Background : South Africa was the African country with the most recorded cases of SARS-CoV-2 during 2020, experiencing 2 waves of infection During the first wave, diagnostics were largely based on reverse transcription-linked PCR (RT-PCR) The Abbott PanBio antigen test was deployed during the 2nd wave which may have been driven by emergence of the B 1 351 variant At the time of evaluation in mid-November 2020, B 1 351 was the dominant circulating virus in Nelson Mandela Bay, in the Eastern Cape Province Methods : Used PanBio antigen swabs (collected from patients with genetically characterised virus) were first validated as suitable for PCR A prospective study was then undertaken to evaluate assay performance in the field Testing was conducted at mobile community testing centres on 677 ambulant patients Used swabs were kept and tested by RT-PCR Results : During initial validation, used swabs in proprietary lysis buffer were found to be suitable for PCR and secondly, the PB assay reliably detected patients infected with B 1 351 In the field study, of 146 RT-PCR positive individuals, 101 were RTD positive in the clinic The RTD had a sensitivity of 69 2% (95%CI 61 4, 75 8) and specificity of 99 0% (95%CI 98 8, 99 3) Sensitivity was dependent on the amount of viral RNA in clinical samples, as reflected by the PCR cycle threshold (CT) value Conclusions : The assay reliably detected B 1 351 infections in ambulatory ill patients during initial validation and in field testing In the field, assay sensitivity was >90% in patients with high viral loads who are expected to be most infectious Negative and positive predictive values were also >90%

Field performance evaluation of the PanBio rapid SARS-CoV-2 antigen assay in an epidemic driven by the B.1.351 variant in the Eastern Cape, South Africa

Abstract A plethora of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic tests are available, each with different performance specifications, detection methods, and targets. This narrative review aims to summarize the diagnostic technologies available and how they are best selected to tackle SARS-CoV-2 infection as the pandemic evolves. Seven key settings have been identified where diagnostic tests are being deployed: symptomatic individuals presenting for diagnostic testing and/or treatment of COVID-19 symptoms; asymptomatic individuals accessing healthcare for planned non-COVID-19-related reasons; patients needing to access emergency care (symptom status unknown); patients being discharged from healthcare following hospitalization for COVID-19; healthy individuals in both single event settings (e.g. airports, restaurants, hotels, concerts, and sporting events) and repeat access settings (e.g. workplaces, schools, and universities); and vaccinated individuals. While molecular diagnostics remain central to SARS-CoV-2 testing strategies, we have offered some discussion on the considerations for when other tools and technologies may be useful, when centralized/point-of-care testing is appropriate, and how the various additional diagnostics can be deployed in differently resourced settings. As the pandemic evolves, molecular testing remains important for definitive diagnosis, but increasingly widespread point-of-care testing is essential to the re-opening of society.

https://www.tandfonline.com/doi/pdf/10.1080/10408363.2022.2045250?needAccess=true

Choice of SARS-CoV-2 diagnostic test: challenges and key considerations for the future

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. SUMMARY Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The global COVID-19 pandemic continues to threaten the lives of hundreds of millions of people, with a severe negative impact on the global economy. Although several COVID-19 vaccines are currently being administered, none of them is 100% effective. Moreover, SARS-CoV-2 variants remain an important worldwide public health issue. Hence, the accelerated development of efficacious antiviral agents is urgently needed. Coronavirus depends on various host cell factors for replication. An ongoing research objective is the identification of host factors that could be exploited as targets for drugs and compounds effective against SARS-CoV-2. In the present review, we discuss the molecular mechanisms of SARS-CoV-2 and related coronaviruses, focusing on the host factors or pathways involved in SARS-CoV-2 replication that have been identified by genome-wide CRISPR screening.

Molecular Virology of SARS-CoV-2 and Related Coronaviruses

The coronavirus disease 2019 (Covid-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and presents a global health emergency that needs urgent intervention Viruses constantly change through mutation, and new variants of a virus are expected to occur over time In the United Kingdom (UK), a new variant called B117 has emerged with an unusually large number of mutations The aim of this study is to evaluate the level of protection of sera from 12 patients infected and later healed in Apulia Region (Italy) with Covid-19 between March and November 2020, when the English variant was not circulating in this territory yet, against the new VOC 202012/01 variant by seroneutralization assay The sera of patients had already been tested before, using a virus belonging to the lineage B1 and showed an antibody neutralizing titer ranging between 1:160 and 1:320 All the 12 sera donors confirmed the same titers of neutralizing antibodies obtained with a strain belonging to the lineage B117 (VOC 202012/01) These data indicate that antibodies produced in subjects infected with variants of Sars-CoV-2 strain before the appearance of the English one, seem to have a neutralizing power also against this variant

VOC 202012/01 Variant Is Effectively Neutralized by Antibodies Produced by Patients Infected before Its Diffusion in Italy.

The reliability of saliva for the detection of SARS-CoV-2 in symptomatic and asymptomatic patients: Insights on the diagnostic performance and utility for COVID-19 screening.

Background. The highly variable manifestation of the COVID-19 disease, from completely asymptomatic to fatal, is both a clinical and a public health issue. The criteria for discharge of hospitalized patients have been based so far on the negative result of Real-Time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) tests, but the persistence of viral fragments may exceed that of the integral virus by weeks. The aim of our study was to verify the clearance of the virus at viral culture in patients hospitalized for COVID-19 that have clinically recovered but are still positive on nasopharyngeal swab. Methods. The study was conducted in hospitalized patients with positive RT-PCR on nasopharyngeal swab. Patients included were from asymptomatic to severe cases and performed nasopharyngeal control swabbing on day 14 for asymptomatic patient or at least three days after remission of symptoms. RT-PCR positive specimens were sent to a biosafety level 3 laboratory for viral culture. Results. We performed a combined analysis of RT-PCR and a highly sensitive in vitro culture from 84 samples of hospitalized patients. The average age was 46 ± 20.29, and 40.5% of the subjects had radiologically confirmed pneumonia, with average PaO2 of 72.35 ± 12.12and P/F ratio of 315 ± 83.15. Ct values for the N gene were lower in the first swab than in the control one (p < 0.001). The samples from 83 patients were negative at viral culture, and RT-PCR on the respective supernatants always confirmed the absence of viral growth. Conclusions. Our preliminary results demonstrate that patients clinically recovered for at least three days show the viral clearance at viral culture, and presumably they continued to not be contagious.

https://www.mdpi.com/2077-0383/10/2/309/pdf

Real Time PCR and Culture-Based Virus Isolation Test in Clinically Recovered Patients: Is the Subject Still Infectious for SARS-CoV2?

OBJECTIVES: The present study aimed to explore differences in COVID-19 outcomes between male and female cases in the Apulian District of Foggia, Italy. DESIGN AND SETTING: We performed a retrospective epidemiological study among all COVID-19 confirmed cases that occurred in the Apulian District of Foggia from 29 February to 30 June 2020. The surveillance data from a regional registry (GIAVA-COVID) were used. MAIN OUTCOMES: The main outcome measures were the proportion of hospitalisations, virus clearance and the case fatality rate. RESULTS: A total of 1175 cases (50.7% female; median age: 55 years) were identified among 55 131 tests performed. The proportion of hospitalisation with COVID-19 diagnosis was 45.4% in men versus 37.9% in women (p<0.01), while the average length of stay in hospitals was 31.3±14.6 days in women versus 26.8±14.4 days in men (p<0.01). The proportion of cases who achieved virus clearance was higher in women (84.2%; days to clearance: 28.0±12.1) than in men (79.3%; days to clearance: 29.4±12.9; p<0.05). Men were associated with a significantly higher risk of dying from COVID-19 than women (case fatality rate 16.1% vs 10.4%; p<0.01). The mean time, from diagnosis to death, was 14.5±14.4 days in women compared with 10.6±10.7 days in men (p<0.01). The male sex, age ≥55 years and presence of at least one underlying comorbidity significantly raised the risk of hospitalisation, persistent infection and death (p<0.05). CONCLUSIONS: This study suggests that more attention should be paid to sex as a variable for the interpretation of COVID-19 data. Sex-disaggregated data will help clinicians to make appropriate patient-tailored medical decisions.

https://bmjopen.bmj.com/content/bmjopen/11/10/e051506.full.pdf

Sex and gender differences in COVID-19: an Italian local register-based study.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the first coronavirus that has caused a pandemic. Assessing the prevalence of anti-SARS-CoV-2 in healthcare worker groups offers a unique opportunity to study the correlation between seroconversion and immunization because of their occupational exposure and a higher risk of contagion. The study enrolled 3242 asymptomatic employees of "Policlinico Riuniti", Foggia. After the first screening, we collected sequential serum samples for up to 23 weeks from the same subjects. In order to perform a longitudinal follow-up study and get information about the titration of IgG levels, we analyzed data from subjects (33) with at least two consecutive serological IgG-positive tests; 62 (1.9%; 95% CI: 1.4-2.3) tested positive for at least one anti-SARS-CoV-2 antibody. The seroprevalence was lower in the high-risk group 1.4% (6/428; 95% CI: 0.5-2.6) vs. the intermediate-risk group 2.0% (55/2736; 95% CI: 1.5-2.5). Overall, within eight weeks, we detected a mean reduction of -17% in IgG levels. Our data suggest a reduction of about 9.27 AU/mL every week (R2 = 0.35, p = 0.0003). This study revealed the prevalence of SARS-CoV-2 antibodies among Foggia's hospital healthcare staff (1.9%). Moreover, the IgG level reduction suggests that the serological response fades fast in asymptomatic infections.

https://www.mdpi.com/1660-4601/17/24/9324/pdf

Vitangelo Dattoli

Papers

Real Time PCR and Culture-Based Virus Isolation Test in Clinically Recovered Patients: Is the Subject Still Infectious for SARS-CoV2?

Sex and gender differences in COVID-19: an Italian local register-based study.

SARS-COV-2 Serological Profile in Healthcare Professionals of a Southern Italy Hospital.