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SARS Cov2 laboratory

Epidemiology: - viral loads of Omicron-infected patients appear to peak on 4th day of symptoms [111]* * implications for maximum sensitivity detecting Omicron infection Laboratory: - complete blood count (CBC) - lymphopenia (63%) [1,11], neutropenia may occur in the elderly [8] - elevated RDW on admission & increasing RDW during hospitalization associated with higher mortality risk [42] - pulse oximetry may reveal hypoxemia (even in the absence of dyspnea) [22] - normal pCO2 may play role in silent hypoxemia - SaO2 q4h - prothrombin time, plasma fibrinogen [21] - elevated serum LDH, elevated serum C-reactive protein, elevated serum IL6 & serum ferritin (markers of inflammation), elevated D-dimer - elevated plasma D-dimer risk factor for mortality in Wuhan patients [5] - plasma D-dimer is elevated in most Covid-19 patients - a normal plasma D-dimer excluses pulmonary embolism [93] - elevated serum troponin-T associated with increased mortality [20] - serum procalcitonin to rule out bacterial pneumonia associated with less antibiotic initiation [110] - high serum cortisol on admission predicts mortality [54] - chemistry panel - high serum glucose on hospital admission predicts severity & mortality (RR=2) [59] - liver function tests (may be elevated due to COVID-19 &/or due to treatment) [39] - elevated serum ALT & serum AST (14-53%) [39] - elevated serum bilirubin (total) (17%) [39] - vitamin D deficiency of unclear relationship to COVID-19 [43] - serum 25-OH vitamin D < 30 ng/mL may be associated with higher mortality [43] - low serum 25-OH vitamin D associated with higher serum C-reactive protein & lymphopenia [43] - no consistent relationship of vitamin D deficiency with COVID-19 - SARS-CoV2 seropositivity is not associated with low serum 25-OH vitamin D independent of other risk factors [85] - low serum testosterone in men associated with severe cases of Covid-19 [86] - average serum testosterone of men admitted to ICU 49 ng/dL - by day 3 of hospitalization average serum testosterone 19 ng/dL - low serum testosterone found to correlate with signs of inflammation [86] - no proof that low serum testosterone causes more severe Covid-19 [86] - low serum testosterone may serve as a risk factor or prognostic indicator [36] - neurofilament light chain in serum - elevated levels in critically ill patients with COVID-19 encephalopathy relative to critically ill patients without COVID-19 [97] - elevated levels predict unfavorable short-term outcome, including in-hospital mortality [97] - neuronal injury may be common & pronounced in critically ill COVID-19 patients - total tau in serum, p-tau181 in serum & GFAP in serum are significantly elevated in patients with Covid-19 encephalopathy & in Covid-19 patients who die in-hospital - total tau in serum & GFAP in serum are significantly lower in patients with Covid-19 who are discharged home - do not perform stool testing for COVID-19 [39] === SARS CoV2 RNA === - SARS-CoV2 RNA - specimen: (% positive in patients with known COVID-19) [7] - bronchoalveolar lavage (93%), sputum (72%), nasal swab (63%). bronchial brush biopsy (46%) pharyngeal swabs (32%), feces (29-41%), blood (1%) - 70% of patients with persistently positive stool RNA even after respiratory RNA had become negative [24,50] - found in semen of 16% of men with COVID-19 [33] - not found in urine [7] - highest viral loads found in nasal swabs [7] - video on obtaining nasopharyngeal swab (standard for screening) [25] - illustration of obtaining nasopharyngeal swab [53] - self-collected midnasal swabs with 80% sensitivity & 98% specificity relative to nasopharyngeal swab in symptomatic patients - saliva yields greater detection sensitivity & consistency throughout the course of infection than nasopharyngeal swabs [30,38] - SalivaDirect used by NBA is FDA-approved for emergency use - saliva & healthcare worker-collected nasopharyngeal swabs performed similarly & better than self-collected nasal swabs [44] - saliva testing has similar sensitivity & specificity to nasopharyngeal testing [70] - saliva testing sensitivity 71% of nasopharyngeal testing during 1st week of Covid-19 infection [91] - saliva more likely positive in symptomatic vs asymptomatic people (88% vs 58%) - saliva testing performs best in patients with high nasopharyngeal viral loads - sensitivity of saliva vs nasopharyngeal testing drops to <20% after 4 weeks [91] - no discussion of false positives with nasopharyngeal testing found - conjunctival swabs positive from one eye but not the other in 23% [77] - sensitivity of a negative RT-PCR is 70% (seems to refer to predictive value of a negative test); sensitivity of a positive RT-PCR is allegedly better [18] - RT-PCR becomes positive 5-7 days after exposure - RT-PCR may remain positive after clinical recovery - 2.7% of adults, 3.4% of children [31] - 1 in 6 patients recovered from COVID-19 retest positive >= 2 weeks later [57] - attributed to persistence of dead virus [31] - median duration to negative RT-PCR tests of upper respiratory tract is 11 days (95% CI 10-12 days) [12]; 3 weeks [29]; 17 days [57] - median duration of viral RNA in stool samples is 17-22 days, compared with 15-18 days in lower respiratory tract & 16-17 days in serum samples [26,57] - for patients with severe disease, median duration of the virus in respiratory samples is 21 days, versus 14 days with mild disease [26] - viral load does not appear to correlate with symptoms [53] - higher viral loads may be seen with less severe COVID-19 [2] - higher viral loads predict more severe disease [65] - transplant recipients more likely to have higher viral loads [65] - maximum shedding duration is 83 days from upper respiratory tract, 59 days 126 days in stools, & 60 days in serum [57] - China is beginning testing anal swabs [72] - if feces cannot be obtained, a saline-soaked cotton swab ~ 1-2 inches long is inserted into the anus, & tested for active traces of the virus [72] - live virus is not detected beyond day 9 of illness, despite persistently high viral loads inferred from PCR cycle threshold values [57] - ref [32] shows time course virus-specific testing likely positive - - CDC recommends against testing same nursing home resident > once a day [51] - CDC says COVID-19 patients no longer need testing to come out of isolation if: - 10 days have past since onset of symptoms - afebrile for > 24 hours (no antipyretics) - asymptomatic (dyspnea & diarrhea specifically cited) [15] - CDC calls for all individuals even if fully vaccinated to be tested for COVID-19 following exposure even if asymptomatic [89,34] - assay using CRISPR technology as specific & more sensitive than RT-PCR in detecting SARS-CoV2 from clinical samples & may be done in <30 minutes [47] - process is isothermal reverse transcriptase loop mediated isothermal amplification (RT-LAMP) with DNA endonuclease-targeted CRISPR trans reporter (DETECTR) [47] - rt-PCR detection of B.1.1.7 variant (UK) may result in false negatives with: - Accula SARS-CoV-2 Test (Mesa Biotech Inc.) - Linea COVID-19 Assay Kit (Applied DNA Sciences, Inc.) - TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, Inc.) - Xpert Xpress SARS-CoV-2, Xpert Xpress SARS-CoV-2 DoD, Xpert Omni SARS-CoV-2 (Cepheid) - rt-PCR detection of omicron variant with Tide Laboratories LLC is expected to fail due to a 9-nucleotide deletion in the N-gene, spanning positions 28370-28362; the single genetic target of this test covers the portion of the N-gene where the deletions occur [95] - a PCR that uses flurescently labeled probes called "sloppy molecular beacons" that glow in different colors when they attach to RNA or DNA can identify all current variants of SARS CoV2, including alpha, beta, gamma, delta & omicron [100] - when the sample is heated, the probes fall off at different temperatures characteristic of the probe sequence & the Covid-19 variant & their color disappears - color & temperature of color transition identify the variant [100] - Roche is launching a SARS-CoV-2 variant test to help monitor emerging SARS-CoV2 mutations [78] - viral rebound occurs in 31% [108] - 95% show reduction of viral load with next measurement - doe not correlate with symptom rebound [108] === Serology === - Serology: [74] - qualitative detection of IgM & IgG Ab against SARS-CoV-2 in serum, plasma (EDTA or citrate), or whole blood (FDA approved for emergency use) [17] - most antibodies recognize viral nucleocapsid antigen [32] - optimal specificity & sensitivity at day 14 [46] - antibody (especially IgA) to spike protein more likely to confer immunity - 3 specific Ab SARS-CoV-2 infection (10% false-negatives, 5% false-positives) [46] - 30% of patients with very low levels of SARS-CoV-2-specific antibodies; 6% with undetectable antibody titers [23] - 94% of COVID-19 patients show a decline in antibody levels at 60 days & 28% have undetectable levels; lower antibody levels associated with less severe disease [62] - sensitivity of IgG/IgM Ab for SARS-CoV-2 during 1st week of symptoms is 30%, increasing to 91% during the 3rd week [56] - specificity of IgG/IgM Ab for SARS-CoV-2 is > 98% [56] - no evidence antibodies confer immunity [27,55] - SARS CoV-2 spike protein specific IgG with plasma 1/2 life of 36 days [16] - FDA authorizes SARS CoV2 neutralizing antibodies test [49] - no evidence that neutralizing Ab test detects confers any level of immunity [49] - presence of anti-spike or anti-nucleocapsid IgG antibodies associated with reduced risk of SARS-CoV-2 reinfection in health care workers in the ensuing 6 months [64] - semi-quantitative COVID-19 IgG testing kit (COVID-SeroKlir) FDA-approved & approved by the European Union. [58] - anti-spike-protein IgG3 best for determining immunity [69] - SARS-CoV2 IgG Ab reached a peak sensitivity of 0.75 112 days after positive RT-PCR [75] - antibodies to the receptor binding domain of the spike glycoprotein are present in 99% of Covid-19 confirmed survivors, 55% of Covid-19 unconfirmed persons & 11% of persons without Covid-19 [101] - SARS-CoV2 serology to assess immunity is flawed, utility questionable [93] === Viral culture === - in hospitalized patients with COVID-19 median time from symptom onset to - negative viral culture is 7 days - negative RT-PCR is 34 days [73] === Blood bank === - Blood bank: - blood type (see COVID-19 (SARS CoV2) Genetics: subsection) - T-detect COVID test identifies prior infection through T-cell DNA - estimated prevalence of SARS CoV2 in blood donations 1.16/100,000 [87] - estimated viral loads of positive donations 1000-4000 copies/mL - no infectivity observed in cell cultures of any blood donation [87] === Point-of-care tests === - Point of care diagnostic tests - SARS CoV2 antigen testing - Sofia SARS Antigen Fluorescent Immunoassay [28] - BD Veritor system - false positives noted [48] - among symptomatic, sensitivity of 80%, specificity of 99%, positive predictive value (PPV) of 94%, negative predictive value (NPV) of 96% [68] - among asymptomatic, sensitivity of 41%, a specificity of 98%, PPV of 33%, & NPV of 99% [68] - Abbott BinaxNOW rapid antigen test is 64% sensitive among symptomatic & 36% sensitive among asymptomatic; specificity is 100% [71] - Abbott BinaxNOW rapid antigen test is able to detect Omicron variant with similar performance [95] - Quidel QuickVue antigen test is able to detect Omicron variant with similar performance as with other variants [95] - Cepheid point of care test will deliver results ~45 minutes [9] - Abbott labs delivers RT-PCR test with results in 15 minutes [10] - caution using Abbott Fast COVID Test (may aerosolize virus) [10] - sensitivity < 70% [35] (test used by White House) - CovidNudge is a point of care RT-PCR test with 94% sensitivity & 100% specificity [41] - NIRVANA, can simultaneously detect & sequence SARS-CoV2, influenza & other viruses [80] - FDA warns of false negative Curative Inc rapid RT-PCR tests used in Los Angeles & other large metropolitan areas [67] - analyzed by Curative's KorvaLabs thus may not be entirely 'point of care' - QIAstat-Dx Respiratory SARS-CoV-2 Panel provides results in 1.7 hours - sensitivity & specificity 99% compared with PCR [45] - FDA issues emergency use authorization for Abbott BinaxNOW COVID-19 Ag Card, showing results directly on testing card (akin to typical pregnancy test) [37] - Abbott's Panbio COVID-19 Ag Rapid Test Device with > 42% false positives [96] - UC San Francisco developing rapid test that identifies spike protein Ab (sensitivity 89%) & N-protein Ab (sensitivity 98%), specificity 98% for both [83] - test results in 30 minutes - test uses SARS-CoV2 viral protein antigens spike-protein receptor-binding domain & N-protein terminal sequence fused to luminescent enzyme - luminescence read with commercially available handheld luminometer [83] - a point of care test combines two different CRISPR-Cas enzymes, Cas13 & Csm6, providing results in < 1 hour [90] - highly specific detection of antigens with nasopharyngeal swab specimens [92] - detection of SARS-CoV-2 nucleocapsid & spike receptor binding domain proteins down to 1 ng/mL (33 pM) - results take less than 5 min [92] - employs fluidic-atomic force microscopy mediated nanomechanical deflection method - FDA-approves emergency use authorization for point-of-care test detects SARS CoV2 variants of concern & both influenza A & influenza B with a single nasal swab [105] - this test is done by RT-PCR [106] - SARS-CoV2 breathalyzer detects SARS-CoV2 aerosols in two exhaled breaths with results in < 60 seconds [109] * Omicron variant tends to stay localized in the upper respiratory tract, thus individuals may remain Covid-19 positive past the 5 day isolation period. A positive antigen test in the post 5-day isolation period may mean you are potentially infective. [99] === Home-based testing === - FDA approves first at-home COVID-19 diagnostic test (Lucira) available by prescription, results in 30 minutes or less [52] - FDA approves diagnostic test for at home collection of patient samples to detect both COVID-19 & influenza A & B (flu) [61] - RT-PCR for COVID-19 + Flu for use with Quest Diagnostics Self-Collection Kit - collected sample is shipeed to a Quest Diagnostics laboratory for analysis [61] - Ellume at home over-the-counter rapid COVID-19 test detects nucleocapsid antigens shed by SARS-Cov2 detected in self collected nasal swabs & analyzes them with a single use lateral flow immunoassay within a bluetooth-enabled analyzer, which transmits the result to a smartphone placed nearby with results in 20 minutes (screening test, confirmation needed, cost estimate $30) [63] - symptomatic persons initially testing negative with a home antigen test should test again in 1-2 days because test sensitivity seems to peak several days after illness onset [102] - Medicare will not pay for home Covid-19 tests at retailers [98] - 8 of 20 at-home tests listed on FDA's website [104] had shelf-life extended - Abbott BinaxNOW & the iHealth test had 3 or 6 month extensions depending upon lot number [103] - shelf-life ranges from 4 months for Cue Health home test, to 18 months for Celltrion's DiaTrust test [103] - unsupervised SARS-CoV2 rapid antigen testing with 3 commercial kits with 70-81% sensitivity during the Omicron period in the Netherlands [104] === Symptom-based screening === - Given that COVID-19 may be transmitted through aerosolized breath from asymptomatic individuals, symptom-based screening is likely ineffective [19] - also see screening for COVID-19 === Regulation === - Ref [6] discusses regulation of laboratory-developed tests, issues of access & quality === False positive tests === * If false positive COVID-19 test suspected [LAJH] - SaO2 q4 hours. - O2 via NP to keep O2 sat > 90% - CBC, BMP, serum C-reactive protein, serum LDH, serum ferritin, & plasma D-dimer q3 days if < 2 L O2; qd of > 2 L O2 === Testing of nursing home staff === - frequent testing & immunity-based staffing interventions may reduce transmission of SARS-CoV-2 in nursing homes [88] * CMS requires nursing home staff to be tested for COVID-19 [36] === Detection of aerosolized SARS-CoV2 === * French hospital tests breathalyser to detect COVID-19 [13] - dogs can be trained to sniff out human cases of COVID-19 [14] in 1 week - Miami Heat, NBA basketball team using dogs to screen fans [14] - dogs can detect COVID-19 in crowded places, including airports, with sensitivity of 92-97% & specificity of 91% [84]; - also see screening for Covid-19 === Pooled surveillance === * Pooled surveillance testing may be useful for screening populations [60] === SARS CoV-2 in sewage === * Following SARS CoV-2 in sewage may provide population prevalence of virus in watershed of sewage drainage [76] === CDC Information for Laboratories === * See CDC Information for Laboratories [3] === SARS-CoV2 Viral Mutations: Impact on COVID-19 Tests === * See FDA: SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests [79].

Related

screening for COVID-19; screening for SARS-CoV2 severe acute respiratory syndrome coronavirus 2; SARS-CoV2; Wuhan coronavirus

References

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