Virus World

The 20-month-long infection is the longest known and highlights how prolonged infections enable the pandemic virus to accumulate genetic changes—potentially spawning new variants of concern. A Covid-19 patient with a weakened immune system incubated a highly mutated novel strain over 613 days before succumbing to an underlying illness, researchers in the Netherlands found. The patient, a 72-year-old man with a blood disorder, failed to mount a strong immune response to multiple Covid shots before catching the omicron variant in February 2022. Detailed analysis of specimens collected from more than two dozen nose and throat swabs found the coronavirus developed resistance to sotrovimab, a Covid antibody treatment, within a few weeks, scientists at the University of Amsterdam’s Centre for Experimental and Molecular Medicine said. It later acquired over 50 mutations, including some that suggested an enhanced ability to evade immune defenses, they said.

The 20-month-long SARS-CoV-2 infection is the longest known, according to the researchers, who are presenting the case at a medical meeting in Barcelona next week. While his mutant virus wasn’t known to have infected other people, it highlights how prolonged infections enable the pandemic virus to accumulate genetic changes, potentially spawning new variants of concern. “This case underscores the risk of persistent SARS-CoV-2 infections in immunocompromised individuals,” the authors said. “We emphasize the importance of continuing genomic surveillance of SARS-CoV-2 evolution in immunocompromised individuals with persistent infections.” Scientists studying genomic data collected from wastewater samples have reported evidence of individuals in the community shedding heavily mutated coronaviruses for more than four years. Such persistent infections may also be causing patients to experience long Covid symptoms, research suggests.

Two European patients are confirmed to have been re-infected with COVID-19, raising concerns about people's immunity to the coronavirus as the world struggles to tame the pandemic. The cases, in Belgium and the Netherlands, follow a report this week by researchers in Hong Kong about a man there who had contracted a different strain of the virus four and a half months after being declared recovered - the first such second infection to be documented. That has raised fears about the efficacy of potential vaccines against the virus, which has killed hundreds of thousands of people, though experts say there would need to be many more cases of re-infection for these to be justified. Belgian virologist Marc Van Ranst said the Belgian case was a woman who had contracted COVID-19 for the first time in March and then again with a different coronavirus strain in June. Further cases of re-infection were likely to surface, he said. Van Ranst told Reuters TV the woman, in her 50s, had very few antibodies after the first infection, although they might have limited the sickness. Re-infection cases were probably limited exceptions, he said, although it was too soon to tell and many were likely to surface in coming weeks.  He added that the new coronavirus appeared more stable than the influenza virus, but it was changing. 

“Viruses mutate and that means that a potential vaccine is not going to be a vaccine that will last forever, for 10 years, probably not even five years. Just as for flu, this will have to be redesigned quite regularly,” he said. Van Ranst, who sits on some Belgian COVID-19 committees, said vaccine designers would not be surprised. “We would have loved the virus to be more stable than it is, but you can’t force nature.”

Genetic Testing

The National Institute for Public Health in the Netherlands said it had also observed a Dutch case of re-infection with a different strain of the virus. “It is clear there has been a first and a second infection with a substantial quantity of virus. Enough to be able to determine the genetic code of the virus, that is what showed they were indeed different,” said Marion Koopmans, a leading virologist in the Netherlands and a member of the World Health Organization’s scientific advisory group. She added the elderly Dutch patient had a weakened immune system, which explained the patient’s situation. “People are worried and ask if re-infection is ‘standard’. I don’t think it is,” she added. WHO spokeswoman Margaret Harris told a U.N. briefing in Geneva regarding the Hong Kong case that, while there were anecdotal reports of re-infections, it was important to have clear documentation.

Microbiologists at research institute KWR conducted a series of RNA-analyses at municipal waste water treatment plants (WWTP) in the Netherlands. The analyses showed the presence of RNA gene fragments of the COVID-19 virus in incoming sewage water. According to KWR the screening of the COVID-19 virus at municipal waste water plants can be used to signal new outbreaks in advance and play an important role to follow the evolution of the pandemic.

RNA-analysis is a method to measure the presence of viruses through capturing virus particles and detect specific gene fragments. The method does not discriminate between inactive and infectious particles. The KWR microbiologists say they have not yet been able to quantify the presence of these fragments. Their first findings indicate that the concentration of the virus at the WWTP is low.  Currently researchers are examining all samples multiple times and are looking at the reproducibility of the results. Furthermore, they double check and focus on fragments of multiple genes, to strengthen their results about the presence of the virus. The detection of COVID-19 in the sewage water at the Dutch WWTP does not really come as a surprise. Sewage water contains many viruses and the detection of the new coronavirus from human faeces was to be expected. Study results released by Chinese microbiologists in 2005 showed that SARS-CoV RNA had been detected in the sewage water of Chinese hospitals where SARS-patients were treated.

KWR suggests the use of the RNA-analyses of the SARS-CoV-2 in sewage water as a tool to measure the virus circulation in cities or smaller municipalities. The concentration level of the virus can be an indicator for the number of virus infections in the population and can signal in advance a new outbreak, for instance when a lock down is lifted. Similarly, these analyses can help monitor the effect of measures put in place to mitigate the spreading of the pandemic, according to KWR.

We present early vaccine effectiveness (VE) estimates of the 2023 seasonal COVID-19 vaccination campaign using XBB.1.5 vaccine against COVID-19 hospitalization and ICU admission in previously vaccinated adults ≥60 years old in the Netherlands. We compared vaccination status of 2050 hospitalizations including 92 ICU admissions with age group-, sex-, region- and date-specific population vaccination coverage between 9 October and 5 December 2023. VE against hospitalization was 70.7% (95% CI: 66.6; 74.3), VE against ICU admission was 73.3% (95% CI: 42.2; 87.6).

Preprint in medRxiv (Dec. 13, 2023):

https://doi.org/10.1101/2023.12.12.23299855 

The blood from seriously ill Covid-19 patients on ventilators was found by researchers to be highly inflammatory and harmful to the body. Antibodies  generated by the immune system to neutralise