Possible recombination between two variants of concern in a COVID-19 patient

He, Yaqing; Ma, Wenping; Dang, Shengyuan; Chen, Long; Zhang, Renli; Mei, Shujiang; Wei, Xinyi; Lv, Qiuying; Peng, Bo; Chen, Jiancheng; Kong, Dongfeng; Sun, Ying; Tang, Xiujuan; Wu, Weihua; Chen, Zhigao; Li, Shimin; Jia, Wei‐Hua; Zou, Xuan; Li, Mingkun; Feng, Tiejian; Ren, Lili; Wang, Jianwei

doi:10.1080/22221751.2022.2032375

Cited by 32 publications

(37 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Virus co-infection and recombination can amplify pathogenicity, for example, the well-studied "model organism" adenovirus [14][15][16][17][18][19][20] , and also in coronaviruses [21][22][23] . SARS-CoV-2 has been shown to co-infect and recombine 26,43 . In host populations with disproportionate immunocompromised conditions, such as Africa 44 , the possibility of long-term infections of SARS-CoV-2 variants may be higher than in populations otherwise healthy and/or vaccinated.…”

Section: Co-infections Of Different Sars-cov-2 Variants In the Popula...mentioning

confidence: 99%

“…Delta) in a 14-day period. Furthermore, putative evidence of recombination in the Orf1ab and spike genes was shown 26 . Such recombination events may not be rare, especially considering that there are hundreds of variants circulating in the general population.…”

Section: Co-infections Of Different Sars-cov-2 Variants In the Popula...mentioning

confidence: 99%

“…The patient was found to be coinfected with two SARS-CoV-2 variants: Beta and Delta, with the ratio of the relative abundance between the two variants maintained at 1:9 (Beta: Delta) in a 14-day period. Furthermore, putative evidence of recombination in the Orf1ab and spike genes was shown 26 . Such recombination events may not be rare, especially considering that there are hundreds of variants circulating in the general population.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

Lan

et al. 2022

Preprint

View full text Add to dashboard Cite

The current pandemic of COVID-19 is fueled by more infectious emergent Omicron variants. Ongoing concerns of emergent variants include possible recombinants, as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral pathogens. Although recombination events among SARS-CoV-1 and MERS-CoV were well-documented, it has been difficult to detect the recombination signatures in SARS-CoV-2 variants due to their high degree of sequence similarity. In this study, we identified diverse recombination events between two Omicron major subvariants (BA.1 and BA.2) and other variants of concern (VOCs) and variants of interest (VOIs), suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of SARS-CoV-2. Through scanning high-quality completed Omicron spike gene sequences, eighteen core mutations of BA.1 variants (frequency >99%) were identified (eight in NTD, five near the S1/S2 cleavage site, and five in S2). BA.2 variants share three additional amino acid deletions with the Alpha variants. BA.1 subvariants share nine common amino acid mutations (three more than BA.2) in the spike protein with most VOCs, suggesting a possible recombination origin of Omicron from these VOCs. There are three more Alpha-related mutations (del69-70, del144) in BA.1 than BA.2, and therefore BA.1 may be phylogenetically closer to the Alpha variant. Revertant mutations are found in some dominant mutations (frequency >95%) in the BA.1 subvariant. Most notably, multiple additional amino acid mutations in the Delta spike protein were also identified in the recently emerged Omicron isolates, which implied possible recombination events occurred between the Omicron and Delta variants during the on-going pandemic. Monitoring the evolving SARS-CoV-2 genomes especially for recombination is critically important for recognition of abrupt changes to viral attributes including its epitopes which may call for vaccine modifications.

show abstract

Section: Co-infections Of Different Sars-cov-2 Variants In the Popula...mentioning

confidence: 99%

Section: Co-infections Of Different Sars-cov-2 Variants In the Popula...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

Lan

et al. 2022

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, 1,175 (0.2%) pu-tative recombinant genomes were identified among 537,360 genomes, and it was reported that up to 5% of SARS-CoV-2 that circulated in the USA and UK might be recombinants [18]. Moreover, the number of cases of detection of recombinant genomes is growing [10,[13][14][15][16][17][18][19][20][21][22][23][24][25]. Recently, 7 coronaviruses have been reported to be able to integrate se-quences putatively from insects [36].…”

Section: Discussionmentioning

confidence: 99%

“…Regarding SARS-CoV-2, coinfection in the same patient with distinct variants has been reported [8][9][10][11][12][13][14]. In addition, several studies have described or suspected genetic recombinations for this virus [10,[13][14][15][16][17][18][19][20][21][22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient

Burel

Colson

Lagier

et al. 2022

Preprint

View full text Add to dashboard Cite

Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but a single patient sample was analyzed, and the virus was not isolated. Here, we report the gradual creation of a hybrid genome of B.1.160 and Alpha variants in a lymphoma patient chronically infected for 14 months, and we isolated the recombinant virus. The hybrid genome was obtained by next-generation sequencing, and recombination sites were confirmed by PCR. This consisted of a parental B.1.160 backbone interspersed with two fragments, including the spike gene, from an Alpha variant. Analysis of seven sequential samples from the patient decoded the recombination steps, including the initial infection with a B.1.160 variant, then a concurrent infection with this variant and an Alpha variant, the generation of hybrid genomes, and eventually the emergence of a predominant recombinant virus isolated at the end of the patient follow-up. This case exemplifies the recombination process of SARS-CoV-2 in real life, and it calls for intensifying genomic surveillance in patients coinfected with different SARS-CoV-2 variants, and more generally with several RNA viruses, as this may lead to the creation of new viruses.

show abstract

Analyzing the emerging patterns of SARS‐CoV‐2 Omicron subvariants for the development of next‐gen vaccine: An observational study

Mohapatra,

Mishra,

Kandi

et al. 2023

Health Science Reports

View full text Add to dashboard Cite

Background and AimUnderstanding the prevalence and impact of SARS‐CoV‐2 variants has assumed paramount importance. This study statistically analyzed to effectively track the emergence and spread of the variants and highlights the importance of such investigations in developing potential next‐gen vaccine to combat the continuously emerging Omicron subvariants.MethodsTransmission fitness advantage and effective reproductive number (Re) of epidemiologically relevant SARS‐CoV‐2 sublineages through time during the study period based on the GISAID data were estimated.ResultsThe analyses covered the period from January to June 2023 around an array of sequenced samples. The dominance of the XBB variant strain, accounting for approximately 57.63% of the cases, was identified during the timeframe. XBB.1.5 exhibited 37.95% prevalence rate from March to June 2023. Multiple variants showed considerable global influence throughout the study, as sporadically documented. Notably, the XBB variant demonstrated an estimated relative 28% weekly growth advantage compared with others. Numerous variants were resistant to the over‐the‐counter vaccines and breakthrough infections were reported. Similarly, the efficacy of mAB‐based therapy appeared limited. However, it's important to underscore the perceived benefits of these preventive and therapeutic measures were restricted to specific variants.ConclusionGiven the observed trends, a comprehensive next‐gen vaccine coupled with an advanced vaccination strategy could be a potential panacea in the fight against the pandemic. The findings suggest that targeted vaccine development could be an effective strategy to prevent infections. The study also highlights the need of global collaborations to rapidly develop and distribute the vaccines to ensure global human health.

show abstract

Possible recombination between two variants of concern in a COVID-19 patient

Cited by 32 publications

References 16 publications

Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient

Analyzing the emerging patterns of SARS‐CoV‐2 Omicron subvariants for the development of next‐gen vaccine: An observational study

Contact Info

Product

Resources

About