Brazil: novel #coronavirus variant VUI-NP13L reported along with 2 cases of coinfection with B.1.1.28

“We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations.”

ScienceDirect.com preprint:  Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

 

 

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Imperial College: #SARSCoV2 #coronavirus variant #P1 is more transmissible, evasive, and growing rapidly in Brazil

Researchers estimate that the P.1 VOC is between 1.4–2.2 times more transmissible than non-VOC lineages. In addition, they estimate that the P.1 VOC evades 25-61% of protective immunity arising from infection with previously circulating variants.

Statistical analysis of genome data suggests that the P.1 lineage has likely been circulating in Manaus since early November 2020.

This lineage has been identified in over 20 countries worldwide and continues to spread, including several recently confirmed cases in the UK.

Global collaborative efforts on rapid virus genome sequencing are allowing us to identify SARS-CoV-2 lineages of concerns in near real-time.

Several genetic changes – substitutions and deletions – in this new P.1 lineage may have immunological significance. The team identified 17 mutations for this VOC, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor: a protein on the cell surface functioning as an entrance into the cell for SARS-CoV-2. Using analysis of genome sequence data, researchers were able to date back the emergence of the P.1 VOC to early November 2020.
More transmissible and evasive

The researchers found that the new P.1 lineage is growing rapidly in Brazil, is likely more transmissible than other variants, and may have the ability to evade protective immunity. The researchers estimate that the P.1 VOC is between 1.4–2.2 times more transmissible than non-VOC lineages. In addition, they estimate that the P.1 VOC evades 25-61% of protective immunity arising from infection with previously circulating variants. The exact trade-off between increased transmissibility and evading immunity is not currently known.

Imperial College report

 

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More #E484K #B1128 #coronavirus co-infections reported in #Brazil

B.1.1.28 (E484K) is able to establish successful coinfection events co-occurring simultaneously with different lineages of SARS-CoV-2.

The novel variant B.1.1.28 (E484K) previously described in Rio de Janeiro is currently spread across the southernmost state of Brazil.

The novel variant VUI-NP13L was also identified by causing a local outbreak in Rio Grande do Sul.

Medrxix paper  – Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil

 

 

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So where’s the Flu? Not a single case of #influenza #flu detected by Public Health England this year

Not a single case of influenza has been detected by public health officials in England for the past seven weeks, with infection rates at historic lows amid the ongoing Covid-19 restrictions.

The social restrictions brought in to curb transmission of coronavirus, combined with increased uptake of the flu vaccine, have both been credited with driving down infections.

The Independent Article

 

An alternative possibility to social distancing causing the drop in flu infections:

“Our study shows that during coinfections, one virus can block another simply by being the first to infect the available host cells; there is no need for viral interference through immune response interactions. We use the model to calculate the duration of detectable coinfection and examine how it varies as initial viral dose and time of infection are varied. We find that rhinovirus, the fastest-growing virus, reduces replication of the remaining viruses during a coinfection, while parainfluenza virus, the slowest-growing virus is suppressed in the presence of other viruses.”

Coinfections of the Respiratory Tract

 

 

 

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#Coinfection with #influenza A virus enhances #SARSCoV2 infectivity

“In this study, we tested whether IAV infection could affect the subsequent SARS-CoV-2 infection in both cultured cells and mice. Our results demonstrate that preinfection with IAV strongly enhances the infectivity of SARS-CoV-2 by boosting viral entry into cells and elevating the viral load, leading to more severe lung damage in infected mice. These data suggest a clear auxo-action of IAV on SARS-CoV-2 infection, which underscores the great risk of influenza virus and SARS-CoV-2 coinfection to public health.”

Nature.com Cell Research Paper

 

 
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Predicting mammalian hosts in which novel coronaviruses can be generated

“..the most immediate threat to public health is recombination of other coronaviruses with SARS-CoV-2. Such recombination could readily produce further novel viruses with both the infectivity of SARS-CoV-2 and additional pathogenicity or viral tropism from elsewhere in the Coronaviridae”

The most prominent result for a SARS-CoV-2 recombination host is the domestic pig (Sus scrofa), having the most predicted associations of all included non-human mammals. The pig is a major known mammalian coronavirus host, harbouring both a large number of observed coronaviruses, as well as a wide diversity. Given the large number of predicted viral associations presented here, the pig’s close association to humans, its known reservoir status for many other zoonotic viruses, and its involvement in genetic recombination of some of these viruses, the pig is predicted to be one of the foremost candidates an important recombination host.

Nature.com article

 

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Co-infection with 2 distinct #sarscov2 lineages reported in a patient in Portugal

“The patient had co-infection by two SARS-CoV-2 lineages, which were affiliated in distinct clades and diverging by six variants. The 20A lineage was absolute at the diagnosis (shared with the patient’s mother), but nine days later, the 20B lineage had 3% frequency, and two months later, the 20B lineage had 100% frequency”

https://pubmed.ncbi.nlm.nih.gov/33540596/

 

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Brazil co-infection sees patients infected with two variants of #coronavirus at the same time

“We were the first to identify two independent events of co-infection caused by the occurrence of B.1.1.28 (E484K) with either B.1.1.248 or B.1.91 lineages. Also, clustering analysis revealed the occurrence of a novel cluster of samples circulating in the state (named VUI-NP13L) characterized by 12 lineage-defining mutations.”

https://www.medrxiv.org/content/10.1101/2021.01.21.21249764v1

 

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