The first case of co-infection by two COVID-19 Omicron subvariants

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The first case of co-infection by two COVID-19 Omicron subvariants

The first case of co-infection by two COVID-19 Omicron subvariants.

Circulation of infectious SARS-CoV-2 variants and suboptimal vaccine protection create conditions for simultaneous infection with multiple strains, which may generate cross-lineage SARS-CoV-2 recombinants with new unpredictable characteristics . Since the first wave of the epidemic, co-infections have been reported.

Co-infection with omicron and delta has been found in immunocompetent and immunocompromised patients living in different geographic regions. Because these variants are characterized by distinct genomic sequences, their co-occurrence can be rapidly identified.

Although recombination between closely related variants is difficult to identify, this does not preclude them from occurring. As of mid-2022, a total of 637 cases of omicron BA.1 and BA.2 recombinants, known as XE, have been confirmed in the UK, and the number is still increasing. These data also suggest that intraline recombination produces highly transmissible chimeric strains.

Recently, China reported the first case of a patient co-infected with two subvariants of coronavirus Omicron. The patient is a 67-year-old woman who lives in Yunyang County, Chongqing City.

The woman tested positive in two samples for the virus, which contained features of the subvariants BA.5.2.48 and BF.7.14, the Chinese Center for Disease Control and Prevention Weekly reported.

On February 7, 2023, the 67-year-old female patient in Yunyang County, Chongqing City was found to have a history of malignant tumors and had received chemotherapy, radiotherapy, and targeted treatments within the past 6 months. Suspected of low immunity, but no other underlying diseases, smoking history, drinking habits. The patient had received the Sinovac vaccine against coronavirus disease 2019 (COVID-19) twice .

On December 23, 2022, the patient reported loss of appetite.
On December 29, she developed fatigue, cough, and tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen.

On January 4, 2023, she developed chills and fever (body temperature 38.9°C), accompanied by cough symptoms. She was admitted to the Yunyang County Hospital of Traditional Chinese Medicine, but no obvious improvement was seen, and she was discharged on January 5.
On January 6, she was admitted to the Department of Infectious Diseases, the Third Affiliated Hospital of Chongqing Medical University. She continues to have a fever and cough.
From January 6 to February 12, a total of 8 people in the hospital tested positive for nucleic acid.

During the investigation, her family members and neighbors were found to be infected in late December, indicating potential exposure. During her two hospitalizations, she may have been exposed to other people infected with SARS-CoV-2.

Samples from the patient’s upper respiratory tract were collected on January 28 and February 7, 2023, and named YB20230158 and YB20230202, respectively, to exclude contamination.

Using detection methods such as PCR and phylogenetic analysis, it was found that these two samples formed an independent clade, which was different from Omicron subvariants BA.5.2.48 and BF.7.14.

Analysis of mutation sites showed that both samples contained specific definition sites of Omicron subvariants BA.5.2.48 and BF.7.14.

Phylogenetic analysis of two co-infecting strains from a patient with Omicron BF.7.14 and BA.5.2.48.

The heterozygosity status and specific mutation frequencies at these positions were verified using IGV 2.10.2 , indicating that the patient was co-infected with the Omicron subvariants BA.5.2.48 and BF.7.14.

Since the start of the pandemic, there have been reports of co-infections with Omicron, Delta, and influenza around the world.

Proper detection of co-infections is critical to understanding the clinical impact and risks of potential recombinants, French researchers said in a paper in the journal Nature last October.

But in a peer-reviewed article published in the medical journal Cureus, researchers in India say co-infection played no or very small role in increasing India’s second wave of Covid-19.

The reports of the Chinese cases came as the World Health Organization (WHO) declared that the pandemic phase of the virus was on track to end. It also comes a week after the third anniversary of the World Health Organization declaring the Covid-19 pandemic.

However, no new variants emerged after China reopened in the first few weeks of the first wave of Covid-19, George Gao Fu, former director of the Chinese Center for Disease Control and Prevention, and a colleague published in The Lancet in early February According to the study, this wave is mainly caused by the BA.5.2 and BF.7 subvariants that have spread in other parts of the world.

According to the “National SARS-CoV-2 Infection Epidemic Report” issued by the Chinese Center for Disease Control and Prevention, the main strain of SARS-CoV-2 circulating in Chongqing is BA.5.2.48 (>90%), followed by BF.7.14 (approx. 3.8%).

So far, there is no report of co-infection between BA.5.2.48 and BF.7.14 in China, especially in Chongqing, where the proportion of BF.7.14 is low, so the report is more meaningful. Surveillance for SARS-CoV-2 variants should be promoted as an important strategy for identifying co-infection and recombinant cases.

Surveillance of SARS-CoV-2 variants, especially in key populations with immunocompromise, is becoming increasingly important as the risk of co-circulation of variants in an area increases.

Source :

https://weekly.chinacdc.cn/en/article/doi/10.46234/ccdcw2023.046
https://www.scmp.com/news/china/science/article/3214021/coronavirus-china-reports-first-case-coinfection-two-omicron-subvariants?module=perpetual_scroll_0&pgtype=article&campaign=3214021

The first case of co-infection by two COVID-19 Omicron subvariants.

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