SARS-CoV-2 transmission by asymptomatic healthcare workers positive to screening swab: an Italian study.

BACKGROUND: SARS-CoV-2 spreads primarily through respiratory droplets of symptomatic individuals. With respect to asymptomatic individuals, there are conflicting results in the literature and a lack of studies specifically examining transmission in healthcare settings. METHODS: The aim of this retrospective study, conducted in a northeastern Italian region, was to estimate the contagiousness of asymptomatic healthcare workers (HCWs) who tested positive for SARS-CoV-2. Asymptomatic HCWs who tested positive for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (rRT-PCR) at a regular screening nasopharyngeal or oropharyngeal swab between 1 February 2020 and 15 September 2020 were considered index cases. Contacts who were at high risk of infection and had follow-up swabs were included. Contacts were considered infected if they had a positive follow-up swab and/or symptoms associated with COVID-19 confirmed by a positive test within 14 days of exposure. Information was taken from records previously collected to identify contacts. Infectivity was estimated using the attack rate (AR) with a 95% confidence interval (95% CI). RESULTS: Thirty-eight asymptomatic HCWs who were positive at the screening swab and 778 contacts were identified. Contacts included 63.8% of colleagues, 25.6% of patients, 7.7% of family members and 3.0% of other contacts. Seven contacts tested positive for SARS-CoV-2 (AR: 0.91%, 95% CI: 0.89-0.93). Five of them were family members (AR: 8.3%), one was a colleague (0.2%) and one was a contact of other type (4.2%). CONCLUSIONS: Viral spread by asymptomatic HCWs was less than in other settings. Identification of risk factors for transmission and reliable indicators of infectivity would be important to prioritize preventive measures.

Local occurrence and fast spread of B.1.1.7 lineage: A glimpse into Friuli Venezia Giulia.

In-depth study of the entire SARS-CoV-2 genome has uncovered many mutations, which have replaced the lineage that characterized the first wave of infections all around the world. In December 2020, the outbreak of variant of concern (VOC) 202012/01 (lineage B.1.1.7) in the United Kingdom defined a turning point during the pandemic, immediately posing a worldwide threat on the Covid-19 vaccination campaign. Here, we reported the evolution of B.1.1.7 lineage-related infections, analyzing samples collected from January 1st 2021, until April 15th 2021, in Friuli Venezia Giulia, a northeastern region of Italy. A cohort of 1508 nasopharyngeal swabs was analyzed by High Resolution Melting (HRM) and 479 randomly selected samples underwent Next Generation Sequencing analysis (NGS), uncovering a steady and continuous accumulation of B.1.1.7 lineage-related specimens, joined by sporadic cases of other known lineages (i.e. harboring the Spike glycoprotein p.E484K mutation). All the SARS-CoV-2 genome has been analyzed in order to highlight all the rare mutations that may eventually result in a new variant of interest. This work suggests that a thorough monitoring of the SARS-CoV-2 genome by NGS is essential to contain any new variant that could jeopardize all the efforts that have been made so far to resolve the emergence of the pandemic.

High Viral Load in Upper Respiratory Specimens of Persons With SARS-CoV-2 Infection in a Northern Italian Area.

BACKGROUND: An assessment of viral load in biologic specimens of subjects with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may have important implications for public health planning. The aim of this study was to estimate the prevalence of high viral load in upper respiratory specimens of patients with SARS-CoV-2 infection during the first Italian wave (spring) and at the beginning of the second wave (summer) of the COVID-19 epidemic, through the measurement of cycle threshold (Ct) values from real-time reverse transcription-polymerase chain reaction tests conducted at the University Hospital of Udine, Italy, serving 530,000 inhabitants. METHODS: We compared the prevalence of high viral load, defined as Ct ≤ 20 at the first positive test result, in 262 subjects from the spring and 453 from the summer period. Logistic regression was used to account for potential confounding due to sex, age, and severity of infection. RESULTS: In the spring, 9.2% of subjects had Ct ≤ 20 versus 21.4% in the summer. After adjusting for confounders, the likelihood of having high viral load was 2.9 times higher in the summer than in the spring (95% confidence interval, 1.7-5.0). CONCLUSIONS: In this Italian area, more COVID-19 patients had high viral load in the spring epidemic wave than at the beginning of the second, during the summer. Cycle threshold values may represent useful information to monitor viral load at a population level in subjects with SARS-CoV-2 infection.

The Fall in Antibody Response to SARS-CoV-2: a Longitudinal Study of Asymptomatic to Critically Ill Patients Up to 10 Months after Recovery.

The aim of this study was to assess the long-term dynamics and factors associated with the serological response against the severe acute respiratory syndrome coronavirus 2 after primary infection. A prospective longitudinal study was conducted with monthly serological follow-up during the first 4 months, and then at 6, 8, and 10 months after the disease onset of all recovered adult in- and outpatients with coronavirus disease 2019 (COVID-19) attending Udine Hospital (Italy) during the first wave (from March to May 2020). A total of 546 individuals were included (289 female, mean age 53.1 years), mostly with mild COVID-19 (370, 68.3%). Patients were followed for a median of 302 days (interquartile range, 186 to 311). The overall seroconversion rate within 2 months was 32% for IgM and 90% for IgG. Seroreversion was observed in 90% of patients for IgM at 4 months and in 47% for IgG at 10 months. Older age, number of symptoms at acute onset, and severity of acute COVID-19 were all independent predictors of long-term immunity both for IgM (ß, linear regression coefficient, 1.10, P = 0.001; ß 5.15 P = 0.014; ß 43.84 P = 0.021, respectively) and for IgG (ß 1.43 P < 0.001; ß 10.46 P < 0.001; ß 46.79 P < 0.001, respectively), whereas the initial IgG peak was associated only with IgG duration (ß 1.12, P < 0.001). IgM antibodies disappeared at 4 months, and IgG antibodies declined in about half of patients 10 months after acute COVID-19. These effects varied depending on the intensity of the initial antibody response, age, and burden of acute COVID-19.

Validation of a One-Step Reverse Transcription-Droplet Digital PCR (RT-ddPCR) Approach to Detect and Quantify SARS-CoV-2 RNA in Nasopharyngeal Swabs.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. Quantitative reverse transcription-PCR (RT-qPCR) is, to this day, the preferred methodology for viral RNA detection, even if not without problems. To overcome some of the limitations still existing for the detection and quantification of nucleic acids in various applications, the use of one-step reverse transcription-droplet digital PCR (RT-ddPCR) has been established. The purpose of this study was, then, to evaluate the efficacy of ddPCR for the detection of SARS-CoV-2 RNA in nasopharyngeal swabs, optimizing the detection of low-viral load-burdened samples. METHODS: The RT-ddPCR workflow was validated for sensitivity, specificity, linearity, reproducibility, and precision using samples from 90 COVID-19-infected patients referred to the Department of Laboratory Medicine of the University Hospital of Udine (Italy). RESULTS: The present study shows that RT-ddPCR allows the detection of as low as 10.3 copies of a SARS-COV-2 E-gene per sample with a higher level of accuracy and precision, especially at low concentration. CONCLUSION: During the postpeak phase of the SARS-CoV-2 pandemic, it is essential to rely on a highly robust molecular biology method to identify infected subjects, whether they have symptoms or not, in order to prepare appropriate containment measures.

A Streamlined Approach to Rapidly Detect SARS-CoV-2 Infection Avoiding RNA Extraction: Workflow Validation.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has rapidly spread worldwide from the beginning of 2020. The presence of viral RNA in samples by nucleic acid (NA) molecular analysis is the only method available to diagnose COVID-19 disease and to assess patients' viral load. Since the demand for laboratory reagents has increased, there has been a worldwide shortage of RNA extraction kits. We, therefore, developed a fast and cost-effective viral genome isolation method that, combined with quantitative RT-PCR assay, detects SARS-CoV-2 RNA in patient samples. The method relies on the addition of Proteinase K followed by a controlled heat-shock incubation and, then, E gene evaluation by RT-qPCR. It was validated for sensitivity, specificity, linearity, reproducibility, and precision. It detects as low as 10 viral copies/sample, is rapid, and has been characterized in 60 COVID-19-infected patients. Compared to automated extraction methods, our pretreatment guarantees the same positivity rate with the advantage of shortening the time of the analysis and reducing its cost. This is a rapid workflow meant to aid the healthcare system in the rapid identification of infected patients, such as during a pathogen-related outbreak. For its intrinsic characteristics, this workflow is suitable for large-scale screenings.

Frequency of nasopharyngeal swab collection and positivity for SARS-CoV-2 infection in the population of the Italian province of Udine with and without chronic conditions.

Severity of SARS-CoV-2 infection is associated with comorbidities. However, no information is available on the frequency of nasopharyngeal swab collection and positivity depending on comorbidities. Using a cross-sectional design, we assessed the prevalence of SARS-CoV-2 tests and of positivity in the general population of the 530,000-inhabitant Italian province of Udine and in subgroups affected by chronic conditions in the first weeks of SARS-CoV-2 epidemic. Anonymous health databases were used as source of information to identify persons with 14 chronic conditions. From laboratory records we assessed the likelihood of real-time reverse-transcriptase polymerase chain reaction for SARS-CoV-2 and the frequency of positivity from February 29 to April 19, 2020, i.e., 7 weeks from the first case detected in the study area. Sex and age-stratified proportions were calculated in comorbidity subgroups. Multivariate regression was used to adjust for confounders. In the province, 236,623 persons had ≥1 chronic condition; 869 had positive tests. Persons with comorbidities were tested more than the others. However, most chronic conditions were not significantly associated with the prevalence of positivity, except psychiatric and neurological diseases and diabetes. In conclusion, despite more frequent testing, patients with most chronic diseases where equally likely to be diagnosed with SARS-CoV-2 as the general population. Chronic patients should adhere to general recommendations for preventing SARS-CoV-2 infection, but ad hoc restrictions do not seem necessary.