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1.
J Otolaryngol Head Neck Surg ; 50(1): 5, 2021 Jan 28.
Article in English | MEDLINE | ID: covidwho-1090606

ABSTRACT

BACKGROUND: The primary method of surveillance for the presence of SARS-CoV-2 is with nasopharyngeal swabs. Given the significant demand for nasopharyngeal swabs, a large number of previously untrained and unfamiliar staff are now performing this test. It was noted that there was significant heterogeneity in instructions for performing nasopharyngeal swabs in Canada, in contrast to the guidance provided by the Centers for Disease Control and Prevention (CDC), and the Pan American Health Organization (PAHO). The objective of this study was to review the instructions provided across Canada and contrast them to those of the CDC and PAHO. METHODS: A standard series of steps for nasopharyngeal swab performance was outlined based on the CDC, PAHO, and New England Journal of Medicine instructions. A comprehensive search was performed in August 2020 to identify nasopharyngeal swab guidelines provided by public health in the provinces and territories of Canada. Regional health authority guidance was also collected. Instructions provided were contrasted against the standardized steps. RESULTS: Instructions were identified for all provinces and territories, and for 81 regional health authorities. From the provincial and territorial guidelines, 10/13 (77%) cleared the nasal passages before swab insertion, 11/13 (85%) tilted the patient's head back slightly, 12/13 (92%) inserted the swab parallel to the palate, but only 3/13 (23%) inserted the swab to at least a depth of two-thirds the distance between the patient's nose and ear. A clear majority (81%) of regional health authority guidelines followed their respective provincial guidelines. For depth of insertion, Quebec provided a pictogram but no distance or technique for estimation. Six provinces and territories - Northwest Territories, Nunavut, Ontario, Saskatchewan, Prince Edward Island and Alberta - recommended 4 cm or one-half the distance from nostrils to ear. British Columbia and Manitoba recommended a 7 cm depth of insertion. Nova Scotia recommended one-half to two-thirds the distance from nose to ear. Lastly, Newfoundland, New Brunswick and the Yukon recommended an insertion from nose to the external ear canal. CONCLUSION: There is significant heterogeneity in guidance for nasopharyngeal swab performance across Canada. The instructions provided by the majority of provinces and territories in Canada would not be effective in reaching the nasopharynx.


Subject(s)
/diagnosis , Nasopharynx/virology , Specimen Handling , Canada , Guideline Adherence , Humans , Nasal Cavity/virology , Practice Guidelines as Topic
2.
BMJ ; 372: n334, 2021 02 17.
Article in English | MEDLINE | ID: covidwho-1088219

ABSTRACT

OBJECTIVE: To directly measure the fatal impact of coronavirus disease 2019 (covid-19) in an urban African population. DESIGN: Prospective systematic postmortem surveillance study. SETTING: Zambia's largest tertiary care referral hospital. PARTICIPANTS: Deceased people of all ages at the University Teaching Hospital morgue in Lusaka, Zambia, enrolled within 48 hours of death. MAIN OUTCOME MEASURE: Postmortem nasopharyngeal swabs were tested via reverse transcriptase quantitative polymerase chain reaction (PCR) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Deaths were stratified by covis-19 status, location, age, sex, and underlying risk factors. RESULTS: 372 participants were enrolled between June and September 2020; PCR results were available for 364 (97.8%). SARS-CoV-2 was detected in 58/364 (15.9%) according to the recommended cycle threshold value of <40 and in 70/364 (19.2%) when expanded to any level of PCR detection. The median age at death among people with a positive test for SARS-CoV-2 was 48 (interquartile range 36-72) years, and 69% (n=48) were male. Most deaths in people with covid-19 (51/70; 73%) occurred in the community; none had been tested for SARS-CoV-2 before death. Among the 19/70 people who died in hospital, six were tested before death. Among the 52/70 people with data on symptoms, 44/52 had typical symptoms of covid-19 (cough, fever, shortness of breath), of whom only five were tested before death. Covid-19 was identified in seven children, only one of whom had been tested before death. The proportion of deaths with covid-19 increased with age, but 76% (n=53) of people who died were aged under 60 years. The five most common comorbidities among people who died with covid-19 were tuberculosis (22; 31%), hypertension (19; 27%), HIV/AIDS (16; 23%), alcohol misuse (12; 17%), and diabetes (9; 13%). CONCLUSIONS: Contrary to expectations, deaths with covid-19 were common in Lusaka. Most occurred in the community, where testing capacity is lacking. However, few people who died at facilities were tested, despite presenting with typical symptoms of covid-19. Therefore, cases of covid-19 were under-reported because testing was rarely done not because covid-19 was rare. If these data are generalizable, the impact of covid-19 in Africa has been vastly underestimated.


Subject(s)
/mortality , /isolation & purification , Adult , Age Distribution , Age Factors , Aged , Autopsy , /virology , Female , Humans , Male , Middle Aged , Nasopharynx/virology , Prospective Studies , Risk Factors , Sex Factors , Urban Population/statistics & numerical data , Zambia/epidemiology
3.
Front Public Health ; 8: 593491, 2020.
Article in English | MEDLINE | ID: covidwho-1081109

ABSTRACT

Background: SARS-CoV-2-infected subjects have been proven contagious in the symptomatic, pre-symptomatic and asymptomatic phase. The identification of these patients is crucial in order to prevent virus circulation. No reliable data on the sensitivity of nasopharyngeal swabs (NPS) are available because of the lack of a shared reference standard to identify SARS-CoV-2 infected patients. The aim of our study was to collect data on patients with a known diagnosis of COVID-19 who underwent serial testing to assess NPS sensitivity. Methods: The study was a multi-center, observational, retrospective clinical study with consecutive enrollment. We enrolled patients who met all of the following inclusion criteria: clinical recovery, documented SARS-CoV-2 infection (≥1 positive rRT-PCR result) and ≥1 positive NPS among the first two follow-up swabs. A positive NPS not preceded by a negative nasopharyngeal swab collected 24-48 h earlier was considered a true positive. A negative NPS followed by a positive NPS collected 24-48 h later was regarded as a false negative. The primary outcome was to define sensitivity of SARS-CoV-2 detection with NPS. Results: Three hundred and ninety three NPS were evaluated in 233 patients; the sensitivity was 77% (95% CI, 73 to 81%). Sensitivity of the first follow-up NPS (n = 233) was 79% (95% CI, 73 to 84%) with no significant variations over time. We found no statistically significant differences in the sensitivity of the first follow-up NPS according to time since symptom onset, age, sex, number of comorbidities, and onset symptoms. Conclusions: NPS utility in the diagnostic algorithm of COVID-19 should be reconsidered.


Subject(s)
/methods , Nasopharynx/virology , /isolation & purification , Adult , Aged , /instrumentation , Chi-Square Distribution , Female , Humans , Male , Middle Aged , RNA, Viral/analysis , Retrospective Studies , Sensitivity and Specificity , Viral Load
4.
Curr Oncol ; 28(1): 847-852, 2021 02 08.
Article in English | MEDLINE | ID: covidwho-1069796

ABSTRACT

The pandemic of SARS-CoV-2 is a serious global challenge affecting millions of people worldwide. Cancer patients are at risk for infection exposure and serious complications. A prompt diagnosis of SARS-CoV-2 infection is crucial for the timely adoption of isolation measures and the appropriate management of cancer treatments. In lung cancer patients the symptoms of infection 19 may resemble those exhibited by the underlying oncologic condition, possibly leading to diagnostic overlap and delays. Moreover, cancer patients might display a prolonged positivity of nasopharyngeal RT-PCR assays for SARS-CoV-2, causing long interruptions or delay of cancer treatments. However, the association between the positivity of RT-PCR assays and the patient's infectivity remains uncertain. We describe the case of a patient with non-small cell lung cancer, and a severe ab extrinseco compression of the trachea, whose palliative radiotherapy was delayed because of the prolonged positivity of nasopharyngeal swabs for SARS-CoV-2. The patient did not show clinical symptoms suggestive of active infection, but the persistent positivity of RT-PCR assays imposed the continuation of isolation measures and the delay of radiotherapy for over two months. Finally, the negative result of SARS-CoV-2 viral culture allowed us to verify the absence of viral activity and to rule out the infectivity of the patient, who could finally continue her cancer treatment.


Subject(s)
/diagnosis , Carcinoma, Non-Small-Cell Lung/virology , Lung Neoplasms/virology , /isolation & purification , Aged , Carrier State/diagnosis , Female , Humans , Nasopharynx/virology , RNA, Viral/genetics , Time-to-Treatment
5.
J Med Case Rep ; 15(1): 65, 2021 Feb 08.
Article in English | MEDLINE | ID: covidwho-1069586

ABSTRACT

INTRODUCTION: The coronavirus disease 2019 (COVID-19) pandemic has caused irreparable damage to society, and the damage continues. Pediatricians are confronted with COVID-19 in a variety of presentations, which may lead to delayed diagnosis and treatment. Early diagnosis of the disease plays an important role in preventing transmission of the virus in the community. CASE PRESENTATION: Here we report a 27-month-old previously healthy Iranian female child who presented with fever and bloody diarrhea, diagnosed with COVID-19 based on contact history, exclusion of enteric bacterial pathogens and parasites, and positive stool and nasopharyngeal severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcriptase polymerase chain reaction (RT-PCR) tests. The patient had viral shedding for more than a month. CONCLUSIONS: The pediatric population usually does not present with typical clinical features of COVID-19, which are respiratory involvement. Dysentery may be the only presentation of this disease, and long-term isolation should be considered, as the viral shedding may last for more than a month.


Subject(s)
/diagnosis , Dysentery/virology , /complications , Child, Preschool , Feces/virology , Female , Fever/virology , Humans , Nasopharynx/virology , Reverse Transcriptase Polymerase Chain Reaction , Virus Shedding
6.
Epidemiol Prev ; 44(5-6 Suppl 2): 200-206, 2020.
Article in Italian | MEDLINE | ID: covidwho-1068140

ABSTRACT

BACKGROUND: to avoid a new spread of the SARS-CoV-2 infection, the post lockdown period requires the implementation of effective strategies for the case finding and contact tracing. The presence of asymptomatic subjects in the population, that are responsible for about 30% of the new infections, may complicate this phase. Serological tests for the measurement of immune response could represent an effective tool for the rapid monitoring of the population with asymptomatic infections and for estimating the proportion of immune in a territory, too. OBJECTIVES: to describe the distribution of the immune response to SARS-CoV-2 infection in the population of the Municipality of Borgosesia (Piedmont Region, Northern Italy) and to estimate the efficacy of this strategy for the identification of asymptomatic cases. DESIGN: Cross-sectional study with administration of a rapid test to assess the seroprevalence of anti-SARS-CoV-2 IgG/IgM antibodies. SETTING AND PARTICIPANTS: all subjects resident in Borgosesia over the age of 18, where invited to participate. A rapid serological test was administered to enrolled participants to detect the presence of SARS-CoV-2 IgG and IgM antibodies on peripheral blood. Subjects with IgG or IgM positivity were offered to perform a swab test for viral RNA research. MAIN OUTCOME MEASURES: the prevalence of IgM and IgG, and the relative risks of having positive swab test and of having symptoms similar to those of COVID-19 in the recent past has been estimated. RESULTS: 4,987 subjects participated to study, 44.5% of the adult population of Borgosesia. The average age was 55 years. There was a greater participation of women (54.4%), of people with a higher education level (37.3%) and of people without specific previous symptoms (95.1%). 245 people had a positive test for IgM or IgG, and the estimated prevalence was of 4.9%. 209 out of 245 subjects who were positive to the rapid test underwent to the RT-PCR test and this allowed to isolate 24 positive subjects. CONCLUSIONS: the seroprevalence values ​​estimated for subjects residing in the city of Borgosesia which underwent the rapid test for the detection of type M and type G antibodies on peripheral blood, confirmed the population-based estimates reported in literature, in particular with the results of the Italian survey of seroprevalence. Furthermore, the implementation of this test allowed the identification and isolation of completely asymptomatic subjects, that could have been identified only through screening with tests for viral RNA.


Subject(s)
Antibodies, Viral/blood , Asymptomatic Infections/epidemiology , Immunoglobulin G/blood , Immunoglobulin M/blood , Pandemics , /immunology , Adult , Aged , Aged, 80 and over , Contact Tracing , Cross-Sectional Studies , Educational Status , Female , Humans , Italy/epidemiology , Male , Middle Aged , Nasopharynx/virology , Population Surveillance , Quarantine , RNA, Viral/analysis , Seroepidemiologic Studies , Urban Population , Young Adult
7.
Epidemiol Prev ; 44(5-6 Suppl 2): 42-50, 2020.
Article in Italian | MEDLINE | ID: covidwho-1068123

ABSTRACT

The article compares two of the most followed indices in the monitoring of COVID-19 epidemic cases: the Rt and the RDt indices. The first was disseminated by the Italian National Institute of Health (ISS) and the second, which is more usable due to the lower difficulty of calculation and the availability of data, was adopted by various regional and local institutions.The rationale for the Rt index refers to that for the R0 index, the basic reproduction number, which is used by infectivologists as a measure of contagiousness of a given infectious agent in a completely susceptible population. The RDt index, on the other hand, is borrowed from the techniques of time series analysis for the trend of an event measurement that develops as a function of time. The RDt index does not take into account the time of infection, but the date of the diagnosis of positivity and for this reason it is defined as diagnostic replication index, as it aims to describe the intensity of the development of frequency for cases recognized as positive in the population.The comparison between different possible applications of the methods and the use of different types of monitoring data was limited to four areas for which complete individual data were available in March and April 2020. The main problems in the use of Rt, which is based on the date of symptoms onset, arise from the lack of completeness of this information due both to the difficulty in the recording and to the absence in asymptomatic subjects.The general trend of RDt, at least at an intermediate lag of 6 or 7 days, is very similar to that of Rt, as confirmed by the very high value of the correlation index between the two indices. The maximum correlation between Rt and RDt is reached at lag 7 with a value of R exceeding 0.97 (R2=0.944).The two indices, albeit formally distinct, are both valid; they show specific aspects of the phenomenon, but provide basically similar information to the public health decision-maker. Their distinction lies not so much in the method of calculation, rather in the use of different information, i.e., the beginning of symptoms and the swabs outcome.Therefore, it is not appropriate to make a judgment of preference for one of the two indices, but only to invite people to understand their different potentials so that they can choose the one they consider the most appropriate for the purpose they want to use it for.


Subject(s)
Basic Reproduction Number , Epidemiological Monitoring , Pandemics , /pathogenicity , Decision Making , Health Policy , Humans , Incidence , Italy/epidemiology , Nasopharynx/virology , Risk , Symptom Assessment , Time Factors
8.
Epidemiol Prev ; 44(5-6 Suppl 2): 33-41, 2020.
Article in Italian | MEDLINE | ID: covidwho-1068122

ABSTRACT

BACKGROUND: the ability to implement effective preventive and control measures is rooted in public health surveillance to promptly identify and isolate contagious patients. OBJECTIVES: to describe some organizational aspects and resources involved in the control of COVID-19 pandemic. DESIGN: observational cross sectional study. SETTING AND PARTICIPANTS: a survey of methods and tools adopted by the competent service (Prevention department) in the Local public health units (LHU) of the regional Health services has been performed in May 2020. The survey collected data related to activities carried out during the month of April 2020 on the surveillance system for collection of suspected cases, their virological ascertainment, the isolation procedures and contact-tracing activities by means of an online questionnaire filled in by the public health structure of the regional health system. A convenience sample of Prevention departments was recruited. RESULTS: in 44 Prevention departments of 14 Regions/Autonomous Provinces (caring for 40% of the population residing in Italy), different services were swiftly engaged in pandemic response. Reports of suspected cases were about 3 times the number of confirmed cases in the same month. Local reporting form was used in 46% of the LHUs while a regional form was available in 42% of the Departments (in 9/14 Regions). In one fourth the forms were not always used and 2% had no forms for the reporting of suspected cases. Data were recorded in 52% of LHUs on local databases, while in 20% a regional database (in 7 Regions) had been created. A proportion of 11% did not record the data for further elaboration. The virological assessment with nasopharyngeal swabs out of the hospital setting was carried out on the average in 7 points in each LHU (median 5) and the average daily capacity was 350 (71 per 100,000) swabs. The rate of subjects newly tested during the month of April was of 893 per 100,000 new people. Data collected at the swabbing were recorded on a regional platform in 17 LHUs (39%) of 8 Regions. In 7% LHUs only positive specimens were recorded electronically. Local files were used in 27% LHUs. The interview with confirmed cases was carried out with a local questionnaire in 52% LHUs, while 14% stated that a standardized form was not used. The data collected about cases were recorded on a regional IT platform in 30% Departments (in 8 Regions) and in 41% data were registered only locally. For each confirmed case in April, a median of 4 contacts were identified. Only 13 (30%) Departments in 9 Regions have registered contact data on a regional database. Ten Departments (23%) have only hard copies, while 56% recorded data on local databases. About 5 health professionals for 100,000 resident population were involved in each LHU in each of the following activities as receiving reports of suspected cases, swabs collection, interviews of cases and contact identifications. CONCLUSIONS: the pandemic required rapidly a great organizational effort and great flexibility to increase response capacity, which now must be strengthened and maintained. Several different tools (forms and electronic files) have been developed in each LHU and used for the same surveillance operational processes with a loss in local efficiency. The inhomogeneous data collection and recording is an obstacle for further analyses and risk identifications and is a missed opportunity for the advancement of our knowledge on pandemic epidemiology analysis. In Italy, updating the pandemic response plans is the priority, at national, regional and local level, and the occasion to fill the gaps and to improve surveillance systems to the interruption of COVID-19 transmission.


Subject(s)
/prevention & control , Communicable Disease Control/organization & administration , Pandemics/prevention & control , Public Health Administration/methods , /isolation & purification , /diagnosis , /transmission , Communicable Disease Control/methods , Contact Tracing , Cross-Sectional Studies , Electronic Health Records , Forms and Records Control , Geography, Medical , Health Care Surveys , Humans , Italy/epidemiology , Nasopharynx/virology , Population Surveillance
12.
Diagn Microbiol Infect Dis ; 99(3): 115260, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1065005

ABSTRACT

The BioFire® COVID-19 Test and Respiratory Panel 2.1 (RP2.1) are rapid, fully automated assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal swabs. In the case of the RP2.1, an additional 21 viral and bacterial pathogens can be detected. Both tests have received emergency use authorization from the U.S. Food & Drug Administration and Interim Order authorization from Health Canada for use in clinical laboratories. We evaluated the performance characteristics of these tests in comparison to a laboratory-developed real-time PCR assay targeting the viral RNA-dependent RNA polymerase and E genes. A total of 78 tests were performed using the BioFire COVID-19 Test, including 30 clinical specimens and 48 tests in a limit of detection study; 57 tests were performed using the RP2.1 for evaluation of SARS-CoV-2 detection, including 30 clinical specimens and 27 tests for limit of detection. Results showed 100% concordance between the BioFire assays and the laboratory-developed test for all clinical samples tested, and acceptable performance of both BioFire assays at their stated limits of detection. Conclusively, the BioFire COVID-19 Test and RP2.1 are highly sensitive assays that can be effectively used in the clinical laboratory for rapid SARS-CoV-2 testing.


Subject(s)
/methods , Nasopharynx/virology , /isolation & purification , /standards , Clinical Laboratory Techniques/methods , Diagnostic Tests, Routine , Humans , Limit of Detection , Multiplex Polymerase Chain Reaction , Real-Time Polymerase Chain Reaction/methods , Reproducibility of Results , Sensitivity and Specificity
13.
Sci Adv ; 7(6)2021 02.
Article in English | MEDLINE | ID: covidwho-1066793

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.


Subject(s)
/diagnosis , Nasopharynx/virology , RNA, Viral/metabolism , /genetics , Area Under Curve , /pathology , Gene Library , Humans , Machine Learning , RNA, Viral/blood , ROC Curve , Reverse Transcriptase Polymerase Chain Reaction , Sensitivity and Specificity , Transcriptome
14.
Proc Natl Acad Sci U S A ; 118(8)2021 02 23.
Article in English | MEDLINE | ID: covidwho-1066042

ABSTRACT

The characterization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral kinetics in hospitalized patients and its association with mortality is unknown. We analyzed death and nasopharyngeal viral kinetics in 655 hospitalized patients from the prospective French COVID cohort. The model predicted a median peak viral load that coincided with symptom onset. Patients with age ≥65 y had a smaller loss rate of infected cells, leading to a delayed median time to viral clearance occurring 16 d after symptom onset as compared to 13 d in younger patients (P < 10-4). In multivariate analysis, the risk factors associated with mortality were age ≥65 y, male gender, and presence of chronic pulmonary disease (hazard ratio [HR] > 2.0). Using a joint model, viral dynamics after hospital admission was an independent predictor of mortality (HR = 1.31, P < 10-3). Finally, we used our model to simulate the effects of effective pharmacological interventions on time to viral clearance and mortality. A treatment able to reduce viral production by 90% upon hospital admission would shorten the time to viral clearance by 2.0 and 2.9 d in patients of age <65 y and ≥65 y, respectively. Assuming that the association between viral dynamics and mortality would remain similar to that observed in our population, this could translate into a reduction of mortality from 19 to 14% in patients of age ≥65 y with risk factors. Our results show that viral dynamics is associated with mortality in hospitalized patients. Strategies aiming to reduce viral load could have an effect on mortality rate in this population.


Subject(s)
/mortality , Models, Theoretical , Nasopharynx/virology , RNA, Viral/analysis , Viral Load , Aged , Antibodies, Viral/blood , /epidemiology , Female , France/epidemiology , Hospitalization , Humans , Kinetics , Male , Prognosis , Prospective Studies , RNA, Viral/genetics , Risk Factors , Survival Rate
15.
Sci Rep ; 11(1): 3134, 2021 02 04.
Article in English | MEDLINE | ID: covidwho-1065962

ABSTRACT

We aimed to test the sensitivity of naso-oropharyngeal saliva and self-administered nasal (SN) swab compared to nasopharyngeal (NP) swab for COVID-19 testing in a large cohort of migrant workers in Singapore. We also tested the utility of next-generation sequencing (NGS) for diagnosis of COVID-19. Saliva, NP and SN swabs were collected from subjects who presented with acute respiratory infection, their asymptomatic roommates, and prior confirmed cases who were undergoing isolation at a community care facility in June 2020. All samples were tested using RT-PCR. SARS-CoV-2 amplicon-based NGS with phylogenetic analysis was done for 30 samples. We recruited 200 subjects, of which 91 and 46 were tested twice and thrice respectively. In total, 62.0%, 44.5%, and 37.7% of saliva, NP and SN samples were positive. Cycle threshold (Ct) values were lower during the earlier period of infection across all sample types. The percentage of test-positive saliva was higher than NP and SN swabs. We found a strong correlation between viral genome coverage by NGS and Ct values for SARS-CoV-2. Phylogenetic analyses revealed Clade O and lineage B.6 known to be circulating in Singapore. We found saliva to be a sensitive and viable sample for COVID-19 diagnosis.


Subject(s)
/diagnosis , Nasal Mucosa/virology , RNA, Viral/isolation & purification , Saliva/virology , Specimen Handling , Adult , Cohort Studies , Female , Humans , Male , Nasopharynx/virology , /isolation & purification , Sensitivity and Specificity , Singapore/epidemiology
16.
Sci Rep ; 11(1): 3044, 2021 02 04.
Article in English | MEDLINE | ID: covidwho-1065949

ABSTRACT

The role of children in the spread of the SARS-CoV-2 coronavirus has become a matter of urgent debate as societies in the US and abroad consider how to safely reopen schools. Small studies have suggested higher viral loads in young children. Here we present a multicenter investigation on over five thousand SARS-CoV-2 cases confirmed by real-time reverse transcription (RT) PCR assay. Notably, we found no discernable difference in amount of viral nucleic acid among young children and adults.


Subject(s)
Nasopharynx/virology , RNA, Viral/analysis , Viral Load , Adolescent , Adult , Aged , Aged, 80 and over , /virology , California/epidemiology , Child , Child, Preschool , Female , Humans , Male , Middle Aged , /physiology , Young Adult
17.
Sci Rep ; 11(1): 1820, 2021 01 19.
Article in English | MEDLINE | ID: covidwho-1065931

ABSTRACT

RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.


Subject(s)
/diagnosis , Molecular Diagnostic Techniques/methods , Nucleic Acid Amplification Techniques/methods , /genetics , /virology , Hot Temperature , Humans , Nasopharynx/virology , RNA, Viral/metabolism , RNA-Directed DNA Polymerase/metabolism , Reagent Kits, Diagnostic , Sensitivity and Specificity , Virus Inactivation
18.
J Proteome Res ; 20(2): 1434-1443, 2021 02 05.
Article in English | MEDLINE | ID: covidwho-1065788

ABSTRACT

Alternative methods to RT-PCR for SARS-CoV-2 detection are investigated to provide complementary data on viral proteins, increase the number of tests performed, or identify false positive/negative results. Here, we have developed a simple mass spectrometry assay for SARS-CoV-2 in nasopharyngeal swab samples using common laboratory reagents. The method employs high sensitivity and selectivity targeted mass spectrometry detection, monitoring nine constitutive peptides representative of the three main viral proteins and a straightforward pellet digestion protocol for convenient routine applications. Absolute quantification of N, M, and S proteins was achieved by addition of isotope-labeled versions of best peptides. Limit of detection, recovery, precision, and linearity were thoroughly evaluated in four representative viral transport media (VTM) containing distinct total protein content. The protocol was sensitive in all swab media with limit of detection determined at 2 × 103 pfu/mL, corresponding to as low as 30 pfu injected into the LC-MS/MS system. When tested on VTM-stored nasopharyngeal swab samples from positive and control patients, sensitivity was similar to or better than rapid immunoassay dipsticks, revealing a corresponding RT-PCR detection threshold at Ct ∼ 24. The study represents the first thorough evaluation of sensitivity and robustness of targeted mass spectrometry in nasal swabs, constituting a promising SARS-CoV-2 antigen assay for the first-line diagnosis of COVID-19 and compatible with the constraints of clinical settings. The raw files generated in this study can be found on PASSEL (Peptide Atlas) under data set identifier PASS01646.


Subject(s)
/diagnosis , Chromatography, Liquid/methods , Nasopharynx/virology , Spike Glycoprotein, Coronavirus/metabolism , Tandem Mass Spectrometry/methods , /virology , Culture Media , Humans , Nucleocapsid/metabolism , Proteomics/methods , Reproducibility of Results , Sensitivity and Specificity , Specimen Handling/instrumentation , Specimen Handling/methods , Viral Proteins/metabolism
19.
Epidemiol Infect ; 149: e24, 2021 01 14.
Article in English | MEDLINE | ID: covidwho-1065752

ABSTRACT

The severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is highly contagious, and the coronavirus disease 2019 (COVID-19) pandemic caused by it has forced many countries to adopt 'lockdown' measures to prevent the spread of the epidemic through social isolation of citizens. Some countries proposed universal mask wearing as a protection measure of public health to strengthen national prevention efforts and to limit the wider spread of the epidemic. In order to reveal the epidemic prevention efficacy of masks, this paper systematically evaluates the experimental studies of various masks and filter materials, summarises the general characteristics of the filtration efficiency of isolation masks with particle size, and reveals the actual efficacy of masks by combining the volume distribution characteristics of human exhaled droplets with different particle sizes and the SARS-CoV-2 virus load of nasopharynx and throat swabs from patients. The existing measured data show that the filtration efficiency of all kinds of masks for large particles and extra-large droplets is close to 100%. From the perspective of filtering the total number of pathogens discharged in the environment and protecting vulnerable individuals from breathing live viruses, the mask has a higher protective effect. If considering the weighted average filtration efficiency with different particle sizes, the filtration efficiencies of the N95 mask and the ordinary mask are 99.4% and 98.5%, respectively. The mask can avoid releasing active viruses to the environment from the source of infection, thus maximising the protection of vulnerable individuals by reducing the probability of inhaling a virus. Therefore, if the whole society strictly implements the policy of publicly wearing masks, the risk of large-scale spread of the epidemic can be greatly reduced. Compared with the overall cost of social isolation, limited personal freedoms and forced suspension of economic activities, the inconvenience for citizens caused by wearing masks is perfectly acceptable.


Subject(s)
/epidemiology , Masks/standards , Aerosols , Humans , Nasopharynx/virology , Oropharynx/virology , Particle Size , Viral Load
20.
Epidemiol Infect ; 149: e18, 2021 01 11.
Article in English | MEDLINE | ID: covidwho-1065749

ABSTRACT

It is important to understand the temporal trend of the paediatric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load to estimate the transmission potential of children in schools and communities. We determined the differences in SARS-CoV-2 viral load dynamics between nasopharyngeal samples of infected asymptomatic and symptomatic children. Serial cycle threshold values of SARS-CoV-2 from the nasopharynx of a cohort of infected children were collected for analysis. Among 17 infected children, 10 (58.8%) were symptomatic. Symptomatic children, when compared to asymptomatic children, had higher viral loads (mean cycle threshold on day 7 of illness 28.6 vs. 36.7, P = 0.02). Peak SARS-CoV-2 viral loads occurred around day 2 of illness in infected children. Although we were unable to directly demonstrate infectivity, the detection of significant amount of virus in the upper airway of asymptomatic children suggest that they have the potential to shed and transmit SARS-CoV-2. Our study highlights the importance of contact tracing and screening for SARS-CoV-2 in children with epidemiological risk factors regardless of their symptom status, in order to improve containment of the virus in the community, including educational settings.


Subject(s)
Nasopharynx/virology , RNA, Viral/analysis , Viral Load , Adolescent , Child , Child, Preschool , Female , Humans , Infant , Male , Polymerase Chain Reaction , /genetics
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