei Province, Wuhan, China, in late 2019. Declared a pandemic by the World Health Organization on March 11th, 2020, COVID-19 has challenged healthcare systems to limit the spread of community and hospital-acquired disease. This article uses a patient case to highlight the importance of infection control during the height of the SARS-CoV-2 surge at a Level I affiliated community hospital in Western New York.

Beyond clinical trials: Evolutionary and epidemiological considerations for development of a universal influenza vaccine

The prospect of universal influenza vaccines is generating much interest and research at the intersection of immunology, epidemiology, and viral evolution. While the current focus is on developing a vaccine that elicits a broadly cross-reactive immune response in clinical trials, there are important downstream questions about global deployment of a universal influenza vaccine that should be explored to minimize unintended consequences and maximize benefits. Here, we review and synthesize the questions most relevant to predicting the population benefits of universal influenza vaccines and discuss how existing information could be mined to begin to address these questions. We review three research topics where computational modeling could bring valuable evidence: immune imprinting, viral evolution, and transmission. We address the positive and negative consequences of imprinting, in which early childhood exposure to influenza shapes and limits immune responses to future infections via memory of conserved influenza antigens. However, the mechanisms at play, their effectiveness, breadth of protection, and the ability to "reprogram" already imprinted individuals, remains heavily debated. We describe instances of rapid influenza evolution that illustrate the plasticity of the influenza virus in the face of drug pressure and discuss how novel vaccines could introduce new selective pressures on the evolution of the virus. We examine the possible unintended consequences of broadly protective (but infection-permissive) vaccines on the dynamics of epidemic and pandemic influenza, compared to conventional vaccines that have been shown to provide herd immunity benefits. In conclusion, computational modeling offers a valuable tool to anticipate the benefits of ambitious universal influenza vaccine programs, while balancing the risks from endemic influenza strains and unpredictable pandemic viruses. Moving forward, it will be important to mine the vast amount of data generated in clinical studies of universal influenza vaccines to ensure that the benefits and consequences of these vaccine programs have been carefully modeled and explored.

Minimizing transmission of COVID-19 while delivering optimal cancer care in a National Cancer Centre

The COVID-19 pandemic has disrupted current models of healthcare and adaptations will likely continue. With the gradual easing of lockdown measures worldwide, cancer centres must be prepared to implement novel means to prevent repeated waves of infection. There are two limitations unique to oncology - a higher susceptibility of patients to COVID-19 and the multidisciplinary approach required of cancer management. We describe the measures implemented in the largest cancer centre in Singapore to continue optimal cancer care in spite of the ongoing pandemic, with no nosocomial infections reported in our centre to date. We adopted a multipronged approach, with an overall committee supervising the entire COVID-19 management effort. A screening clinic was setup to triage patients prior to entry to the centre. Each Oncology Division within the cancer centre designed solutions tailored to the specific needs of their discipline. We explore in detail the screening criteria and workflow of the screening clinic, as well as modifications by individual divisions to reduce infection risk to patients and healthcare professionals. This approach can be modelled by other cancer centres during this prolonged COVID-19 pandemic.

A Review of Multi-Compartment Infectious Disease Models

Multi-compartment models have been playing a central role in modelling infectious disease dynamics since the early 20th century. They are a class of mathematical models widely used for describing the mechanism of an evolving epidemic. Integrated with certain sampling schemes, such mechanistic models can be applied to analyse public health surveillance data, such as assessing the effectiveness of preventive measures (e.g. social distancing and quarantine) and forecasting disease spread patterns. This review begins with a nationwide macromechanistic model and related statistical analyses, including model specification, estimation, inference and prediction. Then, it presents a community-level micromodel that enables high-resolution analyses of regional surveillance data to provide current and future risk information useful for local government and residents to make decisions on reopenings of local business and personal travels. r software and scripts are provided whenever appropriate to illustrate the numerical detail of algorithms and calculations. The coronavirus disease 2019 pandemic surveillance data from the state of Michigan are used for the illustration throughout this paper.