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SARS-CoV-2 re-infection confirmed by whole-genome sequencing

Researchers have confirmed a case of re-infection, which suggests that SARS-CoV-2 may continue to circulate among the population despite herd immunity.


SARS-CoV-2 has rapidly spread across the world affecting millions of individuals and causing more than 0.8 million deaths. The high transmissibility of the virus through airborne, droplet and contact routes has led to large outbreaks in restaurants, bars, cruise ships, workplaces and healthcare environments.

One of the key questions since the start of the pandemic has been whether SARS-CoV-2 re-infection can occur. Despite rapid accumulation of neutralising antibodies after infection, recent studies have shown that antibody titres start to decline as early as 1-2 months after acute infection. A previous case report suggested that re-infection can occur. However, the researchers failed to perform viral genome analysis to confirm this.

In this recent study, published in Clinical Infectious Diseases, researchers encountered another report of re-infection occurring 4.5 months after the first episode. The team used whole-genome analysis to differentiate between re-infection and prolonged viral shedding. They also supported this with epidemiological, clinical and serological data.


The patient was a 33-year-old male living in Hong Kong. During the first episode, he presented with a cough and sputum, sore throat, fever and headache for three days. Specialists confirmed the diagnosis by RT-PCR of a posterior oropharyngeal saliva sample. The patient was hospitalised with symptoms in March 2020 and later released in mid-April 2020. During the second asymptomatic episode, the patient returned to Hong Kong from Spain via the UK in August. He tested positive for the virus during entry screening at Hong Kong airport. He was hospitalised again; however, he remained asymptomatic.

Serological evidence showed elevated levels of C-reactive protein and SARS-CoV-2 IgG. Genome analysis revealed that the viral genomes from the first and second episodes belonged to distinct lineages. The genomes had 24 nucleotide differences. The team found that the viral genome from the first episode was phylogenetically closely related to strains collected in March/April. The second virus genome, however, was closely related to strains collected in July/August.


This study reports the first case of re-infection of SARS-CoV-2. Evidence supports that the second episode was in fact re-infection rather than prolonged viral shedding. This confirmation is key because it suggests that herd immunity is unlikely to eliminate SARS-CoV-2. It is likely that the virus will continue to circulate in the human population, as is the case for other coronaviruses. Importantly, it emphasises that vaccination should still be considered for those previously infected. These individuals must also comply with epidemiological control measures issued by governments. It is important that researchers investigate cases of re-infection further to gain a better understanding of immune markers that are associated with protection against disease. This in turn will help with vaccine design.

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Coronavirus / covid-19 / WGS