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1.
Emerg Infect Dis ; 28(4): 873-876, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1771002

ABSTRACT

The Surveillance for Emerging Threats to Mothers and Babies Network conducts longitudinal surveillance of pregnant persons in the United States with laboratory-confirmed severe acute respiratory syndrome coronavirus 2 infection during pregnancy. Of 6,551 infected pregnant persons in this analysis, 142 (2.2%) had positive RNA tests >90 days and up to 416 days after infection.


Subject(s)
COVID-19 , Pregnancy Complications, Infectious , COVID-19/diagnosis , Female , Humans , Laboratories , Pregnancy , Pregnancy Complications, Infectious/epidemiology , RNA, Viral , SARS-CoV-2/genetics , Serologic Tests , United States
2.
Front Microbiol ; 12: 786042, 2021.
Article in English | MEDLINE | ID: covidwho-1630865

ABSTRACT

The fast spread of COVID-19 is related to the highly infectious nature of SARS-CoV-2. The disease is suggested to be transmitted through saliva droplets and nasal discharge. The saliva quantification of SARS-CoV-2 in real-time PCR from asymptomatic or mild COVID-19 adults has not been fully documented. This study analyzed the relationship between salivary viral load on demographics and clinical characteristics including symptoms, co-morbidities in 160 adults diagnosed as COVID-19 positive patients recruited between September and December 2020 in four French centers. Median initial viral load was 4.12 log10 copies/mL (IQR 2.95-5.16; range 0-10.19 log10 copies/mL). 68.6% of adults had no viral load detected. A median load reduction of 23% was observed between 0-2 days and 3-5 days, and of 11% between 3-5 days and 6-9 days for the delay from onset of symptoms to saliva sampling. No significant median difference between no-symptoms vs. symptoms patients was observed. Charge was consistently similar for the majority of the clinical symptoms excepted for headache with a median load value of 3.78 log10 copies/mL [1.95-4.58] (P < 0.003). SARS-CoV-2 RNA viral load was associated with headache and gastro-intestinal symptoms. The study found no statistically significant difference in viral loads between age groups, sex, or presence de co-morbidity. Our data suggest that oral cavity is an important site for SARS-CoV-2 infection and implicate saliva as a potential route of SARS-CoV-2 transmission.

3.
J Virol Methods ; 297: 114250, 2021 11.
Article in English | MEDLINE | ID: covidwho-1461648

ABSTRACT

Recent publications have highlighted the emergence of mutations in the M1 gene of both influenza A H1N1pdm09 and H3N2 subtypes affecting the performance of commercial RT-PCR assays. Respiratory samples from the 2018/2019 season positive by our in-house RT-PCR for influenza A were analysed for the prevalence and impact of any M1 gene mutations. Sequence information was used to re-design primers for our routine assay and their performance assessed. Forty-five samples, consisting of 11 H1N1pdm09 and 34 H3N2 subtypes, together with the NIBSC H1N1 control were sequenced. All samples displayed the core mutations for H1N1 M1(C154T; G174A and G238A) and for H3N2 M1(C153T; C163T and G189T); three of the H1N1pdm09 viruses also showed a small number of point mutations. None of the mutations appeared to affect either the sensitivity or efficiency of the RT-PCR when compared to the re-designed primers. Although the mutations we found agreed with those in the publications cited we did not encounter any problems with our routine diagnostic assay and no improvements were found when the primers were modified to suit those mutations. However, it is likely that the influenza A virus M1 gene will accumulate further mutations that could impact RT-PCR assays and, therefore, it would be prudent to implement routine sequencing of samples during the influenza seasons to ensure no loss in assay performance.


Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza, Human , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , London/epidemiology , Seasons
4.
Ann Lab Med ; 41(6): 588-592, 2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1264322

ABSTRACT

The rapid antigen test (RAT) for coronavirus disease (COVID-19) represents a potent diagnostic method in situations of limited molecular testing resources. However, considerable performance variance has been reported with the RAT. We evaluated the clinical performance of Standard Q COVID-19 RAT (SQ-RAT; SD Biosensor, Suwon, Korea), the first RAT approved by the Korean Ministry of Food and Drug Safety. In total, 680 nasopharyngeal swabs previously tested using real-time reverse-transcription PCR (rRT-PCR) were retested using SQ-RAT. The clinical sensitivity of SQ-RAT relative to that of rRT-PCR was 28.7% for all specimens and was 81.4% for specimens with RNA-dependent RNA polymerase gene (RdRp) threshold cycle (Ct) values ≤23.37, which is the limit of detection of SQ-RAT. The specificity was 100%. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis was assessed based on the Ct distribution at diagnosis of 33,294 COVID-19 cases in Korea extracted from the laboratory surveillance system of Korean Society for Laboratory Medicine. The clinical sensitivity of SQ-RAT for COVID-19 diagnosis in the Korean population was 41.8%. Considering the molecular testing capacity in Korea, use of the RAT for COVID-19 diagnosis appears to be limited.


Subject(s)
COVID-19/diagnosis , RNA-Dependent RNA Polymerase/genetics , SARS-CoV-2/genetics , COVID-19/virology , COVID-19 Testing/methods , Humans , Nasopharynx/virology , RNA, Viral/analysis , RNA, Viral/metabolism , Real-Time Polymerase Chain Reaction , Republic of Korea , SARS-CoV-2/isolation & purification
5.
Int J Infect Dis ; 102: 299-302, 2021 Jan.
Article in English | MEDLINE | ID: covidwho-1060235

ABSTRACT

Real-time reverse transcription PCR is currently the most sensitive method to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Defining whether a patient could be contagious or not contagious in the presence of residual SARS-CoV-2 RNA is of extreme importance in the context of public health. In this prospective multicenter study, virus isolation was prospectively attempted in 387 nasal swabs from clinically recovered patients showing low viral load (quantification cycle, Cq, value greater than 30). The median Cq value was 36.8 (range 30.0-39.4). Overall, a cytopathic effect was detected in nine samples, corresponding to a culture positivity rate of 2.3% (9/387). The results of this study help to dissect true virus replication and residual viral RNA detection in recovered patients.


Subject(s)
COVID-19/virology , Quarantine , RNA, Viral/genetics , SARS-CoV-2/isolation & purification , Adult , COVID-19/diagnosis , COVID-19/transmission , COVID-19 Testing , Disease Progression , Female , Humans , Male , Middle Aged , Nose/virology , Prospective Studies , Real-Time Polymerase Chain Reaction , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Time Factors , Viral Load , Young Adult
6.
J Microbiol Immunol Infect ; 54(2): 164-174, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-548385

ABSTRACT

Laboratory-based diagnostic measures including virological and serological tests are essential for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Real-time reverse transcription-polymerase chain reactions (rRT-PCR) can detect SARS-COV-2 by targeting open reading frame-1 antibodies (ORF1ab), envelope protein, nucleocapsid protein, RNA-dependent RNA polymerase genes, and the N1, N2, and N3 (3N) target genes. Therefore, rRT-PCR remains the primary method of diagnosing SARS-CoV-2 despite being limited by false-negative results, long turnaround, complex protocols, and a need for skilled personnel. Serological diagnosis of coronavirus disease 2019 (COVID-19) is simple and does not require complex techniques and equipment, rendering it suitable for rapid detection and massive screening. However, serological tests cannot confirm SARS-CoV-2, and results will be false-negative when antibody concentrations fall below detection limits. Balancing the increased use of laboratory tests, risk of testing errors, need for tests, burden on healthcare systems, benefits of early diagnosis, and risk of unnecessary exposure is a significant and persistent challenge in diagnosing COVID-19.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , SARS-CoV-2 , COVID-19/immunology , COVID-19/virology , COVID-19 Nucleic Acid Testing/methods , COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19 Serological Testing/methods , COVID-19 Serological Testing/statistics & numerical data , COVID-19 Testing/statistics & numerical data , False Negative Reactions , False Positive Reactions , Humans , In Vitro Techniques , Pandemics , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
7.
Emerg Infect Dis ; 26(8)2020 Aug.
Article in English | MEDLINE | ID: covidwho-245493

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified as the etiologic agent associated with coronavirus disease, which emerged in late 2019. In response, we developed a diagnostic panel consisting of 3 real-time reverse transcription PCR assays targeting the nucleocapsid gene and evaluated use of these assays for detecting SARS-CoV-2 infection. All assays demonstrated a linear dynamic range of 8 orders of magnitude and an analytical limit of detection of 5 copies/reaction of quantified RNA transcripts and 1 x 10-1.5 50% tissue culture infectious dose/mL of cell-cultured SARS-CoV-2. All assays performed comparably with nasopharyngeal and oropharyngeal secretions, serum, and fecal specimens spiked with cultured virus. We obtained no false-positive amplifications with other human coronaviruses or common respiratory pathogens. Results from all 3 assays were highly correlated during clinical specimen testing. On February 4, 2020, the Food and Drug Administration issued an Emergency Use Authorization to enable emergency use of this panel.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/diagnosis , Nucleocapsid Proteins/genetics , Pneumonia, Viral/diagnosis , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction/methods , Biomarkers/analysis , COVID-19 , Centers for Disease Control and Prevention, U.S. , Coronavirus Infections/virology , Coronavirus Nucleocapsid Proteins , DNA Primers/chemical synthesis , DNA Primers/genetics , Feces/virology , Fluoresceins/chemistry , Fluorescent Dyes/chemistry , Humans , Limit of Detection , Nasopharynx/virology , Pandemics , Phosphoproteins , Pneumonia, Viral/virology , Real-Time Polymerase Chain Reaction/standards , Reproducibility of Results , SARS-CoV-2 , Sputum/virology , United States
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