ABSTRACT
Introduction- The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods- We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested by RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results- A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.
Subject(s)
COVID-19ABSTRACT
The SARS-CoV-2 Omicron variant has demonstrated increased transmissibility and ability to escape natural and vaccine-induced immunity. We aimed to characterize the duration of Omicron’s shedding by comparing viral isolation to rapid antigen test (RAT) and real-time polymerase chain reaction (RT-PCR) positivity. Thus, we performed a cross-sectional study of 30 vaccinated individuals with mild COVID-19 to evaluate the ability to infect Vero cells at day 5, 7, 10 and 14 since symptoms onset. Viral growth was observed in 46% and 20% of respiratory samples at day 5 and 7, respectively, while all were negative from day 10. RAT showed 100% of sensitivity during the first 7 days of symptoms compared to viral isolation, being a better infectivity predictor than RT-PCR Ct values. In conclusion, immunocompetent vaccinated individuals with Omicron infection can still transmit the virus on the 7th day of symptoms. This data may impact decisions on end-isolation protocols for mild COVID-19.
Subject(s)
COVID-19ABSTRACT
Background: The Gamma variant has been considered the predominant SARS-CoV-2 lineage in Brazil during the first half of 2021. We aimed to characterise the clinical presentation of COVID-19 caused by the Gamma variant in comparison with strains that are not variants of concern (non-VoC).Method: We performed a prospective cohort study including symptomatic COVID-19 cases among healthcare workers from January 22 to May 15, 2021. Positive samples for SARS-CoV-2 RT-PCR underwent whole genome sequencing. COVID-19 symptoms, caused by the Gamma variant or non-VoC, and risk factors for Gamma variant infection were evaluated using multiple logistic regression analyses.Findings: We included 423 COVID-19 cases, of which 415 (98%) with mild disease. One hundred and seventy-five (41%) patients had been fully immunised, of which 173/175 (99%) had received CoronaVac. There were 313 (74%) Gamma variant cases and 110 (26%) non-VoC cases. Hyposmia/anosmia and dysgeusia were present in 129 (30%) and 108 (26%) of cases, respectively. Lower frequencies of hyposmia/anosmia (OR=0.304, p <0.001) and dysgeusia (OR=0.385, p =0.011) were the only symptoms significantly associated with Gamma variant infection. COVID-19 immunisation, previous COVID-19 and age were not associated with Gamma variant infection.Interpretation: The increase in Gamma variant cases should raise the awareness that COVID-19 may present more often with cold-like symptoms because of a decreased frequency of hyposmia/anosmia and dysgeusia.Funding: Supported by the Itau Unibanco “Todos pela saúde” program”.Declaration of Interest: None to declare. Ethical Approval: This study was approved by the Hospital’s Ethics Committee (CAAE: 42708721.0.0000.0068).
Subject(s)
COVID-19 , Olfaction Disorders , DysgeusiaABSTRACT
Abstract This report describes a persistent SARS-CoV-2 infection of at least 218 days in a male, in his forties who had undergone a prior autologous hematopoietic stem cell transplant due to a diffuse large B-cell lymphoma. He did not manifest a humoral immune response to the virus. Whole-genome sequencing and viral cultures confirmed a continual infection with a replication-positive virus that had undergone genetic variation for at least 196 days following symptom onset.
Subject(s)
COVID-19 , Lymphoma, B-CellABSTRACT
Objectives: Rapid diagnostics is pivotal to curb SARS-CoV-2 transmission, and saliva has emerged as a practical alternative to naso/oropharyngeal (NOP) specimens. We aimed to develop a direct RT-LAMP workflow for viral detection in saliva, and to provide more information regarding its potential in COVID-19 diagnostics. Methods: Clinical and contrived specimens were used to screen/optimize formulations and sample processing protocols. Salivary viral load was determined in symptomatic patients to evaluate clinical performance (n = 90) and to characterize saliva based on age, gender and time from onset of symptoms (n = 49). Results: The devised workflow achieved 93.2% sensitivity, 97% specificity, and 0.895 Kappa for salivas containing >102 copies/L. Further analyses in saliva showed peak viral load in the first days of symptoms and lower viral loads in females, particularly among young individuals (<38 years). NOP RT-PCR data did not yield relevant associations. Conclusions: This novel saliva RT-LAMP workflow can be applied to point-of-care testing. This work reinforces that saliva better correlates with transmission dynamics than NOP specimens, and reveals gender differences that may reflect higher transmission by males. To maximize detection, testing should be done immediately after symptom onset, especially in females.
Subject(s)
COVID-19ABSTRACT
Abstract Objectives: To evaluate if antibodies induced by infection with SARS-CoV-2 B.1.128 neutralize the P.1 variant. Methods: Convalescent sera from 60 individuals who had mild symptoms that did not require hospitalization following a documented SARS-CoV-2 infection (B.1.128 lineage) were assayed for neutralizing antibody titer against their original strain and against the SARS-CoV-2 P.1 variant. Results: Fifty-six (94%) and 50 (84 %) sera were positive for neutralizing antibodies against the ancestral and P.1 strains, respectively, and remained positive throughout the 6-week study period. Neutralization titers were consistently higher against the ancestral strain (p[≤] 0.001), but in the majority of patients (57.8%) differences did not differ by more than a single dilution. Conclusions: Neutralizing antibodies that were generated following a mild infection with SARS-CoV-2 B.1.128 were effective in vitro, and likely protective, against the SARS-CoV-2 P.1. variant in the majority of individuals.
Subject(s)
COVID-19ABSTRACT
RT-qPCR is used world-wide to test and trace the spread of SARS-CoV-2. Extraction-less or direct RT-PCR is an open-access qualitative method for SARS-CoV-2 detection from nasopharyngeal (NP) or oral pharyngeal (OP) samples with the potential to generate actionable data more quickly, at a lower cost, and with fewer experimental resources than full RT-qPCR. This study engaged ten global testing sites, including laboratories currently experiencing testing limitations due to reagent or equipment shortages, in an international inter-laboratory ring trial. Participating labs were provided a common protocol, common reagents, aliquots of identical pooled clinical samples and purified nucleic acids, and used their existing in-house equipment. We observed 100% concordance across labs in the correct identification of all positive and negative samples, with highly similar Ct values observed. The test also performed well when applied to locally collected patient NP samples, provided the viral transport media did not contain charcoal or guanidine, both of which appeared to potently inhibit the RT-PCR reaction. Our results suggest that open access, direct RT-PCR assays are a feasible option for more efficient COVID-19 testing as demanded by the continuing pandemic.
Subject(s)
COVID-19ABSTRACT
It has been estimated that individuals with COVID-19 can shed replication-competent virus up to a maximum of twenty days after initiation of symptoms. This report describes two patients with mild forms of the disease who shed replication-competent virus for 24 and 37 days, respectively, after symptom onset.
Subject(s)
COVID-19ABSTRACT
SARS-CoV-2 cross-transmission has become an concern in hospitals. We investigate healthcare workers(HCWs) knowledge about SARS-CoV-2 cross-transmission and conceptions whether the virus can remain on HCWs mobile phones(MPs) and be part of the chain of transmission. A cross-sectional study was conducted at a COVID-19 Intensive Care Unit of a teaching-hospital. Fifty-one MPs were swabbed and a questionnaire about hand hygiene and MP use and disinfection was applied after an educational campaign. Although most of HCWs believed on the importance of cross-transmission and increased hand hygiene adhesion and MP disinfection during the pandemic, SARS-CoV-2 RNA was detected in two MPs(culture of the samples was negative). Implementation of official hospital policies to guide HCWs regarding disinfection and care of personal MP are needed.
Subject(s)
COVID-19ABSTRACT
SARS-CoV-2 quickly spread in the worldwide population by contact with oral and respiratory secretions of infected individuals, imposing social restrictions to control the infection. Massive testing is essential to breaking the chain of COVID-19 transmission. The aim of this study was to compare the performance of at-home self-collected samples - saliva and combined nasal-oropharyngeal swabs (NOP) - for SARS-CoV-2 detection in a telemedicine platform for COVID-19 surveillance. We analyzed 201 patients who met the criteria of suspected COVID-19. NOP sampling were combined (nostrils and oropharynx) and saliva collected using a cotton pad device. Detection of SARS-COV-2 was performed by using the Altona RealStar SARS-CoV-2 RT-PCR Kit 1.0. According to our data, there was an overall significant agreement (k coefficient value of 0.58) between the performances of saliva and NOP. Assuming that positive results in either sample represent true infections, 70 patients positive for SARS-CoV-2 were identified, with 52/70 being positive in NOP and 55/70 in saliva. This corresponds to sensitivities of 74.2% (95% CI; 63.7% to 83.1%) for NOP and 78.6% (95% CI; 67.6% to 86.6%) for saliva. We also found a strong correlation (Beta coefficients < 1) between the cycle threshold values in saliva and NOP. Ageusia was the only symptom associated with patients SARS-CoV-2 positive only in NOP (p=0.028). In conclusion, our data show the feasibility of using at-home self-collected samples (especially saliva), as an adequate alternative for SARS-CoV-2 detection. This new approach of testing can be useful to develop strategies for COVID-19 surveillance and for guiding public health decisions.
Subject(s)
COVID-19 , Respiratory Tract InfectionsABSTRACT
The association between coronaviruses and central nervous system (CNS) demyelinating lesions has been previously shown. However, no case has been described of an association between the novel coronavirus (SARS-COV-2) and CNS demyelinating disease so far. SARS-COV-2 was previously detected in cerebrospinal fluid (CSF) sample of a patient with encephalitis. However, the virus identity was not confirmed by deep sequencing of SARS-COV-2 detected in the CSF. Here, we report a case of a patient with mild respiratory symptoms and neurological manifestations compatible with Clinically Isolated Syndrome. The viral genome of SARS-COV-2 was detected and sequenced in CSF with 99.74 to 100% similarity between the patient virus and worldwide sequences. This report suggests a possible association of SARS COV-2 infection with neurological symptoms of demyelinating disease, even in the absence of relevant upper respiratory tract infection signs.