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Issue 2: Basic science of SAR2-CoV-2 (MARCH 12, 2020)
- The SARS-CoV-2 or COVID-19-virus is a novel beta-coronavirus, and is the fifth of this group to be identified1.
- To date, two active strains have been characterized: the less-aggressive ancestral S strain and the evolved, prevalent variant L strain; the latter accounts for ~70% of cases2.
- The genomic sequences of SARS-CoV-2 viruses isolated from a number of patients share sequence identity higher than 99.9%, suggesting a very recent host shift into humans; where pangolins possibly provided a partial spike gene (S) to SARS-CoV-23,4.
- The SARS-CoV-2 binds to the angiotensin converting enzyme II (ACE2) via the receptor binding domain of the S protein, where membrane fusion and entry into human cells is initiated 1.
- A pooled analysis of COVID-19 cases reported a median incubation time of 5.1 days, and 97.5% of cases developed within 11.5 days (95% CI: 8.2-15.6 days). Conservatively therefore, 101 out of every 10,000 cases (99th percentile, 482) will develop symptoms after 14 days of active monitoring or quarantine5.
- Another recent, but small, study suggests that the serial interval (i.e., time between disease onset in direct infector-infectee pairs) is shorter, at 4.0 days6.
- Notably, virus reproduction follows exponential growth with a reproduction number between 2.24-3.587.
- Confirmation of cases of COVID-19 is based on detection of unique sequences of virus RNA by nucleic acid amplification tests (NAAT) such as real-time reverse transcription polymerase chain reaction (rRT-PCR) and confirmation by nucleic acid sequencing when necessary8.
- Viral genes targeted so far include the N, E, S and RdRP genes.
- A negative test does not necessarily rule out COVID-19 infection. Assessment of overall specimen quality and repeat testing may be warranted8.
- At minimum, respiratory material should be collected from upper respiratory specimens: nasopharyngeal and oropharyngeal swab or wash in ambulatory patients; and/or lower respiratory specimens from sputum (if produced) and/or endotracheal aspirate or bronchoalveolar lavage in patients with more severe respiratory disease8.
- There are no specific therapies directed at SARS-CoV-2, but broad-spectrum antiviral agents such as remdesivir have shown good effects9.
- Several clinical trials are being conducted in China to assess efficacy of LPV/RTV and 157 IFNα-2b or chloroquine in hospitalized COVID-19 patients.