ABSTRACT
The ARTIC protocol uses a multiplexed PCR approach with two primer pools tiling the entire SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genome. Primer pool updates are necessary for accurate amplicon sequencing of evolving SARS-CoV-2 variants with novel mutations. The suitability of the ARTIC V4 and updated V4.1 primer scheme was assessed using whole genome sequencing of Omicron from clinical samples using Oxford Nanopore Technology. Analysis of Omicron BA.1 genomes revealed that 93.22â% of clinical samples generated improved genome coverage at 50× read depth with V4.1 primers when compared to V4 primers. Additionally, the V4.1 primers improved coverage of BA.1 across amplicons 76 and 88, which resulted in the detection of the variant-defining mutations G22898A, A26530G and C26577G. The Omicron BA.2 sub-variant (VUI-22JAN-01) replaced BA.1 as the dominant variant by March 2022, and analysis of 168 clinical samples showed reduced coverage across amplicons 15 and 75. Upon further interrogation of primer binding sites, a mutation at C4321T [present in 163/168 (97â%) of samples] was identified as a possible cause of complete dropout of amplicon 15. Furthermore, two mutations were identified within the primer binding regions for amplicon 75: A22786C (present in 90â% of samples) and C22792T (present in 12.5â% of samples). Together, these mutations may result in reduced coverage of amplicon 75, and further primer updates would allow the identification of the two BA.2-defining mutations present in amplicon 75: A22688G and T22679C. This work highlights the need for ongoing surveillance of primer matches as circulating variants evolve and change.
Subject(s)
COVID-19 , Humans , SARS-CoV-2/genetics , Mutation , Binding SitesABSTRACT
COVID-19 emerged in China in late 2019 and quickly spread worldwide. The severe immunomodulation and depletion of lymphocytes caused by the virus and its therapy led to an increase in the incidence of superinfections. COVID-19-associated pulmonary aspergillosis (CAPA) is a new entity with increasing incidence and high associated mortality. We present the case of a 68-year-old patient admitted to our ward after recovering from severe COVID-19 pneumonia. Due to worsening of her clinical condition, chest computed tomography was performed and a lung abscess was documented with the identification of Aspergillus niger. Despite therapy with voriconazole, the patient's condition deteriorated, culminating in her death. LEARNING POINTS: COVID-19-associated pulmonary aspergillosis (CAPA) is a new entity with an increasing incidence.It is a serious and life-threatening complication in patients with severe COVID-19 even in the absence of the classic risk factors for invasive pulmonary aspergillosis.Clinical suspicion is crucial since a timely diagnosis and treatment have a major impact on prognosis.
ABSTRACT
At the time of the first wave of the COVID-19 pandemic, patients with cancer were considered to be at high risk of serious illness and had a higher exposure risk since they needed frequent and nondeferrable hospital visits. Serological tests were not routinely used, and seroprevalence in this population was unknown. A single-center, cross-sectional study was developed to determine the seroprevalence of anti-SARS-CoV-2 antibodies (Abs) in patients with cancer undergoing systemic antineoplastic treatment. One hundred patients were consecutively recruited in a two-week period (6th-20th May 2020), and serum samples were tested for the presence of immunoglobulin M (IgM) and immunoglobulin G (IgG) Abs directed against both spike (S) and nucleocapsid (N) SARS-CoV-2 proteins in two distinct time points (at recruitment and 4-8 weeks later). IgG-positive results were subject to confirmation, in the same serum sample, using two distinct assays. At the time of the first study visit, no patient had a previously confirmed diagnosis of COVID-19, one reported previous contact with a COVID-19 patient, and all had a baseline SARS-CoV-2-negative RT-PCR. Two patients tested positive for SARS-CoV-2 IgG in the first study visit, which was not confirmed in either of the two confirmatory assays. Seventy-two patients were tested at the second study visit, all with negative IgG tests. IgM was persistently positive at both study visits in one patient and was positive in another patient at the second study visit, both with negative RT-PCR and serum IgG. No patient tested positive for RT-PCR within the study timeframe. No evidence of prior or acute SARS-CoV-2 infection was documented in this cohort of patients with cancer undergoing systemic treatment, and no additional exposure risk was documented compared to general population seroprevalence studies. The study was inconclusive regarding the role of SARS-CoV-2 serology in patients with cancer in the early phase of the pandemic. This study did show that, with adherence to recommended preventive measures, it was safe to maintain systemic cancer therapy.