First Documented Transmission of a Newly Minted Hybrid SARS-CoV-2 Variant

In a recent case report, Swedish scientists documented the first known transmission of a novel recombinant SARS-CoV-2 variant. The case highlights how a patient co-infected with two different strains—sublineages of XBB (HV.1) and BA.2.86.1—generated and transmitted a hybrid variant to another patient within a hospital setting.

In October 2023, routine genomic surveillance in Stockholm identified a recombinant variant in a patient (Patient B). This hybrid virus combined genetic material from two distinct lineages: the 5′ part of the genome from HV.1 and the 3′ part from BA.2.86.1. The recombination occurred at the orf1b and S gene junction, producing a novel variant not observed in other Swedish patients.

Meanwhile, another patient (Patient A), co-hospitalized in the same ward, was found to be co-infected with both HV.1 and BA.2.86.1. Sequencing revealed that about 30% of the virus in Patient A came from the BA.2.86.1 lineage. The two patients shared six rare mutations, confirming that Patient A transmitted the recombinant variant to Patient B during their 8-day stay.

HV.1 (EG.5.1.6.1) is part of the Eris (EG.5) family, first identified in China in February 2023 as a descendant of the XBB variant dubbed Gryphon, which spread widely in Singapore and India in 2022. BA.2.86.1 is a descendent of Pirola (BA.2.86), first detected in Israel and Denmark in August 2023. Another offshoot of Pirola, JN.1, first detected in Luxembourg in August 2023, caused last winter’s wave and is expected to be followed by XEC, a recombinant of BA.2.86 sublineages (KS.1.1 (BA.2.86.1.1.13.1.1.1 and KP.3.3 (BA.2.86.1.1.11.1.3.3)), in this year’s winter wave.

Both patients had received five or more COVID-19 vaccine doses, with their most recent dose administered over six months before hospitalization. Despite being admitted for reasons unrelated to COVID-19, this case has provided valuable insight into real-time viral recombination within human hosts.


REFERENCE

Robert Dyrdak, Sofia Stamouli, Shambhu Ganeshappa Aralaguppe, Martin Ekman, Hamzah Safari, Carlo Berg, Elin Movert, Neus Latorre-Margalef, Emmi Andersson, Magnus Gisslén, Joanna Nederby-Öhd, Åsa Sjödin Leufvén, Josette Schoenmakers, Sandra Broddesson, Ben Murrell, Jan Albert, A novel SARS-CoV-2 recombinant transmitted from a patient with an acute co-infection, The Lancet Microbe, 2024, 100998, ISSN 2666-5247,https://doi.org/10.1016/j.lanmic.2024.100998.

(https://www.sciencedirect.com/science/article/pii/S2666524724002660)

Published October 1, 2024



Comments

Post a Comment

Popular posts from this blog

A New Onset of Ulcerative Colitis post-2nd-breakthrough-COVID-19

Image
A 21-year-old non-smoking Caucasian male with a history of acute pancreatitis but no other medical issues or family history had two doses of the BNT162b2 mRNA COVID-19 vaccine.  Four months after the second dose he had his first episode of COVID-19. Although not hypoxic, he felt pretty unwell for a week, with a severe cough, fever, generalized body ache, headache, and loss of taste. He received the third dose of the vaccine two months after recovering from COVID. Nine months after the third dose, he had the second episode of COVID-19, during which he was mildly unwell for three days, recovered, and did not require any anti-viral medication or antibiotics. One week post the second episode of COVID-19, he developed diarrhea and abdominal pain. It then progressed to bloody diarrhea. Ulcerative colitis was diagnosed based on his clinical symptoms, biopsy changes, and the exclusion of other causes.  There are ten published case reports about the newly diagnosed ulcerative colitis associate
Read more

COVID in May

Image
Concerns about a potential resurgence of COVID-19 are mounting as summer 2024 approaches.  This is driven by several indicators, including social media posts, healthcare data, and wastewater surveillance across different regions. Our study findings corroborate this trend.  While many forecasters anticipate a surge, others expect a gradual increase through the end of May, and then a decline again around early June. Reports from social media suggest emerging clusters of COVID-19 in Texas, several Canadian provinces, the UK, and on cruises in northern regions such as a Norwegian cruise to Alaska.  Data from Alberta's Respiratory virus dashboard   (total weekly laboratory-confirmed COVID-19 cases) and wastewater surveillance in Calgary indicate an uptick in COVID-19 cases starting April 2024. The most recent statistics from Alberta Health reveal a significant increase in hospitalizations due to COVID-19, with 114 individuals currently hospitalized—an increase of more than 20% over two
Read more

Chronic SARS-CoV-2 Shedding

Image
Chronic viral shedding, a condition where the virus continues to be released from an individual's body long after the initial infection, has been observed in many infectious diseases, including COVID-19.  In such cases, individuals may remain asymptomatic or experience only mild symptoms while the virus persists. It remains detectable in repeated tests over an extended period and can still infect others even in nasal swab is negative (which happens quite often ). This was evident in our study.    Recent research by Conway et al. (2024) highlights the possibility of chronic SARS-CoV-2 infection, extending over several months and potentially years. Other studies have documented prolonged asymptomatic infections and extended viral shedding in moderate to severe beyond hospital discharge. Analysis of sequencing data on UK samples taken between 2 November 2020 and 15 August 2022 lead to estimates that 0.1–0.5% of infections may become persistent with typically rebounding high viral load
Read more