Diagnosis

Presymptomatic phase

Infection can be 2-14 days before symptoms appear. CDF from https://www.acpjournals.org/doi/10.7326/M20-0504 below.

So, a 10 day quarantine catches about 90% of the cases. 11.5 days (CI, 8.2 to 15.6 days) for 97.5% of infected persons

Symptoms

Major

  • Fever
  • Cough
  • Shortness of breath

Minor

  • Tiredness, body ache, sore throat, diarrhea, vomiting
  • stuffy nose, Loss of smell

Case studies

  • 2021 Apr - puNe. याजुषी.
    • आरम्भे ज्वरः। महती श्रान्तिः। ततोऽग्रे किञ्चिदिव कासः। ज्वरेऽपगते महाश्रान्तिः। स्थातुमपि न शक्यते तादृशी। अधुनैव शनैः शनैः सामान्यकार्याणि कर्तुं शक्नोमि।
    • गृहे अन्येषां तु पूर्वं कासः ततः ज्वरः। पुत्रयोः उभयम्। तयोः शीघ्रमेव लक्षणमुक्तिरभूत्।
    • रोगमुक्तिस्तु टेस्ट कृत्वैव ज्ञायेत। श्रान्तिरेवैकं महत्कष्टम्।
  • 2020 Aug - Devanahalli, BLR. Patient and wife reported fever which came and went for about 4 days. Then, pulse oxymeter showed 92% saturation in patient. He tested positive.
  • When on oxygen, saturation level is 95, but when he goes to toilet etc.., it comes down to 80.

Big list

Respiratory symptoms

  • Breathlessness
  • Cough

Cardiovascular symptoms

  • Chest tightness
  • Chest pain
  • Palpitations

Generalised symptoms

  • Fatigue
  • Fever
  • Pain

Neurological symptoms

  • Cognitive impairment (‘brain fog’, loss of concentration or memory issues)
  • Headache
  • Sleep disturbance
  • Peripheral neuropathy symptoms (pins and needles and numbness)
  • Dizziness
  • Delirium (in older populations)

Gastrointestinal symptoms

  • Abdominal pain
  • Nausea
  • Diarrhoea
  • Anorexia and reduced appetite (in older populations)

Musculoskeletal symptoms

  • Joint pain
  • Muscle pain

Psychological/psychiatric symptoms

  • Symptoms of depression
  • Symptoms of anxiety

Ear, nose and throat symptoms

  • Tinnitus
  • Earache
  • Sore throat
  • Dizziness
  • Loss of taste and/or smell

Dermatological

  • Skin rashes

Tests for infection

  • “RT-PCR remains the gold standard for the diagnosis of COVID-19 in sputum samples. However, the combination of different diagnostic tests is highly recommended to achieve adequate sensitivity and specificity.”

Test metrics

  • See here for intro.

Sample collection

  • Saliva better - “saliva viral load was significantly higher in those with COVID-19 risk factors; that it correlated with increasing levels of disease severity and showed a superior ability over nasopharyngeal viral load as a predictor of mortality over time (AUC=0.90).”
  • nasopharynx swabs.

RNA detection

RT-PCR

  • Intro elsewhere.
  • “The current RT-PCR has a sensitivity at best of 70 percent with a turn around time of 120 minutes.”
  • For RT-PCR tests, rectal stools/swab, urine, and plasma were less sensitive while sputum (97.2% [90.3%-99.7%]) presented higher sensitivity for detecting the virus. pubmed
  • The CT (cycle threshold) value indicates the number of cycles in the RT-PCR test which are needed to amplify viral RNA to a detectable level. A low CT value (less than 25) indicates a high viral load and it significantly improves the chances of genomic sequencing. If the CT value is high, then sequencing becomes difficult.
  • Most RT-PCR kits detect maximum 3 genes of SARS-COV-2 (As of Jan 2022 in India ).

Crisper based

  • A Crisper based diagnostic testing tried out in Thailand offers 97-100 percent sensitivity to detect the virus and has a turn around time of 75 minutes.

Antigen tests

  • detect small viral proteins ( antigens).
  • The tests require rubbing a shallow nasal swab inside your nostrils and then exposing the swab to a few drops of chemicals. They provide results in about 15 minutes.
  • Rapid, inexpensive paper strip tests can tell you whether you are contagious. Research shows that if taken frequently, these tests will drive down infections. RT
  • ICMR advisory, validated kits here.
  • Maximum duration for interpreting a positive or negative test is 30 minutes. After that the test strip should be discarded.

Accuracy

  • False negatives
    • Rapid antigen tests, which do not amplify the virus, are less sensitive than P.C.R. tests.
    • Good at flagging people who have high viral loads
    • overall sensitivity of roughly 85 percent. In some studies, their real-world performance has been even lower.
    • False negatives more likely during the earliest phase of an infection.
    • tests are more sensitive in people with symptoms than without and are most sensitive during the first week of symptoms
    • Compensation by repitition - “tested infected college students and employees every three days, rapid antigen tests successfully identified 98 percent of infections, on par with P.C.R. tests.”
    • home kit sensitivity during tests is more accurate when taking throat swab along with nasal cavity swab.
  • False positives
    • highly specific, which means that they generate relatively few false positives.
    • positive result is more likely to be a false positive when the prevalence of the virus is low
    • Tackling false positives - use different antigen test strip.

Severity tests

Blood tests

  • Get a Complete Blood Count (CBC) and C-reactive Protein (CrP) test as soon as ANY symptoms appear. This is an inexpensive (<1k) and relatively fast (although taking 24+ hours in Delhi now) test that is extremely important to measure severity of infection - detects tissue damage and infection signs.

CT scans

  • High resolution computed tomography (HRCT)
  • At prevalance 15%, 20200822
    • Sensitivity (fraction of positives caught) - 86%
    • Specificity (fraction of negatives marked as negative) - 18%
  • CT scans need you to travel to labs + cost >5k and reports are available in a few hours.
  • CT scan 18+/25 is terrible. 202104 Victoria Hospital BLR shivakumAr

Antibody tests

  • Prick blood and put on test strip.
  • “The combination of IgM and IgG antibodies demonstrated promising results for both parameters (84.5% [82.2%-86.6%]; 91.6% [86.0%-95.4%], respectively). "

Oxygen levels

  • Pulse oximeters help diagnose the infection.
  • For SpO2 below 92-93, you might need hospitalisation. Before making that call, take a 6-min walk test. If levels rise, good. Else go to a hospital where oxygen therapy & some steroids will be given.

Aggregation

  • If O2 sat. is remaining above 95 and CrP is below 5 on Day 5, then in all likelihood one is out of the woods.
  • If the sat is dropping (<93) and CrP is still high by Day 5 -> needs stronger medication