The major findings are described in six sections: the virus, the outbreak, transmission dynamics, disease progression and severity, the China response and knowledge gaps. More detailed descriptions of technical findings are provided in Annex C.
On 30 December 2019, three bronchoalveolar lavage samples were collected from a patient with pneumonia of unknown etiology – a surveillance definition established following the SARS outbreak of 2002-2003 – in Wuhan Jinyintan Hospital. Real-time PCR (RT-PCR) assays on these samples were positive for pan-Betacoronavirus. Using Illumina and nanopore sequencing, the whole genome sequences of the virus were acquired. Bioinformatic analyses indicated that the virus had features typical of the coronavirus family and belonged to the Betacoronavirus 2B lineage. Alignment of the full-length genome sequence of the COVID-19 virus and other available genomes of Betacoronavirus showed the closest relationship was with the bat SARS-like coronavirus strain BatCov RaTG13, identity 96%. Virus isolation was conducted with various cell lines, such as human airway epithelial cells, Vero E6, and Huh-7. Cytopathic effects (CPE) were observed 96 hours after inoculation. Typical crown-like particles were observed under transmission electron microscope (TEM) with negative staining. The cellular infectivity of the isolated viruses could be completely neutralized by the sera collected from convalescent patients. Transgenic human ACE2 mice and Rhesus monkey intranasally challenged by this virus isolate induced multifocal pneumonia with interstitial hyperplasia. The COVID-19 virus was subsequently detected and isolated in the lung and intestinal tissues of the challenged animals.
Whole genome sequencing analysis of 104 strains of the COVID-19 virus isolated from patients in different localities with symptom onset between the end of December 2019 and mid-February 2020 showed 99.9% homology, without significant mutation (Figure 1).
Figure 1. Phylogenetic analysis of the COVID-19 virus and its closely related reference genomes Note: COVID-19 virus is referred to as 2019-nCoV in the figure, the interim virus name WHO announced early in the outbreak.
Post-mortem samples from a 50-year old male patient from Wuhan were taken from the lung, liver, and heart. Histological examination showed bilateral diffuse alveolar damage with cellular fibromyxoid exudates. The lung showed evident desquamation of pneumocytes and hyaline membrane formation, indicating acute respiratory distress syndrome (ARDS). Lung tissue also displayed cellular and fibromyxoid exudation, desquamation of pneumocytes and pulmonary oedema. Interstitial mononuclear inflammatory infiltrates, dominated by lymphocytes, were seen in both lungs. Multinucleated syncytial cells with atypical enlarged pneumocytes characterized by large nuclei, amphophilic granular cytoplasm, and prominent nucleoli were identified in the intraalveolar spaces, showing viral cytopathic-like changes. No obvious intranuclear or intracytoplasmic viral inclusions were identified.
Categories: Origins, Symptoms, Vaccine