The coronavirus (SARS-CoV-2) is a very cunning virus that, despite its simple structure, is constantly mutating.
So far, the new crown virus has had many "doppelgangers" through continuous mutation [1]:
Alpha: First discovered in the UK in September 2020, the variant was severely ill and had a high mortality rate, but low immune escape, and the immune system was able to recognize it and attack it.
Beta: First discovered in South Africa in May 2020, this variant is highly transmissible but usually less severe.
Gamma: First discovered in Brazil in November 2020, this variant causes a high proportion of severe and critical illnesses.
Delta: First discovered in India in October 2020, this is yet another highly transmitted variant.
Omicron: First discovered in South Africa in November 2021, this is a highly contagious variant with atypical symptoms, high occultity, and easy missed diagnosis.
At present, the main epidemic strain worldwide is TheOmexon. It is a "fierce character", fast,highly contagious and stealthily transmitted, and has two "big name" clones, BA.1 and BA.2.
At present, the main strain that is raging in Shanghai, Jilin and other places in the mainland is the Omicron sub-variant BA.2.
Recently, the UK Health Security Agency (UKHSA) released a report that mentioned three recombinant variants of the new crown virus – XD, XE and XF[2].
Recombinant variant refers to a new strain formed by the merger of several popular variant strains, which is equivalent to poisoning.
Recombinant variants are not uncommon, and when the body is infected with 2 or more NEW CORONAVIRUS variants at the same time, it may produce recombinant variants. However, the vast majority of recombinant variants die out quickly, and those that remain are generally strains with virulence and transmission advantages.
We can use the following figure to understand the three recombinant variants of XD, XE and XF in this report.
(Fig. 1 XD, XE, XD recombinant sequence display[2])
From the figure we can derive the following information:
Row 1 orange shows the full genome length of SARS-CoV-2;
The second row uses red, yellow, and orange to represent the composition of SARS-CoV-2;
The 3rd row of green represents the genome of the mutant strain Delta;
The 4th row of deep purple represents the genome of the mutant strain Omicron BA.1;
The 5th row of light purple represents the genome of the mutant strain Omicron BA.2;
Both the XD and XF variants are a recombination of the Omicron BA.1 and Delta variants, but they are combined in different ways, so different variants are formed;
The XE variant is a combination of Omicron BA.1 and BA.2.
Of these 3 recombinant variants, the one that comes the most attention is XE. The main reason is that it is very strong, spreading 9.8% faster than BA.2, which may cause a widespread epidemic [2].
As of 22 March this year, 637 cases of XE infection have been detected in the United Kingdom, and in February this year, two arriving passengers in Hong Kong were found to be infected with the Mixed Virus XE of Omikejong, but fortunately they were isolated and did not flow into the community [3].
In the report, the researchers assessed the growth rate of XE. Growth rate is a measure of the rate at which infections are diagnosed. Through it, we can understand how strong the spread rate of XE is.
Prior to this, the growth rate of BA.2 was 75% higher than that of other Omikejung strains. But XE's growth rate is 9.8% higher than BA.2.
This means that XE will spread faster than BA.2, potentially triggering a new mass epidemic [2].
(Figure 2 Comparison of XE and BA.2 growth rates[2])
There is currently insufficient evidence for the severity of XE infection (severe illness rate, mortality) and immune evasion. But only in terms of propagation, XE is definitely a mutant that should not be underestimated. The WHO also warns not to trivialize or underestimate the dangers of recombinant strains [2].
Is antigen detection good?
Antigen testing, the antigen kit that can currently be tested at home, detects the nucleocapsid protein (NP) of the new coronavirus in a sample. After the new coronavirus mutates, the relative position of the nucleocapsid protein may also mutate (as shown in the table below).
(Table 1 Nucleocapsid protein mutations in the new crown strain[4])
Antigen detection studies compared their ability to detect different variants and found that the sensitivity of antigen detection was only slightly different from that of the original strain.
(Fig. 3 Comparison of detection performance of a certain antigen test on the new coronavirus variant strain[4])
Although there is currently no evidence of the sensitivity of antigen testing to XE, based on data from previous studies, it is inferred that antigen testing should be able to detect XE infection.
Nucleic acid testing remains the most reliable method
Nucleic acid detection, you can directly detect the viral nucleic acid to determine whether it is infected, in the new crown virus detection, the virus nucleic acid multiple targets (ORF1ab gene, N gene, S gene) will be tested.
When confronted with Omikeron, nucleic acid tests cannot detect the S gene in the target gene, which is known as S-Gene Target Failure (SGTF). It was in this way that the examiner was able to distinguish Between Omikeron and other mutants.
However, the emergence of the Omiljung variant BA.2 made it no longer have the so-called "S gene deletion" feature, resulting in its "stealth" when it first appeared. However, with the deepening of understanding of it, after adjusting the detection method, nucleic acid testing can detect BA.2.
The XE infection cases found in the UNITED Kingdom are all confirmed by nucleic acid testing, so we can rest assured that nucleic acid testing can detect XE infection.
To date, there is not enough evidence to understand the effect of vaccines on this variant. But the vaccine's effectiveness against Omikeron has been validated by multiple studies.
On March 22, the University of Hong Kong released a study evaluating the effectiveness of two vaccines, Pfizer/BioNTech vaccine, on Opichron.
The results of the study showed that both Fupitai and Koxing could reduce the risk of severe illness or death after infection with Omilton, and only one dose could be effective [5].
(Fig. 4 Effectiveness of the COVID-19 vaccine on Amiqueron[5])
It can be seen that for the CURRENT leading epidemic of BA.2, the vaccine can play an effective protective role. XE as a combination of BA.1 and BA.2, although the vaccine effect is not yet clear, but it can not be denied vaccination. Standardized vaccination is still one of the most powerful means of protecting yourself.
In addition to vaccination, doing a good job of daily protection, reducing mobility, and treating the various medical problems brought to us by the new crown pneumonia in a scientific and rational manner will also help us better protect ourselves.
Review expert: Pan Lei
Physician of Respiratory and Critical Care Medicine, Shanghai Public Health Clinical Center
bibliography
[1].https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
[2].https://www.gov.uk/government/publications/investigation-of-sars-cov-2-variants-technical-briefings
[3].https://news.sina.cn/gn/2022-04-02/detail-imcwiwss9503449.d.html
[4]. Weishampel ZA， Young J， Fischl M， Fischer RJ， et al. OraSure InteliSwab Rapid Antigen Test performance with the SARS-CoV-2 Variants of Concern Alpha， Beta， Gamma， Delta， and Omicron. medRxiv
[5].http://www.med.hku.hk/en/news/press//-/media/HKU-Med-Fac/News/slides/20220322-wave_5_omicron_PHSM_update_final.ashx
Author: Ye Yichu | Editors: Wu Jiaxiang, Ye Zhengxing
Typesetting: Han Ningning | Operations: Li Yongmin | Coordinator: Ye Yichu