Two Omicron sublineages, one patient: the shortest case of reinfection so far

The history behind the paper: Girardi, V., Gularte, J.S., Demoliner, M. et al. Reinfection by SARS-CoV-2 by divergent Omicron sublineages, 16 days apart. Braz J Microbiol (2023).
Two Omicron sublineages, one patient: the shortest case of reinfection so far

At times, scientific writing is also about telling interesting stories. Obviously, these need to be relevant in the scientific context, being valuable for discussion for other studies. In the midst of facing a pandemic due to an emerging virus, there are stories that can serve to generate insights even on control measures. This was the situation that led us to study and report this case of such a rapid reinfection with the BA.1.1 and BA.2 strains in a patient in southern Brazil.

The patient in this clinical case experienced symptoms of COVID-19 twice, with the first round of symptoms starting on May 23rd 2022 and the second round starting on June 4th  (Fig. 1). The 52-old man, triple vaccinated, had clinically recovered completely, tested negative in RT-qPCR tests after a few days of mild symptoms. He has happily returned to work in office and then began to present more intense symptoms a few days later. The viral detection assay was positive again. Both the health professionals and surveillance teams involved, as we in the laboratory, obviously thought of a prolonged infection with a relapse.

The timeline of the case
Figure 1.  Timeline of the events (clinical signs and sampling) following two consecutive infections by two different Omicron sublineages in a patient from Southern Brazil

Since we had the SARS-CoV-2 positive samples collected on those two occasions, we thought it would be quite interesting to perform genome sequencing on both to check whether the virus genome had suffered any mutations over that period (although the negative assays in the middle of monitoring were still a mystery at that point). Surprisingly, the results showed that the patient was infected with two different sublineages of the Omicron variant of SARS-CoV-2: BA.1.1, for the first round of symptoms, and BA.2 for the second (Table 1).

Table 1. Sequencing results (reads, coverage, and length) and signature mutation at spike protein for both samples evaluated

Total reads
Length (mean)
130 bp
133 bp
Signature mutation at spike protein3
Shared mutations4
Specific mutations
Mutations detected
1bp base pairs; 2First infection, classified as BA.1.1 sublineage (clade 21 K); 3Second infection, classified as BA.2 sublineage (clade 21L); 4According to the website; 5Total number of signature mutations shared between BA.1.1 and BA.2 that was detected.

When you have a result as different as this one, the first thing you have to do is rule out all possibilities of error, contamination, and that's what we did, including resorting to records of tests carried out in other laboratories and other diagnostic tools. Reviewing all possibilities, we were able to conclude that, yes, we were facing a sui generis case of reinfection in a record period, only 16 days apart one from another. It is indeed the shortest one described so far.

Fortunately, the patient recovered. What we learned and wanted to tell other researchers is that people's individual responses to an infection can indeed vary, and that the Omicron variant and its variants can surprise us in terms of their ability to generate reinfections. Also, it's not by chance that we probably see so many SARS-CoV-2 recombinants out there nowadays since co-infections must also be very likely. A lot of good sense and cautiousness is needed when you have a large number of cases of COVID-19 going on in your community (the same must be true for other respiratory viral infections), and general measures of respiratory hygiene must be adopted even by patients that have recently recovered.

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Life Sciences > Biological Sciences > Microbiology > Virology > Virology
Life Sciences > Biological Sciences > Microbiology > Virology > Virus > SARS Virus > SARS-CoV-2 > SARS-CoV-2
Life Sciences > Biological Sciences > Microbiology > Medical Microbiology > Infectious Diseases > COVID19 > COVID19
Life Sciences > Biological Sciences > Biological Techniques > Genomic Analysis > Sequencing > Sequencing
Next-generation sequencing
Life Sciences > Biological Sciences > Biological Techniques > Genomic Analysis > Sequencing > Next-generation sequencing > Next-generation sequencing