High proportion of low cycle threshold value as an early indicator of COVID-19 surge

Kinetics of Viral Shedding for Outbreak Surveillance of Emerging Infectious Diseases: Modeling Approach to SARS-CoV-2 Alpha and Omicron Infection

BACKGROUND

Previous studies have highlighted the importance of viral shedding using cycle threshold (Ct) values obtained via reverse transcription polymerase chain reaction to understand the epidemic trajectories of SARS-CoV-2 infections. However, it is rare to elucidate the transition kinetics of Ct values from the asymptomatic or presymptomatic phase to the symptomatic phase before recovery using individual repeated Ct values.

OBJECTIVE

This study proposes a novel Ct-enshrined compartment model to provide a series of quantitative measures for delineating the full trajectories of the dynamics of viral load from infection until recovery.

METHODS

This Ct-enshrined compartment model was constructed by leveraging Ct-classified states within and between presymptomatic and symptomatic compartments before recovery or death among people with infections. A series of recovery indices were developed to assess the net kinetic movement of Ct-up toward and Ct-down off recovery. The model was applied to (1) a small-scale community-acquired Alpha variant outbreak under the "zero-COVID-19" policy without vaccines in May 2021 and (2) a large-scale community-acquired Omicron variant outbreak with high booster vaccination rates following the lifting of the "zero-COVID-19" policy in April 2022 in Taiwan. The model used Bayesian Markov chain Monte Carlo methods with the Metropolis-Hastings algorithm for parameter estimation. Sensitivity analyses were conducted by varying Ct cutoff values to assess the robustness of the model.

RESULTS

The kinetic indicators revealed a marked difference in viral shedding dynamics between the Alpha and Omicron variants. The Alpha variant exhibited slower viral shedding and lower recovery rates, but the Omicron variant demonstrated swifter viral shedding and higher recovery rates. Specifically, the Alpha variant showed gradual Ct-up transitions and moderate recovery rates, yielding a presymptomatic recovery index slightly higher than 1 (1.10), whereas the Omicron variant had remarkable Ct-up transitions and significantly higher asymptomatic recovery rates, resulting in a presymptomatic recovery index much higher than 1 (152.5). Sensitivity analysis confirmed the robustness of the chosen Ct values of 18 and 25 across different recovery phases. Regarding the impact of vaccination, individuals without booster vaccination had a 19% higher presymptomatic incidence rate compared to those with booster vaccination. Breakthrough infections in boosted individuals initially showed similar Ct-up transition rates but higher rates in later stages compared to nonboosted individuals. Overall, booster vaccination improved recovery rates, particularly during the symptomatic phase, although recovery rates for persistent asymptomatic infection were similar regardless of vaccination status once the Ct level exceeded 25.

CONCLUSIONS

The study provides new insights into dynamic Ct transitions, with the notable finding that Ct-up transitions toward recovery outpaced Ct-down and symptom-surfacing transitions during the presymptomatic phase. The Ct-up against Ct-down transition varies with variants and vaccination status. The proposed Ct-enshrined compartment model is useful for the surveillance of emerging infectious diseases in the future to prevent community-acquired outbreaks.

Long-term trends in cycle threshold values: a comprehensive analysis of COVID-19 dynamics, viral load, and reproduction number in South Korea

Background

With the emergence of COVID-19 cases, governments quickly responded with aggressive testing, contact tracing, isolation and quarantine measures. South Korea's testing strategy primarily relied on real-time reverse-transcriptase polymerase chain reaction (real-time RT-PCR), focusing on cycle threshold (Ct) values, indicative of viral load, to determine COVID-19 positivity. This study examined the long-term time series distribution of Ct values measured in the same laboratory using a nationally standardized testing type and sampling method in South Korea. It aimed to link Ct values, new COVID-19 cases, and the reproduction number (Rt), setting the stage for using Ct values effectively.

Methods

This study analyzed nationally collected 296,347 samples Ct values from February 2020 to January 2022 and examined their associations with the number of new cases and Rt trends. The data were categorized into four COVID-19 periods for in-depth analysis. Statistical methods included time series trend analysis, local regression for smoothing, linear regression for association analysis, and calculation of correlation coefficients.

Results

The median Ct values across four COVID-19 periods decreased gradually from 31.71 in the initial period to 21.27 in the fourth period, indicating higher viral load. The comparison of trends between Ct values and the number of new cases revealed that the decline in Ct values preceded the surge in new cases, particularly evident during the initial stages when new cases did not undergo a significant increase. Also, during variant emergence and vaccination rollout, marked shifts in Ct values were observed. Results from linear regression analysis revealed a significant negative relationship between Ct values and new cases (β = -0.33, p < 0.001, R 2 = 0.67). This implies that as Ct values decrease, new case numbers increase.

Conclusion

This study demonstrates the potential of Ct values as early indicators for predicting confirmed COVID-19 cases during the initial stages of the epidemic and suggests their relevance in large-scale epidemic monitoring, even when case numbers are similar.

A simple PCR-based quick detection of the economically important oriental fruit fly, Bactrocera dorsalis (Hendel) from India

The oriental fruit fly, Bactrocera dorsalis (Hendel), is a significant economic and quarantine pest due to its polyphagous nature. The accurate identification of B. dorsalis is challenging at the egg, maggot, and pupal stages, due to lack of distinct morphological characters and its similarity to other fruit flies. Adult identification requires specialized taxonomist. Existing identification methods are laborious, time consuming, and expensive. Rapid and precise identification is crucial for timely management. By analyzing the variations in the mitochondrial cytochrome oxidase-1 gene sequence (Insect barcoding gene), we developed a species-specific primer (SSP), DorFP1/DorRP1, for accurate identification of B. dorsalis. The optimal annealing temperature for the SSP was determined to be 66°C, with no cross-amplification or primer-dimer formation observed. The SSP was validated with B. dorsalis specimens from various locations in northern and eastern India and tested for cross-specificity with six other economically significant fruit fly species in India. The primer specificity was further confirmed by the analysis of critical threshold (Ct) value from a qPCR assay. Sensitivity analysis showed the primer could detect template DNA concentrations as low as 1 pg/µl, though sensitivity decreased at lower concentrations. Sequencing of the SSP-amplified product revealed over >99% similarity with existing B. dorsalis sequences in the NCBI GenBank. The developed SSP reliably identifies B. dorsalis across all developmental stages and sexes. This assay is expected to significantly impact pest identification, phytosanitary measures, and eradication programs for B. dorsalis.

Kinetics of SARS-CoV-2 Viral Load in Hospitalized Patients

The rapid and accurate detection of infectious people is crucial in controlling outbreaks. The aim of this study was to evaluate the kinetics of the viral load expressed as Ct in COVID-19 hospitalized patients. Nasopharyngeal swab specimens were collected for RT-PCR testing. Forty-one subjects were recruited, of which 48.8% developed severe symptoms and 51.2% showed milder symptoms. The distribution of Ct values measured from the symptom onset showed that the kinetics of the viral load decreased with increasing time. A Ct of 25 (high viral load) was reached after a mean of 9.9 ± 4.8 days from the symptom onset, without a significant difference between patients with severe (10.9 ± 5.7 days) and milder (9.0 ± 3.9 days) symptoms. In 65.8% of cases, a high viral load was maintained for more than 7 days from the symptom onset, especially in patients with severe symptoms (70.6%). A Ct of 30 (moderate viral load) and of 38 (low viral load) were reached after a mean of 16.1 ± 8.1 and 28.5 ± 22.4 days from the symptom onset, respectively, with a significant difference between patients with severe (Ct = 30:17.9 ± 9.8 days; Ct = 38:34.6 ± 29.6 days) and milder (Ct = 30:14.3 ± 5.8 days; Ct = 38:22.7 ± 9.9 days) symptoms. These results provide an understanding of the viral kinetics of SARS-CoV-2 and have implications for pandemic control strategies and practices.

A pilot study on salivary HPV DNA detection to monitor active disease from patients with recurrent respiratory papillomatosis

PURPOSE

Recurrent respiratory papillomatosis (RRP) is a human papillomavirus (HPV)-related disease affecting the upper airway and saliva could be an important non-invasive sampling source for viral screening and clinical monitoring. We investigated whether HPV DNA could be detected in saliva (cellular pellets and supernatant) from RRP patients and influence on clinical manifestation of the disease.

MATERIALS AND METHODS

In this pilot study, saliva samples from 14 RRP patients were obtained in preoperative condition (n = 7) and in disease-free interval (DFI; n = 7). Healthy donors (n = 14) were also included. HPV DNA was investigated by polymerase chain reaction (PCR)-based assays.

RESULTS

From cellular pellets, HPV-positive saliva was only detected from preoperative collections (5/7; 71.4 %) and showed a mean cycle threshold (Ct) value of 24.33 (±1.25), whereas all patients in DFI were HPV-negative (Ct ≥ 32.16), revealing significant difference between these two clinical moments (p = 0.021). Patients in DFI and healthy donors showed similar Ct values. From saliva supernatant, detectable HPV cell-free DNA (cfDNA) occurred in 42.9 % (3/7) and 57.1 % (4/7) of preoperative collections using the commercial cfDNA kits from Norgen and Qiagen, respectively. Salivary cfDNA size distribution obtained by TapeStation analysis showed a predominant size range of 150 to 400 bp in both patients and healthy controls, corresponding to mononucleosomal and dinucleosomal fragments.

CONCLUSIONS

In conclusion, HPV DNA screening in saliva (both cellular pellets and cfDNA) may have clinical utility to monitor active disease of RRP patients.

Beyond the waves: Unraveling pandemic outcomes with genomic insights and immunity analysis - Evidence from 14 countries

OBJECTIVE

Although the World Health Organization and many governments have recategorized COVID-19 as a generally mild to moderately severe disease, consecutive pandemic waves driven by immune escape variants have underscored the need for timely and accurate prediction of the next outbreak. Nevertheless, little attention has been paid to translating genomic data and infection- and vaccine-induced immunity into direct estimates.

METHODS

We retrieved epidemiologic and genomic data shortly before pandemic waves across 14 developed countries from late 2021 to mid-2022 and examined associations between early-stage variant competition, infection- and vaccine-induced immunity, and the time intervals between wave peaks. We applied regression analysis and the generalized estimating equation method to construct an inferential model.

RESULTS

Each per cent increase in the proportion of a new variant was associated with a 1.0% reduction in interpeak intervals on average. Curvilinear associations between vaccine-induced immunity and outcome variables were observed, suggesting that reaching a critical vaccine distribution rate may decrease the caseload of the upcoming wave.

CONCLUSIONS

By leveraging readily accessible pre-outbreak genomic and epidemiologic data, our results not only substantiate the predictive potential of early variant fractions but also propose that immunity acquired through infection alone may not sufficiently mitigate transmission. Conversely, a rapid and widespread vaccination initiative appears to be correlated with a decrease in disease incidence.

Associations of SARS-CoV-2 cycle threshold values with age, gender, sample collection setting, and pandemic period

Cycle threshold (Ct) values in COVID-19 reverse-transcription polymerase chain reaction (RT-PCR) tests estimate the viral load in biological samples. Studies have investigated variables associated with SARS-CoV-2 viral load, aiming to identify factors associated with higher transmissibility. Using the results from tests performed between May/2020-July/2022 obtained from the database of a referent hospital in Sao Paulo, Brazil, we investigated associations between Ct values and patient's age, gender, sample collection setting and pandemic period according to the predominant SARS-CoV-2 variant locally. We also examined variations in Ct values, COVID-19 incidence, mortality, and vaccination coverage over time. The study sample included 42,741 tests. Gender was not significantly associated with Ct values. Age, sample collection setting and the pandemic period were significantly associated with Ct values even after adjustment to the multivariable model. Results showed lower Ct values in older groups, during the Gamma and Delta periods, and in samples collected in emergency units; and higher Ct values in children under 10 years old, home-based tests, during the Omicron period. We found evidence of a linear trend in the association between age and Ct values, with Ct values decreasing as age increases. We found no clear temporal associations between Ct values and local indicators of COVID-19 incidence, mortality, or vaccination between February/2020-November/2022. Our findings suggest that SARS-CoV-2 Ct values, a proxy for viral load and transmissibility, can be influenced by demographic and epidemiological variables.

Viral skin diseases in odontocete cetaceans: gross, histopathological, and molecular characterization of selected pathogens

Fifty-five skin lesions from 31 stranded cetaceans along the Canary coasts (2011-2021) were submitted to macroscopic, histological, and molecular analyses to confirm infection by cetacean poxvirus, herpesvirus and cetacean morbillivirus. They were macroscopically categorized into eight categories with respective subcategories according to their color, shape, size, and consistency. Cetacean poxvirus was detected in 54.54% of the skin lesions through real-time and conventional PCRs based on the DNA polymerase gene. Additionally, herpesvirus and morbillivirus were currently detected from 43.63 and 1.82% of the cutaneous lesions, respectively. Coinfection of poxvirus and herpesvirus was detected in nine of them (16.36%), which makes the present study the first to report coinfection by both pathogens in skin lesions in cetaceans. A plausible approach to histopathological characterization of poxvirus-and herpesvirus-positive skin lesions was established. Hyperkeratosis, acanthosis, ballooning degeneration, and intracytoplasmic inclusion bodies in vacuolized keratinocytes through the stratum spinosum were common findings in poxvirus skin lesions. Alphaherpesvirus was associated with a prominent acanthotic epidermis, moderate necrosis, multifocal dyskeratosis, and irregular keratinocytes with both cellular and nuclei pleomorphism. The common histopathological findings of both pathogens were observed in coinfection lesions. However, those associated with herpesvirus were considerably more remarkable. Relationships between molecular and microscopic findings were observed for the lesions that showed tattoo-like and tortuous patterns. Further multidisciplinary diagnostic studies of infected skin lesions are needed to understand the epidemiology of these emerging infectious diseases.

Proof of concept of the potential of a machine learning algorithm to extract new information from conventional SARS-CoV-2 rRT-PCR results

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been and remains one of the major challenges modern society has faced thus far. Over the past few months, large amounts of information have been collected that are only now beginning to be assimilated. In the present work, the existence of residual information in the massive numbers of rRT-PCRs that tested positive out of the almost half a million tests that were performed during the pandemic is investigated. This residual information is believed to be highly related to a pattern in the number of cycles that are necessary to detect positive samples as such. Thus, a database of more than 20,000 positive samples was collected, and two supervised classification algorithms (a support vector machine and a neural network) were trained to temporally locate each sample based solely and exclusively on the number of cycles determined in the rRT-PCR of each individual. Overall, this study suggests that there is valuable residual information in the rRT-PCR positive samples that can be used to identify patterns in the development of the SARS-CoV-2 pandemic. The successful application of supervised classification algorithms to detect these patterns demonstrates the potential of machine learning techniques to aid in understanding the spread of the virus and its variants.

Systematic Review on the Correlation Between SARS-CoV-2 Real-Time PCR Cycle Threshold Values and Epidemiological Trends

BACKGROUND

The ability to proactively predict the epidemiological dynamics of infectious diseases such as coronavirus disease 2019 (COVID-19) would facilitate efficient public health responses and may help guide patient management. Viral loads of infected people correlate with infectiousness and, therefore, could be used to predict future case rates.

AIM

In this systematic review, we determine whether there is a correlation between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) real-time reverse-transcription polymerase chain reaction (RT-PCR) cycle threshold (Ct) values (a proxy for viral load) and epidemiological trends in patients diagnosed with COVID-19, and whether Ct values are predictive of future cases.

METHODS

A PubMed search was conducted on August 22 2022, based on a search strategy of studies reporting correlations between SARS-CoV-2 Ct values and epidemiological trends.

RESULTS

Data from 16 studies were relevant for inclusion. RT-PCR Ct values were measured from national (n = 3), local (n = 7), single-unit (n = 5), or closed single-unit (n = 1) samples. All studies retrospectively examined the correlation between Ct values and epidemiological trends, and seven evaluated their prediction model prospectively. Five studies used the temporal reproduction number (Rt) as the measure of the population/epidemic growth rate. Eight studies reported a prediction time in the negative cross-correlation between Ct values and new daily cases, with seven reporting a prediction time of ~1-3 weeks, and one reporting 33 days.

CONCLUSION

Ct values are negatively correlated with epidemiological trends and may be useful in predicting subsequent peaks in variant waves of COVID-19 and other circulating pathogens.

Monitoring algorithm of hospitalized patients in a medical center with SARS-CoV-2 (Omicron variant) infection: clinical epidemiological surveillance and immunological assessment

Purpose

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major healthcare threat worldwide. Since it was first identified in November 2021, the Omicron (B.1.1.529) variant of SARS-CoV-2 has evolved into several lineages, including BA.1, BA.2-BA.4, and BA.5. SARS-CoV-2 variants might increase transmissibility, pathogenicity, and resistance to vaccine-induced immunity. Thus, the epidemiological surveillance of circulating lineages using variant phenotyping is essential. The aim of the current study was to characterize the clinical outcome of Omicron BA.2 infections among hospitalized COVID-19 patients and to perform an immunological assessment of such cases against SARS-CoV-2.

Patients and Methods

We evaluated the analytical and clinical performance of the BioIC SARS-CoV-2 immunoglobulin (Ig)M/IgG detection kit, which was used for detecting antibodies against SARS-CoV-2 in 257 patients infected with the Omicron variant.

Results

Poor prognosis was noted in 38 patients, including eight deaths in patients characterized by comorbidities predisposing them to severe COVID-19. The variant-of-concern (VOC) typing and serological analysis identified time-dependent epidemic trends of BA.2 variants emerging in the outbreak of the fourth wave in Taiwan. Of the 257 specimens analyzed, 108 (42%) and 24 (9.3%) were positive for anti-N IgM and IgG respectively.

Conclusion

The VOC typing of these samples allowed for the identification of epidemic trends by time intervals, including the B.1.1.529 variant replacing the B.1.617.2 variant. Moreover, antibody testing might serve as a complementary method for COVID-19 diagnosis. The combination of serological testing results with the reverse transcription-polymerase chain reaction cycle threshold value has potential value in disease prognosis, thereby aiding in epidemic investigations conducted by clinicians or the healthcare department.

Viral shedding patterns of symptomatic SARS-CoV-2 infections by periods of variant predominance and vaccination status in Gyeonggi Province, Korea

OBJECTIVES

We compared the viral cycle threshold (Ct) values of infected patients to better understand viral kinetics by vaccination status during different periods of variant predominance in Gyeonggi Province, Korea.

METHODS

We obtained case-specific data from the coronavirus disease 2019 (COVID-19) surveillance system, Gyeonggi in-depth epidemiological report system, and Health Insurance Review & Assessment Service from January 2020 to January 2022. We defined periods of variant predominance and explored Ct values by analyzing viral sequencing test results. Using a generalized additive model, we performed a nonlinear regression analysis to determine viral kinetics over time.

RESULTS

Cases in the Delta variant's period of predominance had higher viral shedding patterns than cases in other periods. The temporal change of viral shedding did not vary by vaccination status in the Omicron-predominant period, but viral shedding decreased in patients who had completed their third vaccination in the Delta-predominant period. During the Delta-predominant and Omicron-predominant periods, the time from symptom onset to peak viral shedding based on the E gene was approximately 2.4 days (95% confidence interval [CI], 2.2 to 2.5) and 2.1 days (95% CI, 2.0 to 2.1), respectively.

CONCLUSIONS

In one-time tests conducted to diagnose COVID-19 in a large population, although no adjustment for individual characteristics was conducted, it was confirmed that viral shedding differed by the predominant strain and vaccination history. These results show the value of utilizing hundreds of thousands of test data produced at COVID-19 screening test centers.

Dynamic characteristics of a COVID-19 outbreak in Nanjing, Jiangsu province, China

Objectives

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.617.2 (also named the Delta variant) was declared as a variant of concern by the World Health Organization (WHO). This study aimed to describe the outbreak that occurred in Nanjing city triggered by the Delta variant through the epidemiological parameters and to understand the evolving epidemiology of the Delta variant.

Methods

We collected the data of all COVID-19 cases during the outbreak from 20 July 2021 to 24 August 2021 and estimated the distribution of serial interval, basic and time-dependent reproduction numbers (R₀ and R_t), and household secondary attack rate (SAR). We also analyzed the cycle threshold (Ct) values of infections.

Results

A total of 235 cases have been confirmed. The mean value of serial interval was estimated to be 4.79 days with the Weibull distribution. The R₀ was 3.73 [95% confidence interval (CI), 2.66-5.15] as estimated by the exponential growth (EG) method. The R_t decreased from 4.36 on 20 July 2021 to below 1 on 1 August 2021 as estimated by the Bayesian approach. We estimated the household SAR as 27.35% (95% CI, 22.04-33.39%), and the median Ct value of open reading frame 1ab (ORF1ab) genes and nucleocapsid protein (N) genes as 25.25 [interquartile range (IQR), 20.53-29.50] and 23.85 (IQR, 18.70-28.70), respectively.

Conclusions

The Delta variant is more aggressive and transmissible than the original virus types, so continuous non-pharmaceutical interventions are still needed.

Variant-specific symptoms of COVID-19 in a study of 1,542,510 adults in England

Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study monitored the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell or taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and effects on daily activities will become increasingly important.

Oral dysbiosis and its linkage with SARS-CoV-2 infection

The human oral cavity harbours complex microbial communities with various commensal microorganisms that play pivotal roles in maintaining host health and immunity but can elicit local and systemic diseases. The role of commensal microorganisms in SARS-CoV-2 infection and disease susceptibility and enrichment of opportunistic pathobionts in the oral cavity is poorly understood. The present study aims to understand the altered landscape of the oral microbiome and mycobiome in SARS-CoV-2 infected patients (n = 30) and its correlation with risk factors compared to non-infected individuals (n = 24) using targeted amplicon sequencing. Diminution of species richness, an elevated abundance of opportunistic pathogens (Veillonella, Acinetobacter, Klebsiella, Prevotella, Gemella, and Streptococcus) and impaired metabolic pathways were observed in the COVID-19 patients. Similarly, altered oral mycobiome with enrichment of known respiratory disease causing pathogenic fungi were observed in the infected individuals. The data further suggested that reduction in immunomodulatory microorganisms lowers the protection of individuals from SARS-CoV-2. Linear discriminant analysis identified several differentially abundant taxa associated with risk factors (ageing and co-morbidities). We also observed distinct bacterial and fungal community structures of elderly infected patients compared to the younger age group members making them highly vulnerable to SARS-CoV-2 infection and disease severity. Furthermore, we also assessed the dynamics of the oral microbiome and mycobiome in symptomatic and asymptomatic patients, host types, co-morbidities, and viral load in the augmentation of specific pathobionts. Overall, the present study demonstrates the microbiome and mycobiome profiling of the COVID-19 infected individuals, the data further suggests that the SARS-CoV-2 infection triggers the prevalence of specific pathobiont.

Correlation of SARS-CoV-2 Viral Load and Clinical Evolution of Pediatric Patients in a General Hospital From Buenos Aires, Argentina

Background

SARS-CoV-2 infection is associated with a wide range of clinical manifestations and severity. Pediatric cases represent <10% of total cases, with a mortality rate below 1%. Data of correlation between SARS-CoV-2 viral load in respiratory samples and severity of disease in pediatric patients is scarce. The cycle threshold (CT) value for the detection of SARS-CoV-2 could be used as an indirect indicator of viral load in analyzed respiratory samples.

Objective

The aim of this study was to describe CT values and their correlation with clinical manifestations, epidemiology and laboratory parameters in pediatric patients with confirmed COVID-19.

Methods

In this observational, retrospective, analytic and single-center study we included patients under 15 years with confirmed COVID-19 by RT-PCR SARS-CoV-2 admitted to the Isidoro Iriarte Hospital (Argentina) between March 1st 2020 and April 30th 2021.

Results

485 patients were included, the distribution according to disease severity was: 84% (408 patients) presented mild disease, 12% (59 patients) moderate disease and 4% (18 patients) severe disease. Patients with moderate and severe illness had an increased hospitalization rate, prolonged hospitalization, higher frequency of comorbidities and oxygen and antibiotics use. CT values, that could be used as an indirect measure of viral load, was associated with severity of clinical manifestations and age under 12 months. No patient required admission to PICU nor mechanical ventilation. No deaths were registered.

Conclusions

In this study, the viral load of SARS-CoV-2 in respiratory samples, determined by the cycle threshold, was significantly correlated with moderate to severe cases and with age.

Performance evaluation of STANDARD Q COVID-19 Ag home test for the diagnosis of COVID-19 during early symptom onset

BACKGROUND

Surveillance and control of SARS-CoV-2 outbreak through gold standard detection, that is, real-time polymerase chain reaction (RT-PCR), become a great obstacle, especially in overwhelming outbreaks. In this study, we aimed to analyze the performance of rapid antigen home test (RAHT) as an alternative detection method compared with RT-PCR.

METHODS

In total, 79 COVID-19-positive and 217 COVID-19-negative patients confirmed by RT-PCR were enrolled in this study. A duration from symptom onset to COVID-19 confirmation of <5 days was considered a recruiting criterion for COVID-19-positive cases. A nasal cavity specimen was collected for the RAHT, and a nasopharyngeal swab specimen was collected for RT-PCR.

RESULTS

Sensitivity of the STANDARD Q COVID-19 Ag Home Test (SD Biosensor, Korea), compared with RT-PCR, was 94.94% (75/79) (95% [confidence interval] CI, 87.54%-98.60%), and specificity was 100%. Sensitivity was significantly higher in symptomatic patients (98.00%) than in asymptomatic (89.66%) patients (p-value = 0.03). There was no difference in sensitivity according to the duration of symptom onset to confirmation (100% for 0-2 days and 96.97% for 3-5 days, respectively) (p-value = 1.00). The RAHT detected all 51 COVID-19 patients whose Ct values were ≤25 (100%), whereas sensitivity was 73.33% (11/15) among patients with Ct values >25 (p-value = 0.01).

CONCLUSION

The RAHT showed an excellent sensitivity for COVID-19-confirmed cases, especially for those with symptoms. There was a decrease in sensitivity when the Ct value is over 25, indicating that RAHT screening may be useful during the early phase of symptom onset, when the viral numbers are higher and it is more transmissible.

Comparative Evaluation of Six SARS-CoV-2 Real-Time RT-PCR Diagnostic Approaches Shows Substantial Genomic Variant–Dependent Intra- and Inter-Test Variability, Poor Interchangeability of Cycle Threshold and Complementary Turn-Around Times

Several professional societies advise against using real-time Reverse-Transcription PCR (rtRT-PCR) cycle threshold (Ct) values to guide clinical decisions. We comparatively assessed the variability of Ct values generated by six diagnostic approaches by testing serial dilutions of well-characterized isolates of 10 clinically most relevant SARS-CoV-2 genomic variants: Alpha, Beta, Gamma, Delta, Eta, Iota, Omicron, A.27, B.1.258.17, and B.1 with D614G mutation. Comparison of three fully automated rtRT-PCR analyzers and a reference manual rtRT-PCR assay using RNA isolated with three different nucleic acid isolation instruments showed substantial inter-variant intra-test and intra-variant inter-test variability. Ct value differences were dependent on both the rtRT-PCR platform and SARS-CoV-2 genomic variant. Differences ranging from 2.0 to 8.4 Ct values were observed when testing equal concentrations of different SARS-CoV-2 variants. Results confirm that Ct values are an unreliable surrogate for viral load and should not be used as a proxy of infectivity and transmissibility, especially when different rtRT-PCR assays are used in parallel and multiple SARS-CoV-2 variants are circulating. A detailed turn-around time (TAT) comparative assessment showed substantially different TATs, but parallel use of different diagnostic approaches was beneficial and complementary, allowing release of results for more than 81% of non-priority samples within 8 h after admission.

An AIEgen/graphene oxide nanocomposite (AIEgen@GO)-based two-stage "turn-on" nucleic acid biosensor for rapid detection of SARS-CoV-2 viral sequence

The ongoing outbreak of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic has posed significant challenges in early viral diagnosis. Hence, it is urgently desirable to develop a rapid, inexpensive, and sensitive method to aid point-of-care SARS-CoV-2 detection. In this work, we report a highly sequence-specific biosensor based on nanocomposites with aggregation-induced emission luminogens (AIEgen)-labeled oligonucleotide probes on graphene oxide nanosheets (AIEgen@GO) for one step-detection of SARS-CoV-2-specific nucleic acid sequences (Orf1ab or N genes). A dual "turn-on" mechanism based on AIEgen@GO was established for viral nucleic acids detection. Here, the first-stage fluorescence recovery was due to dissociation of the AIEgen from GO surface in the presence of target viral nucleic acid, and the second-stage enhancement of AIE-based fluorescent signal was due to the formation of a nucleic acid duplex to restrict the intramolecular rotation of the AIEgen. Furthermore, the feasibility of our platform for diagnostic application was demonstrated by detecting SARS-CoV-2 virus plasmids containing both Orf1ab and N genes with rapid detection around 1 h and good sensitivity at pM level without amplification. Our platform shows great promise in assisting the initial rapid detection of the SARS-CoV-2 nucleic acid sequence before utilizing quantitative reverse transcription-polymerase chain reaction for second confirmation.

Effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines for reducing susceptibility to infection with the Delta variant (B.1.617.2) of SARS-CoV-2

Background

From January to May 2021 the alpha variant (B.1.1.7) of SARS-CoV-2 was the most commonly detected variant in the UK. Following this, the Delta variant (B.1.617.2) then became the predominant variant. The UK COVID-19 vaccination programme started on 8th December 2020. Prior to the Delta variant, most vaccine effectiveness studies focused on the alpha variant. We therefore aimed to estimate the effectiveness of the BNT162b2 (Pfizer-BioNTech) and the ChAdOx1 nCoV-19 (Oxford-AstraZeneca) vaccines in preventing symptomatic and asymptomatic infection with respect to the Delta variant in a UK setting.

Methods

We used anonymised public health record data linked to infection data (PCR) using the Combined Intelligence for Population Health Action resource. We then constructed an SIR epidemic model to explain SARS-CoV-2 infection data across the Cheshire and Merseyside region of the UK. Vaccines were assumed to be effective after 21 days for 1 dose and 14 days for 2 doses.

Results

We determined that the effectiveness of the Oxford-AstraZeneca vaccine in reducing susceptibility to infection is 39% (95% credible interval [34, 43]) and 64% (95% credible interval [61, 67]) for a single dose and a double dose respectively. For the Pfizer-BioNTech vaccine, the effectiveness is 20% (95% credible interval [10, 28]) and 84% (95% credible interval [82, 86]) for a single-dose and a double dose respectively.

Conclusion

Vaccine effectiveness for reducing susceptibility to SARS-CoV-2 infection shows noticeable improvement after receiving two doses of either vaccine. Findings also suggest that a full course of the Pfizer-BioNTech provides the optimal protection against infection with the Delta variant. This reinforces the need to complete the full course programme to maximise individual protection and reduce transmission.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07239-z.

Association of viral load with age, gender, disease severity and death in SARS-CoV-2 variants

In the current study, the relationship between viral load, demographic characteristics, and disease information in 1007(48.5%) patients with Delta variant (B.1.617.2), and 1070 (51.5%) patients with Alpha variant (B1.1.7) mutations was investigated. We found that there was a significant difference in viral load between patients who died from the Alpha variant and those who were discharged (p<0.05). Nevertheless, no significant difference was observed in patients with Delta variant. The viral load in patients who died from the Alpha variant was significantly higher than those who were discharged (p<0.05). The viral load was found to be higher in females in patients with Delta variant, whereas it was very close in males and females in patients with Alpha variant (p>0.05). No significant difference was detected between the cycle threshold values (Ct) and disease severity. In terms of the mean Ct values, statistical differences were observed in patients with Delta and Alpha variant. The Alpha variant was found to have a higher viral load than the Delta variant. Furthermore, Delta variant was found to be higher in the 40-year-old and under-age group than in the Alpha variant, whereas the Alpha variant was higher in the 40-year-old and older group. While the rate of moderate and severe patients in Alpha variant was found to be higher, the rate of mild survivors was found to be higher in Delta variant. In conclusion, The increase in vaccination prior to the appearance of the Delta variant in our region may have influenced the viral load and clinical status of the patients. This article is protected by copyright. All rights reserved.

High proportion of low cycle threshold value as an early indicator of COVID-19 surge

Many countries in the world are experiencing a recent surge in COVID‐19 cases. This is mainly attributed to the emergence of new SARS‐CoV‐2 variants. Genome sequencing is the only means to detect the evolving virus mutants and emerging variants. Cycle threshold values have an inverse relationship with viral load and lower Ct values are also found to be associated with increased infectivity. In this study, we propose to use Ct values as an early indicator for upcoming COVID‐19 waves. A retrospective cross‐sectional study was carried out to analyze the Ct values of positive samples reported during the first wave and second wave (April 2020–May 2021). Median Ct values of confirmatory genes were taken into consideration for comparison. Ct values below 25, >25–30, and >30 were categorized as high, moderate, and low viral load respectively. Our study found a significantly higher proportion of positive samples with a low Ct value (<25) across age groups and gender during the second wave of the COVID‐19 pandemic. A higher proportion of positive samples with a low Ct value (high viral load) may act as an early indicator of an upcoming surge.

A surge in COVID‐19 cases is predominantly due to emergence of new SARS‐CoV‐2 variants.

Cycle threshold values have an inverse relationship with viral load and also associated with infectivity.

Our study found a significantly higher proportion of positive samples with low Ct value (<25) across age groups and gender during the second wave of COVID‐19 pandemic.

Higher proportion of positive samples with low Ct value (high viral load) may act as an early indicator of an upcoming surge.