Comparison of secondary attack rate and viable virus shedding between patients with SARS-CoV-2 Delta and Omicron variants: A prospective cohort study

Risk period for transmission of SARS-CoV-2 and seasonal influenza: a rapid review

BACKGROUND

Restricting infectious healthcare workers (HCWs) from the workplace is an important infection prevention strategy. The duration of viral shedding or symptoms are often used as proxies for the infectious period in adults but may not accurately estimate it.

OBJECTIVE

To determine the risk period for transmission among previously healthy adults infected with SARS-CoV-2 omicron variant (omicron) or influenza A (influenza) by examining the duration of shedding and symptoms, and day of symptom onset in secondary cases of transmission pairs.

DESIGN

Rapid review.

METHODS

This rapid review adhered to PRISMA-ScR; five databases were searched. The cumulative daily proportion of participants with an outcome of interest was calculated for each study and summarized.

RESULTS

Forty-three studies were included. Shedding resolved among ≥ 70% of participants by the end of day nine post symptom onset for omicron, and day seven for influenza; and for ≥ 90% of participants, by the end of day 10 for omicron and day nine for influenza. Two studies suggested shedding continues > 24 hours post-fever resolution for both viruses. Symptom onset occurred in ≥ 80% of secondary cases by the end of day seven post-primary case symptom onset for omicron and day six for influenza.

CONCLUSIONS

Omicron shedding is consistent with previous recommendations to exclude infected HCWs from work for 10 days; and influenza follows a similar trend. Earlier symptom onset in most secondary cases for both pathogens indicates that, despite persistent viral shedding, most transmission occurs earlier; and the cumulative serial interval might better approximate the duration of infectiousness.

Comparison of Airborne SARS-CoV-2 Omicron and Pre-Delta Variants Around Infected Patients

Transmissibility has increased during the evolution of SARS-CoV-2, possibly by improved airborne transmission. An increased transmission was noted also in many hospitals. We analyzed SARS-CoV-2 in room air of hospitalized Omicron infected patients and compared results with previous findings with pre-Delta variants to study if SARS-CoV-2 was more prevalent in patient rooms after the introduction of Omicron. Only 4 of 75 (5%) air samples, from 3 of 43 included patients, were positive during the early Omicron wave, compared to 14/120 (12%), from 10 of 60 included patients during the initial wave. No certain statistical difference between virus variants could be established, but the tendency was a lower occurrence at Omicron infected patients, also when adjusting for relevant confounders. These finding do not support the initial hypothesis that increased SARS-CoV-2 aerosol emission from diagnosed patients with Omicron could explain any increased risk of hospital transmission.

Deisolation in the Healthcare Setting Following Recent COVID-19 Infection

BACKGROUND

Deisolation of persons infected with SARS-CoV-2, the virus that causes COVID-19, presented a substantial challenge for healthcare workers and policy makers, particularly during the early phases of the pandemic. Data to guide deisolation of SARS-CoV-2-infected patients remain limited, and the risk of transmitting and acquiring infection has changed with the evolution of SARS-CoV-2 variants and population immunity from previous vaccination or infection, or both.

AIMS

This review examines the evidence to guide the deisolation of SARS-CoV-2-infected inpatients within the hospital setting when clinically improving and also of healthcare workers with COVID-19 prior to returning to work.

METHODS

A review was performed using relevant search terms in Medline, EMBASE, Google Scholar, and PubMed.

RESULTS AND DISCUSSION

The evidence is reviewed with regards to the nature of SARS-CoV-2 transmission, the role of testing to guide deisolation, and the impact of SARS-CoV-2-specific immunity. A paradigm and recommendations are proposed to guide deisolation for inpatients and return to work for healthcare workers.

SARS-CoV-2 subgenomic RNA: formation process and rapid molecular diagnostic methods

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which caused coronavirus disease-2019 (COVID-19) is spreading worldwide and posing enormous losses to human health and socio-economic. Due to the limitations of medical and health conditions, it is still a huge challenge to develop appropriate discharge standards for patients with COVID-19 and to use medical resources in a timely and effective manner. Similar to other coronaviruses, SARS-CoV-2 has a very complex discontinuous transcription process to generate subgenomic RNA (sgRNA). Some studies support that sgRNA of SARS-CoV-2 can only exist when the virus is active and is an indicator of virus replication. The results of sgRNA detection in patients can be used to evaluate the condition of hospitalized patients, which is expected to save medical resources, especially personal protective equipment. There have been numerous investigations using different methods, especially molecular methods to detect sgRNA. Here, we introduce the process of SARS-CoV-2 sgRNA formation and the commonly used molecular diagnostic methods to bring a new idea for clinical detection in the future.

Duration of SARS-CoV-2 shedding: A systematic review

Background

Positive viral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cultures indicate shedding of infectious virus and corresponding transmission risk of coronavirus disease 2019 (COVID-19). The research question of this systematic review was: Is there a discernible pattern in the timing of SARS-CoV-2 virus isolation, and what is the proportion of positive and negative results for isolation of SARS-CoV-2 virus with viral culture relative to the onset of clinical symptoms or the day of diagnosis, as indicated by longitudinal studies?

Methods

We systematically searched PubMed and Embase from inception to 16 February 2023 for English-language studies with serial viral culture testing within symptomatic or asymptomatic SARS-CoV-2 infected persons during the post-vaccination period. Outcomes of interest were the daily culture status per study and the overall daily culture positivity rate of SARS-CoV-2. We critically appraised the selected studies using the Newcastle-Ottawa quality assessment scale.

Results

We included 14 viral shedding studies in this systematic review. Positive viral SARS-CoV-2 cultures were detected in samples ranging from 4 days before to 18 days after symptom onset. The daily culture SARS-CoV-2 positivity rate since symptom onset or diagnosis showed a steep decline between day 5 and 9, starting with a peak ranging from 44% to 50% on days -1 to 5, decreasing to 28% on day 7 and 11% on day 9, and finally ranging between 0% and 8% on days 10-17.

Conclusions

Viral shedding peaked within 5 days since symptom onset or diagnosis and the culture positivity rate rapidly declined hereafter. This systematic review provides an overview of current evidence on the daily SARS-CoV-2 culture positivity rates during the post-vaccination period. These findings could be used to estimate the effectiveness of public health control measures, including treatment and preventive strategies, to reduce the spread of COVID-19.

Comparison of surveillance systems for monitoring COVID-19 in England: a retrospective observational study

BACKGROUND

During the COVID-19 pandemic, cases were tracked using multiple surveillance systems. Some systems were completely novel, and others incorporated multiple data streams to estimate case incidence and prevalence. How well these different surveillance systems worked as epidemic indicators is unclear, which has implications for future disease surveillance and outbreak management. The aim of this study was to compare case counts, prevalence and incidence, timeliness, and comprehensiveness of different COVID-19 surveillance systems in England.

METHODS

For this retrospective observational study of COVID-19 surveillance systems in England, data from 12 surveillance systems were extracted from publicly available sources (Jan 1, 2020-Nov 30, 2021). The main outcomes were correlations between different indicators of COVID-19 incidence or prevalence. These data were integrated as daily time-series and comparisons undertaken using Spearman correlation between candidate alternatives and the most timely (updated daily, clinical case register) and the least biased (from comprehensive household sampling) COVID-19 epidemic indicators, with comparisons focused on the period of Sept 1, 2020-Nov 30, 2021.

FINDINGS

Spearman statistic correlations during the full focus period between the least biased indicator (from household surveys) and other epidemic indicator time-series were 0·94 (95% CI 0·92 to 0·95; clinical cases, the most timely indicator), 0·92 (0·90 to 0·94; estimates of incidence generated after incorporating information about self-reported case status on the ZoeApp, which is a digital app), 0·67 (95% CI 0·60 to 0·73, emergency department attendances), 0·64 (95% CI 0·60 to 0·68, NHS 111 website visits), 0·63 (95% CI 0·56 to 0·69, wastewater viral genome concentrations), 0·60 (95% CI 0·52 to 0·66, admissions to hospital with positive COVID-19 status), 0·45 (95% CI 0·36 to 0·52, NHS 111 calls), 0·08 (95% CI -0·03 to 0·18, Google search rank for "covid"), -0·04 (95% CI -0·12 to 0·05, in-hours consultations with general practitioners), and -0·37 (95% CI -0·46 to -0·28, Google search rank for "coronavirus"). Time lags (-14 to +14 days) did not markedly improve these rho statistics. Clinical cases (the most timely indicator) captured a more consistent proportion of cases than the self-report digital app did.

INTERPRETATION

A suite of monitoring systems is useful. The household survey system was the most comprehensive and least biased epidemic monitor, but not very timely. Data from laboratory testing, the self-reporting digital app, and attendances to emergency departments were comparatively useful, fairly accurate, and timely epidemic trackers.

FUNDING

National Institute for Health and Care Research Health Protection Research Unit in Emergency Preparedness and Response, a partnership between the UK Health Security Agency, King's College London, and the University of East Anglia.

Clinical and virological features of asymptomatic and mild symptomatic patients with SARS-CoV-2 Omicron infection at Shanghai Fangcang shelter hospital

OBJECTIVE

The objective of this study is to evaluate and compare clinical and virological characteristics of asymptomatic and mild symptomatic patients of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2.2 variant infection and identify risk factors associated with the prolonged viral negative conversion duration.

METHODS

We conducted a retrospective observational study in a Shanghai (China) Fangcang shelter hospital from April 9 to May 17, 2022. The patient-related demographic or clinical data were retrospectively recorded. Comparisons of demographic and clinical characteristics between asymptomatic and mild-symptomatic patients were performed. Cox regression was performed to identify the risk factors of prolonged viral negative conversion duration.

RESULTS

A total of 551 patients confirmed with SARS-CoV-2 Omicron variant infection were enrolled in the study. Of these, 297 patients (53.9%) were asymptomatic and 254 patients (46.1%) had mild symptoms. When comparing the clinical and virological characteristics between the asymptomatic and mild symptomatic groups, several clinical parameters, including age, gender, time to viral clearance from the first positive swab, chronic comorbidities, and vaccination dose did not show statistically significant differences. In mild symptomatic patients, the median viral negative conversion duration (NCD) was 7 days (interquartile range [IQR]: 5-9), which was comparable to the median of 7 days (IQR: 5-10) in asymptomatic patients (p = .943). Multivariate Cox analysis revealed that patients age ≥ 60 years had a significantly higher hazard ratio (HR) for prolonged viral NCD (HR: 1.313; 95% confidence interval: 1.014-1.701, p = .039).

CONCLUSION

Asymptomatic and symptomatic patients with non-severe SARS-CoV-2 Omicron BA.2.2 variant infection have similar clinical features and virological courses. Old age was an independent risk factor for prolonged SARS-CoV-2 conversion time.

Viral dynamics of SARS-CoV-2 in immunocompromised patients

OBJECTIVES

Immunocompromised patients infected with SARS-CoV-2 have been shown to shed replicable virus for a prolonged period of time, and the duration of isolation can therefore be difficult to estimate. The objective of this study was to evaluate the viral load dynamic in non-hospitalized immunocompromised patients infected with SARS-CoV-2 and treated with monoclonal antibodies (mAbs) or antivirals.

METHODS

Oropharyngeal swabs for RT-PCR and viral culture were collected from 29 immunocompromised patients before treatment with mAbs or antivirals and at days 5 and 15 after treatment. Overall, 12 patients were infected with the subvariant Omicron BA.1, 12 with Omicron BA.2, two with the Delta variant and for three patients determination of the variant were inconclusive.

RESULTS

Before treatment with mAbs or antivirals, 22 of 29 patients (76% [95% CI, 56-90]) shed replicative SARS-CoV-2. At day 5, 21 patients (72% [95% CI, 53-87]) still tested RT-PCR-positive, but for 14 patients (48% [95% CI, 29-67]) there were no replicative virus in culture. At day 15, 16 patients (55% [95% CI, 36-74%]) tested positive but only two patients (7% [95%CI, 1-23]) had replicative virus.

DISCUSSION

Half of the patients in this cohort had no viable virus after 5 days and only two patients had replicative virus after 15 days. This could indicate that the current CDC recommendations of an isolation period of 20 days for immunocompromised patients infected with SARS-CoV-2 could be reduced, but larger studies are needed to estimate the isolation duration for immunocompromised patients.

Wastewater-based modeling, reconstruction, and prediction for COVID-19 outbreaks in Hungary caused by highly immune evasive variants

(MOTIVATION)

Wastewater-based epidemiology (WBE) has emerged as a promising approach for monitoring the COVID-19 pandemic, since the measurement process is cost-effective and is exposed to fewer potential errors compared to other indicators like hospitalization data or the number of detected cases. Consequently, WBE was gradually becoming a key tool for epidemic surveillance and often the most reliable data source, as the intensity of clinical testing for COVID-19 drastically decreased by the third year of the pandemic. Recent results suggests that the model-based fusion of wastewater measurements with clinical data and other indicators is essential in future epidemic surveillance.

(METHOD)

In this work, we developed a wastewater-based compartmental epidemic model with a two-phase vaccination dynamics and immune evasion. We proposed a multi-step optimization-based data assimilation method for epidemic state reconstruction, parameter estimation, and prediction. The computations make use of the measured viral load in wastewater, the available clinical data (hospital occupancy, delivered vaccine doses, and deaths), the stringency index of the official social distancing rules, and other measures. The current state assessment and the estimation of the current transmission rate and immunity loss allow a plausible prediction of the future progression of the pandemic.

(RESULTS)

Qualitative and quantitative evaluations revealed that the contribution of wastewater data in our computational epidemiological framework makes predictions more reliable. Predictions suggest that at least half of the Hungarian population has lost immunity during the epidemic outbreak caused by the BA.1 and BA.2 subvariants of Omicron in the first half of 2022. We obtained a similar result for the outbreaks caused by the subvariant BA.5 in the second half of 2022.

(APPLICABILITY)

The proposed approach has been used to support COVID management in Hungary and could be customized for other countries as well.

Judicious ending of isolation based on reverse transcription-polymerase chain reaction (RT-PCR) cycle threshold only for patients with coronavirus disease 2019 (COVID-19) requiring in-hospital therapy for longer than 20 days after symptom onset

BACKGROUND

For patients with coronavirus disease 2019 (COVID-19) requiring hospitalization, extending isolation is warranted. As a cautious protocol, ending isolation based on polymerase chain reaction cycle threshold (Ct) value was introduced for patients requiring therapy for >20 days after symptom onset.

METHOD

We compared a Ct-based strategy using Smart Gene® between March 2022 and January 2023 with a preceding control period (March 2021 to February 2022) when two consecutive negative reverse transcription-polymerase chain reaction tests using FilmArray® were required for ending isolation. Ct was evaluated on day 21, and ending isolation was permitted in patients with Ct ≥ 38. Although patients with Ct 35-37 were transferred to a non-COVID-19 ward, isolation was continued.

RESULTS

The duration of stay on a COVID-19 ward in the Ct group was 9.7 days shorter than that in controls. The cumulative number of tests was 3.7 in controls and 1.2 in the Ct group. There was no nosocomial transmission after ending isolation in either group. The number of days from symptom onset to testing was 20.7 ± 2.1 in Ct group, and five patients had Ct < 35, nine Ct 35-37, and 71 Ct ≥ 38. No patients were moderately or severely immunocompromised. Steroid use was an independent risk factor for prolonged low Ct (odds ratio 9.40, 95% confidence interval 2.31-38.15, p = 0.002) CONCLUSIONS: The efficacy of ending isolation based on Ct values could improve bed utilization without the risk of transmission among patients with COVID-19 requiring therapy for >20 days after symptom onset.

Duration of viable virus shedding and polymerase chain reaction positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract: a systematic review and meta-analysis

OBJECTIVES

To assess the duration of viable virus shedding and polymerase chain reaction (PCR) positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract.

METHODS

We systematically searched PubMed, Cochrane, and Web of Science for original articles reporting the duration of viable virus shedding and PCR positivity of the SARS-CoV-2 Omicron variant in the upper respiratory tract from November 11, 2021 to December 11, 2022. This meta-analysis was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and was registered with PROSPERO (CRD42022357349). We used the DerSimonian-Laird random-effects meta-analyses to obtain the pooled value and the 95% confidence intervals.

RESULTS

We included 29 studies and 230,227 patients. The pooled duration of viable virus shedding of the SARS-CoV-2 Omicron variant in the upper respiratory tract was 5.16 days (95% CI: 4.18-6.14), and the average duration of PCR positivity was 10.82 days (95% CI: 10.23-11.42). The duration of viable virus shedding and PCR positivity of the SARS-CoV-2 Omicron variant in symptomatic patients was slightly higher than that in asymptomatic patients, but the difference was not significant (P >0.05).

CONCLUSION

The current study improves our understanding of the status of the literature on the duration of viable virus shedding and PCR positivity of Omicron in the upper respiratory tract. Our findings have implications for pandemic control strategies and infection control measures.