Four successive waves of infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has caused the ongoing pandemic of coronavirus disease 2019 (COVID-19), have hit Hong Kong.
A recent article in the Centers for Disease Control and Prevention (CDC)’s Emerging Infectious Diseases reveals that the last of these was probably due to the introduction of a new variant from Nepal. This novel variant had been circulating in the community for about a month before the last outbreak was reported.
SARS-CoV-2 has been identified as having evolved into several clades from the original Wuhan strain. In the current paper, the researchers focused on the clade GH variant, which has proved to induce low levels of inflammation and of interferon-stimulated genes in human airway cells, in culture.
The Hong Kong outbreaks
Hong Kong had four waves of COVID-19, with a total of 10,400 cases by February 2021. Wave 3 (June-end to September 2020) was traced to a single introduction of a viral variant from clade GR, while wave 4 (November 2020 to the present) is caused by a clade GH variant.
Community introduction and spread
Though the current outbreak began in November 2020, the researchers had already, in early October, found almost identical viral genomes from two clusters of patients from two building complexes in the same district. All showed the same clade GH variant, unlike the cases that occurred during the third wave.
Our results indicate that this newly introduced clade GH virus was circulating in the local community ≈1 month before the beginning of the fourth epidemic wave in Hong Kong.”
However, they found that three of four patients with imported infection in a single cluster near the index cases, as well as two other patients in another district, had the same viral genomes. These patients were all under mandatory quarantine and had arrived on the same flight in the second week of September 2020, from Nepal.
The first three patients were quarantined in another hotel near the two buildings already mentioned, while the other two patients were in a hotel in another district. A fourth patient in the first hotel developed COVID-19 despite having tested negative twice, on arrival and after 12 days, while still quarantined.
This could indicate that either this patient had a very long incubation period after being infected in Nepal, or that he was infected on the flight. He tested positive only after he was released from quarantine. This presents one possible route of introduction of this clade GH virus into the local community.
Of course, it may have arrived via another undetected chain of transmission.
The analysis of the viral genome shows that this virus has the following mutations, namely: RdRp[L323P] affecting the RNA-dependent RNA polymerase, the D614G spike mutation, the open reading frame 3a ORF3a Q57H, ORF3bE14, and the nucleocapsid N S194L mutations.
Of these, the Q57H mutation leads to the ORF3b E14 truncation, which affects ORF3b, a major antagonist of the interferon pathway. This wave 4 virus was compared with the wave 3 virus, which has only D614G, and wave 1, which has neither D614G nor Q57H.
No replication advantage
The study of viral replication in human organ culture and human airway organoids showed that the wave 4 virus in the human bronchial tissue had a rate of replication that was equivalent to that of the wave 1 virus. In lung tissues, however, it was slower to replicate than the other, when assessed at 48 hours, 72 hours, and 96 hours.
In contrast, the wave 3 virus replicated slightly more rapidly than the wave 1 virus in human bronchus cell culture, but not in human lung cultures. Thus, the wave 3 virus may be better at viral replication than the wave 1 virus.
Does not induce inflammation
With regard to the inflammatory nature of the virus, the wave 1 virus had already been shown by these researchers to be incapable of inducing powerful inflammatory mediators, as shown by the low levels of inflammatory cytokines and chemokines in the infected human cells.
The Q57H mutation did not change this property. When tested in human respiratory organoid cultures, the viral ribonucleic acid (RNA) from cells infected with the wave 3 virus or the wave 4 virus was found to be even lower than in cells infected by the wave 1 virus, by about one log unit.
What are the conclusions?
The wave 4 virus thus caused low cytokines, chemokines and interferon-stimulated gene expression, like the wave 1 virus. However, the wave 3 virus caused higher gene expression than wave 1 virus, as shown by measurement of the interferon-γ-induced protein-10.
Despite the major ORF3b deletion, our results demonstrate that the wave 4 virus does not have an enhanced ability to replicate ex vivo and retains potent innate immune evasion capacity in our experimental models.”
The wave 3 virus has some unique mutations, mainly in the ORF1ab and N gene. It is somewhat better at replication than wave 1 or wave 4 viruses, and can elicit a more robust innate immune response, according to the observations made in the experimental models.
However, the findings indicate that the SARS-CoV-2 mutant responsible for the fourth wave of COVID-19 in Hong Kong does not replicate faster than earlier variants, nor does it induce powerful inflammatory reactions. The need for strict containment policies remains imperative, given the highly localized nature of the index cases.