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1.
Journal of the International Aids Society ; 25:129-129, 2022.
Article in English | Web of Science | ID: covidwho-1980567
3.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326899

ABSTRACT

A new SARS-CoV-2 variant of concern, Omicron (B.1.1.529), has been identified based on genomic sequencing and epidemiological data in South Africa. Presumptive Omicron cases in South Africa have grown extremely rapidly, despite high prior exposure and moderate vaccination coverage. The available evidence suggests that Omicron spread is at least in part due to evasion of this immune protection, though Omicron may also exhibit higher intrinsic transmissibility. Using detailed laboratory and epidemiological data from South Africa, we estimate the constraints on these two characteristics of the new variant and their relationship. Our estimates and associated uncertainties provide essential information to inform projection and scenario modeling analyses, which are crucial planning tools for governments around the world.

4.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326897

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1–3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.

6.
Southern African Journal of Infectious Diseases ; 36(1), 2021.
Article in English | EMBASE | ID: covidwho-1348731

ABSTRACT

Background: Serology testing is an important ancillary diagnostic to the reverse transcriptase polymerase chain reaction (RT-PCR) test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to evaluate the performance of the Roche Elecsys™ chemiluminescent immunoassay (Rotkreuz, Switzerland), that detects antibodies against the SARS-CoV-2 nucleocapsid antigen, at an academic laboratory in South Africa. Methods: Serum samples were collected from 312 donors with confirmed positive SARS-CoV-2 RT-PCR tests, with approval from a large university’s human research ethics committee. Negative controls included samples stored prior to December 2019 and from patients who tested negative for SARS-CoV-2 on RT-PCR and were confirmed negative using multiple serology methods (n = 124). Samples were stored at –80 °C and analysed on a Roche cobas™ 602 autoanalyser. Results: Compared with RT-PCR, our evaluation revealed a specificity of 100% and overall sensitivity of 65.1%. The sensitivity in individuals > 14 days’ post-diagnosis was 72.6%, with the highest sensitivity 31–50 days’ post-diagnosis at 88.6%. Results were also compared with in-house serology tests that showed high agreement in majority of categories. Conclusions: The sensitivity at all-time points post-diagnosis was lower than reported in other studies, but sensitivity in appropriate cohorts approached 90% with a high specificity. The lower sensitivity at earlier time points or in individuals without symptomatology may indicate failure to produce antibodies, which was further supported by the comparison against in-house serology tests.

7.
Journal of Clinical Oncology ; 39(15 SUPPL), 2021.
Article in English | EMBASE | ID: covidwho-1339367

ABSTRACT

Background: Patients (pts) with cancer are at increased risk of SARS-CoV-2 infection and severe COVID-19 disease. Longitudinal followup is needed to characterize the severity, sequelae and outcomes in pts with cancer who develop COVID-19. Methods: NCCAPS is a prospective, longitudinal study (NCT04387656) aiming to accrue 2,000 pts with cancer undergoing active treatment or prior stem cell transplant for hematologic or solid tumor malignancy. Adult patients are eligible to enroll within 14 days of their first positive SARS-CoV-2 test;pediatric patients may also enroll retrospectively. Clinical data, patient-reported outcomes, blood specimens, and imaging are collected for up to 2 years. This abstract provides initial baseline and 2-month follow-up data. Results: As of Jan 22, 2021, 585 pts (552 adults and 33 pediatric pts) had complete baseline data and of these pts, 215 adults had 2 months of complete follow-up data. 23.4% of adults and 42.4% of pediatric pts were of nonWhite race and/or Hispanic/Latinx ethnicity. The most common cancer diagnoses were breast (19.6%), lung (9.9%) and multiple myeloma (8.9%) in adults and acute leukemia (AML/ALL;63.6%) in children. The most recent treatment was chemotherapy in 38.2%, immunotherapy in 9.6%, and radiation in 5.4%. Median time from positive SARS-CoV-2 test to study enrollment was 10.5 days in adults and 18 days in pediatric pts. Preliminary analysis of plasma cytokines will be presented. At enrollment, 84.6% of adults had COVID-19 symptoms. 55.9% reported symptoms 2 weeks after their positive SARSCoV-2 test;this fell to 39.0% at 1 month and 28.8% at 2 months (see Table). Of the 215 adults with complete data at 2 months, sequelae included pulmonary (n=22, 10%), cardiovascular (n=12, 6%) thromboembolic (n=9, 4%), bleeding (n=9, 4%) and gastrointestinal (n=11, 5%). 144 (67%) reported at least one cancer treatment disruption in the first 2 months, most commonly delayed therapy (n=98;46%).Of the 348 adults with baseline data and SARS-CoV-2 test date prior to Nov 23, 2020, 6.3% had died (median time from SARS-CoV-2 test to death: 27 days), and 22.1% reported at least one hospitalization for COVID-19. No deaths were reported in the pediatric population. Conclusion: Cancer pts with COVID-19 report ongoing symptoms after acute infection and a substantial number develop sequelae. Cancer treatment disruptions are common in the initial months following SARS-CoV-2 infection. Longer follow-up will inform whether these treatment disruptions are associated with adverse outcomes. (Table Presented).

8.
Journal of Clinical Oncology ; 39(15 SUPPL), 2021.
Article in English | EMBASE | ID: covidwho-1339185

ABSTRACT

Background: The National Cancer Institute supports several national trial networks which responded rapidly to the COVID-19 pandemic to overcome operational barriers to clinical cancer research. The National Clinical Trials Network (NCTN) focuses on late phase treatment trials, while the Experimental Therapeutics Clinical Trials Network (ETCTN) conducts early phase treatment trials. We report findings on the experience and adaptations of these networks during COVID-19. Methods: Using 2019 and 2020 accrual data, we analyzed changes in accrual levels and demographics. We also evaluated changes in trial activation numbers and timelines. In July 2020, we surveyed 255 investigators from academic and community sites to assess changes in research practices and get feedback on modified processes implemented by NCI to address trial conduct during the pandemic. Results: Accrual across the NCTN and ETCTN fell significantly in midMarch 2020, dropping from a weekly average of 307 patients in February to 169 the week of March 23-29. Accrual began to recover in June and July but did not return to pre-pandemic levels until September. Accrual in November and December 2020 followed the patterns seen in 2019, with short-term drops around major holidays. Non-White participants were enrolled to NCTN and ETCTN trials at similar monthly rates throughout 2019 and 2020, with slightly higher overall enrollment in 2020 (23.7% vs. 22.7%). New trials continued to be developed and activated throughout 2020. Between 2017 and 2019, an average of 71 trials were activated per year (NCTN = 46, ETCTN = 25), compared to 84 activated in 2020 (NCTN = 58, ETCTN = 26). The average time to trial activation was similar or slightly longer in 2020 compared to 2019. The investigator survey yielded 111 responses (43.5% response rate). 43% of respondents' sites paused enrollment to phase 1 trials during the pandemic, compared to 18% for phase 3 trials. Many sites temporarily stopped opening new trials and processing specimens. Sites were more likely to keep enrolling to trials offering clear potential benefit and pause complex trials that required more patient contact. Respondents attributed some of the decline in accrual to a reduction in overall patient volume, increased patient concerns, and reduced research staff on site. Respondents were asked to rate the usefulness of modified trial processes NCI put in place during the pandemic. Telehealth was rated most useful (avg. 4.6/5), followed by shipping oral IND agents to enrolled patients (4.5/5), remote informed consent (4.2/5), coordinating care with local providers (3.9/5), and remote auditing (3.7/5). Conclusions: The cancer trials community has an opportunity to learn from working through the challenges of COVID-19. NCI will seek to continue and expand on modifications to clinical trial processes that have the potential to improve operational efficiency, reduce cost, and help bring trials to more patients.

10.
South African Medical Journal ; 111(1):10-13, 2021.
Article in English | EMBASE | ID: covidwho-994168

ABSTRACT

Persistence of symptoms or development of new symptoms relating to SARS-CoV-2 infection late in the course of COVID-19 is an increasingly recognised problem facing the globally infected population and its health systems. 'Long-COVID' or 'COVID long-haulers' generally describes those persons with COVID-19 who experience symptoms for >28 days after diagnosis, whether laboratory confirmed or clinical. Symptoms are as markedly heterogeneous as seen in acute COVID-19 and may be constant, fluctuate, or appear and be replaced by symptoms relating to other systems with varying frequency. Such multisystem involvement requires a holistic approach to management of long-COVID, and descriptions of cohorts from low- and middle-income countries are eagerly awaited. Although many persons with long-COVID will be managed in primary care, others will require greater input from rehabilitation medicine experts. For both eventualities, planning is urgently required to ensure that the South African public health service is ready and able to respond.

12.
S Afr Med J ; 110(9): 842-845, 2020 07 17.
Article in English | MEDLINE | ID: covidwho-743542

ABSTRACT

Antibody tests for the novel coronavirus, SARS-CoV2, have been developed both as rapid diagnostic assays and for high-throughput formal serology platforms. Although these tests may be a useful adjunct to a diagnostic strategy, they have a number of limitations. Because of the antibody and viral dynamics of the coronavirus, their sensitivity can be variable, especially at early time points after symptom onset. Additional data are required on the performance of the tests in the South African population, especially with regard to development and persistence of antibody responses and whether antibodies are protective against reinfection. These tests may, however, be useful in guiding the public health response, providing data for research (including seroprevalence surveys and vaccine initiatives) and development of therapeutic strategies.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections , Immunologic Tests/methods , Pandemics , Pneumonia, Viral , Serologic Tests/methods , Betacoronavirus/genetics , Betacoronavirus/immunology , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Humans , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Pneumonia, Viral/immunology , Reproducibility of Results , SARS-CoV-2 , Sensitivity and Specificity , Seroepidemiologic Studies , South Africa/epidemiology
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