BREAKING! COVID-19 News: Antibody Resistant SARS-CoV-2 Variant Emerges In Patient After Convalescent Plasma Therapy

COVID-19 News: British researchers from University College London, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge University NHS Hospitals Foundation Trust, University of Kent and University of Amsterdam have in a new research discovered the emergence of antibody resistant SARS-CoV-2 variants in a COVID-19 patient who had been treated with neutralizing antibodies from convalescent plasma.


 
Thailand Medical news has been warning since the April that mankind’s usage of antibody based therapeutics would lead to more emerging resistant strains and variants emerging due to the past studies showing the track record of coronaviruses.
 
The SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs.
 
The study team here reports the fatal SARS-CoV-2 escape from neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Little evolutionary change was observed in the viral population over the first 65 days despite two courses of remdesivir.
 
However, following convalescent plasma the study team observed dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 NTD of the Spike protein. As serum neutralisation waned, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. 
 
In vitro, the Spike escape variant conferred decreased sensitivity to multiple units of convalescent plasma/sera from different recovered patients, whilst maintaining infectivity similar to wild type. These data reveal strong positive selection on SARS-CoV-2 during convalescent plasma therapy and identify the combination of Spike mutations D796H and ΔH69/ΔV70 as a broad antibody resistance mechanism against commonly occurring antibody responses to SARS-CoV-2.
 
The study findings were published on a preprint server and are currently being peer reviewed. https://www.medrxiv.org/content/10.1101/2020.12.05.20241927v1
 
The world has been too focused on vaccines and antibody treatments, mostly due to motivation of greed and corruption.
 
The COVID-19 vaccine may help slow down the viral spread and maybe reduce the mortality and morbidity associated with this infection but it is not going to stop the pandemic and in fact in might lead to far more worse problems.
 
Most vaccines are at or near the finishing post already and about to be rolled out, mostly directed against the viral spike antigen. However, there is a worrying increase in the emergence of escape mutations that allow the virus to evade these antibodies' neutralizing effects.
 
This new study indicates a critical cause of the positive selection pressure that underlies this phenomenon.
 
The SARS-CoV-2 coronavirus has several structural proteins, including the key spike glycoprotein. This protein is among the dominant antigens and crucial for viral entry into the host cell. It is the spike receptor-binding domain (RBD) that is bound by neutralizing natural and therapeutic monoclonal antibodies.
 
Numerous mutations have been documented in the viral genome over the pandemic's year-long course, of which some have been particularly successful.
 
Among the most notable includes the spike D614G mutation, which has rapidly risen to the dominant position in every place where it was introduced, displacing the original strain. This mutation confers a definite advantage on the virus in terms of infectivity and transmissibility, accounting for the rapid spread of strains characterized by it.
 
Importantly deletion mutations have also been recognized in different strains within the same host and across different individuals. The most important is H69/V70, a double deletion found in multiple separate strains in Europe.
 
This research follows the emergence of this double mutation in combination with the S2 mutation D796H and broad escape from antibody neutralization in a patient who received convalescent plasma therapy. The patient was immunocompromised because of treatment with the B cell depletion agent rituximab.
 
The detailed research included the measurement of specific anti-SARS-CoV-2 antibodies over time. The initial negative results at day 44 and day 50 following infection were followed by an infusion of three units of convalescent plasma (CP) from three separate donors. These had specific neutralizing antibodies targeting the virus.  
 
The study team compared genomic analyses from 23 successive respiratory samples, mostly from post-intubation nose and throat samples or endotracheal aspirates. Ct values were between 16 and 24. Samples from the call bell and the telephone in the patient’s room yielded viral isolates from the same population on days 59, 92 and 101, indicating environmental contamination.
 
It was found that the infecting strain was of the lineage 20B with the D614G mutation in the spike.
 
However alarmingly over 101 days, the virus population showed marked diversity of viral strains, with the mutation rate being estimated at 30 per year.
 
Also at days 93 and 95, the viral strains were significantly different from the early isolates, though closely related phylogenetically. Rather than being the effect of positive selection pressures, the investigators infer that this reflects rapid mutagenesis within a small subset due to enhancement by genetic drift.
 
It was also found that sequential samples from three other patients who also had viral RNA shedding for four or more weeks were also sequenced, but interestingly, the compositional shift did not occur in these cases, especially concerning the spike protein.
 
The treatment protocol of two courses of remdesivir therapy (by day 54) and two CP infusions (by day 65) failed to change the Ct values up to the first 100 days post-infection.
 
Alarmingly, after day 66, the viral population showed a drastic compositional shift.
 
The study team found that by day 82, the D796H mutation in S2 became almost the sole allele, along with the S1 double mutation H69/V70. This set of mutations then dropped to a very low frequency by days 86 and 89, while spike mutations Y200H and 163 T240I became predominant. Despite the clear divergence, this was not due to superinfection, as the phylogenetic relationship was observed.
 
The team found that on day 93, the set of D796H along with H69/V70 was detected in less than 10% of the samples in a nose and throat sample. Simultaneously, a group of viruses with spike RBD mutation P330S and S1 NTD mutation W64G had increased to almost 100% abundance at this date. The RBD mutation was present in two distinct samples.
 
This divergent sample resulted from the stochastic development of a hitherto undetected subgroup of viruses in the upper respiratory tract.
 
The study team was shocked that after the third course of remdesivir on day 92 and the third CP infusion on day 95, the D796H + H69/V70 strain increased. The researchers consider this to be the effect of positive selection pressure renewed by the third unit of CP.
 
Subsequently the level of inflammation was hyperintense, but Ct values were low through this period, terminated by the patient's death on day 102. The cause of death was multi-organ failure.
 
The study team said that the repeated increase in frequency of the novel viral strain during CP therapy strongly supports the hypothesis that the deletion/mutation combination conferred antibody escape properties.
 
The study team found that the neutralization activity of CP against the wild-type was higher than against the H69/V70 + D796H mutant D614G-carrying spike protein, as tested in a pseudoviral system.
 
It was also found that after two CP units, the triple mutant continued to persist in the patient’s samples. Patient serum both before and after the second unit of CP showed only partial neutralization efficacy against this variant.
 
Importantly the persistence and re-emergence of this variant after the third unit of CP emphasizes its lack of susceptibility and indicates a broad escape mechanism.  
 
The study team tested five randomly selected sera from recovered patients to neutralize activity against wild-type and mutant viruses. The mutant strain resisted neutralization by four of the five sera, with non-significant neutralization activity by the fifth. In contrast, the wild-type virus was up to ten times as susceptible as the mutant strain.
 
More importantly the study team wanted to find out what would be the impact of monoclonal antibodies on the mutant virus?
 
In order to find out, the study team looked at the neutralization activity of a seven-antibody set to an array of epitope groups. There was no difference in the neutralization achieved with any of the epitope clusters. The researchers concluded that the mechanism of immune escape did not belong to these epitopes.
 
The researchers then analyzed a published spike structure, annotating the residues related to the escape. They found the double mutation affected a disordered loop at the tip of the NTD, with multiple sugar residues attached. Therefore, the location could easily disrupt antibody binding. Secondly, the D796H mutation is relatively uncommon. However, because it affects an exposed loop in the S2 spike subunit, a part of the spike that is an important epitope could interfere with antibody binding.
 
For this case, the change in viral population genes in response to CP was capable of being followed over the long-term because of the prolonged viral shedding due to persistent viral replication and the absence of antiviral effect despite remdesivir and CP infusion. Such patients are prone to developing prolonged infections.  
 
The study findings show how the genetic makeup of the virus population shifts with the administration of convalescent plasma therapy. In response, a viral strain emerged carrying a beneficial mutation, which became less abundant, before again rising when exposed to the next unit of convalescent plasma therapy, a feature of positive selection.
 
This research's implications are potentially alarming, in that it suggests the repeated emergence of a resistant SARS-CoV-2 variant, which has been showing a rise in frequency in Europe. This patient's death may not have been due to viral proliferation following the emergence of this escape mutation.
 
The study team however says, “Given that both vaccines and therapeutics are aimed at Spike, our study raises the possibility of virus evasion, particularly in immune-suppressed individuals where prolonged viral replication occurs.”
 
The study findings suggest caution in use of convalescent plasma therapy in patients with immune suppression of both T cell and B cell arms. In such cases, the antibodies administered have little support from cytotoxic T cells, thereby reducing chances of clearance and raising the potential for escape mutations.
 
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