Tag: covid transmission

Modelling Suggests COVID Will Reach Endemic Stage by 2024

COVID heat map. Photo by Giacomo Carra on Unsplash

A new study on coronavirus transmission in rats suggests that COVID will enter the endemic stage in about two years. The study also suggested that infections from high-risk conditions such as close contact with infected individuals produced more robust immunity than by exposure in low-risk settings.

The study, published in PNAS Nexus, made use of rats to determine when and how SARS-CoV-2 would eventually become endemic. Rats, like humans, are susceptible to coronaviruses. By collecting data on coronaviral reinfection rates among rats, the researchers were able to model the potential trajectory of COVID.

SARS-CoV-2 is just one of many coronaviruses, and there are several that cause the common cold. Many livestock animals live with endemic coronaviruses, too, and a key factor identified in the spread of animal and human coronaviruses alike is their tendency to evoke non-sterilising immunity.

“It means that initially there is fairly good immunity, but relatively quickly that wanes,” explained the study’s senior author, Caroline Zeiss, a professor of comparative medicine at Yale School of Medicine. “And so even if an animal or a person has been vaccinated or infected, they will likely become susceptible again.”

Over the past two years, scientists have come to see that SARS-CoV-2 yields non-sterilising immunity as people become re-infected.

The strong similarities between animal and human coronaviruses, animal data helps improve the understanding of SARS-CoV-2, said Prof Zeiss.

“There are many lessons to be learned from animal coronaviruses,” she said.

In this study, Prof Zeiss and her colleagues observed how a coronavirus similar to one that causes the common cold in humans was transmitted through rat populations. The team modelled the exposure scenario to resemble human exposures in the US, where a portion of the population is vaccinated against COVID and where people continue to face natural exposure to SARS-CoV-2. They also reproduced the different types of exposure experienced by people in the US, with some animals exposed through close contact with an infected rat (high risk of infection) and others exposed by being placed in a cage once inhabited by an infected rat (low risk of infection).

Infected animals contracted an upper respiratory tract infection and then recovered. Three to four months later, the rats were then reorganised and re-exposed to the virus. The rates of reinfection showed that natural exposure yielded a mix of immunity levels, with those exposed to more virus through close contact having stronger immunity, while those exposed to lower virus levels by (being placed in a contaminated cage) having higher rates of reinfection.

The takeaway, said Prof Zeiss, is that with natural infection, some individuals will develop better immunity than others. People also need vaccination, which is offered through a set dose and generates predictable immunity. But with both vaccination and natural exposure, the population accumulates broad immunity that pushes the virus toward endemic stability, the study showed.

Mathematical models using the data predicted that the median time for SARS-CoV-2 to become endemic in the United States is 1437 days, or just under four years from the start of the pandemic in March 2020.

In this model’s scenario, 15.4% of the population would be susceptible to infection at any given time after it reaches endemic phrase.

“The virus is constantly going to be circulating,” said Prof Zeiss. So it will be important to keep more vulnerable groups in mind. “We can’t assume that once we reach the endemic state that everybody is safe.”

Four years is the median time predicted by the model, she said, so it could take even longer to reach the endemic stage. And this doesn’t take into account mutations that could make SARS-CoV-2 more harmful.

“Coronaviruses are very unpredictable, so there could be a mutation that makes it more pathogenic,” said Prof Zeiss. “The more likely scenario, though, is that we see an increase in transmissibility and probable decrease in pathogenicity.” That means the virus would be easily transmitted between people but less likely to cause severe illness, much like the common cold.

There is precedent for this trajectory. In the late 1800s, the ‘Russian flu’ killed approximately one million people around the world. Researchers now think that virus was a coronavirus that originated in cattle, which eventually evolved into one of the common cold viruses still in circulation. Reduced pathogenicity associated with the transition from epidemic to endemic status has also been observed in pig coronaviruses. And almost all commercial chicken flocks across the globe are vaccinated for an endemic respiratory coronavirus that has been present since the 1930s.

Longstanding experience with coronaviral infections in other animals can help navigate a pathway to living with SARS-CoV-2.

However, endemic stability in the United States also depends on what happens to the virus elsewhere.

“We are one global community,” Zeiss said. “We don’t know where else these mutations are going to arise. Until we reach endemic stability around the entire globe, we are vulnerable here to having our US endemic stability disrupted by introduction of a new variant.

“But I think overall the picture’s hopeful. I think we will be in endemic stability within the next year or two.”

Source: Yale University

Omicron Viral Load Shedding May Be Unaffected by Vaccination

SARS-CoV-2 virus
SARS-CoV-2 virus. Source: Fusion Medical Animation on Unsplash

A small study published in the New England Journal of Medicine has found that viral load shedding of the omicron variant is similar to other strains, and is not significantly affected by vaccination status.

The SARS-CoV-2 omicron variant has a shorter incubation period and a higher transmission rate than previous variants. Recently, the Centers for Disease Control and Prevention recommended shortening the strict isolation period for infected persons from 10 days to 5 days after symptom onset or initial positive test, followed by 5 days of masking. However, the viral delay kinetics and load shedding of omicron is still unclear.

Using nasal swabs to measure viral load, sequencing, and viral culture, they enrolled 66 participants, including 32 with delta variant and 34 with omicron. Participants who received COVID–specific therapies were excluded; only one participant was asymptomatic.

The characteristics of the participants were similar in the two variant groups except that more participants with omicron infection had received a booster vaccine than had those with delta infection (35% vs 3%). After adjustments for age, sex, and vaccination status, the number of days from an initial positive polymerase-chain-reaction (PCR) assay to a negative PCR assay and the number of days from an initial positive PCR assay to culture conversion were similar in the two variant groups.

The median time from the initial positive PCR assay to culture conversion was 4 days in the delta group and 5 days in the omicron group; the median time from symptom onset or the initial positive PCR assay, whichever was earlier, to culture conversion was 6 days and 8 days, respectively. There were no appreciable between-group differences in the time to PCR conversion or culture conversion according to vaccination status, although the sample size was quite small, which led to imprecision in the estimates.

In these participants with nonsevere COVID, the viral decay kinetics were similar with omicron infection and delta infection. No large differences in the median duration of viral shedding was seen among participants who were unvaccinated, vaccinated but not boosted, and those who were vaccinated and boosted.

Discussing limitations, the authors cautioned that the small sample size limits precision, and there are possible residual confounding variables. Further studies are need to properly correlate culture positivity with infectivity.

They conclude by saying: “Our data suggest that some persons who are infected with the omicron and delta SARS-CoV-2 variants shed culturable virus more than 5 days after symptom onset or an initial positive test.”

How Effective was Masking for SA in Preventing COVID?

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COVID restrictions have finally come to an end altogether in South Africa, as Health Minister Joe Phaahla gazetted a number of changes to the rules, as reported by BusinessTech. This means the end of mask use requirements, social gatherings restrictions and COVID border testing. Prof Shabir Madhi was welcoming of the move in a recent tweet, having criticised SA’s lockdowns as overly harsh and economically damaging. Around the world, many had questioned the widespread use of masks, or their use by some subset of the population, such as children – and even questioned locally by a scientist who argued that it didn’t and wouldn’t work in a South African setting, where people are less adherent to regulations.

Professor Salim Abdool Karim likened such a viewpoint to saying Africans with HIV can’t use ARVs because they didn’t have watches to take them at the right time, reminiscent of “a colonial mentality”.

The case for public mask use is well established. Experiments had shown that even simple cloth masks were moderately effective at hindering the transmission of SARS-CoV-2–containing aerosol particle from infected individuals, though they were less effective at protecting a wearer against infection. Predictably, N95 masks and others are better at doing the job than simple cloth face coverings.

There are no real-world studies for South Africa comparing mask use vs non-mask use as mask wearing was compulsory from the early stages of the outbreak. It would have been downright unethical to ask people to not wear masks, although some people may have had exemptions due to medical conditions or other important reasons. There is a country with good COVID surveillance and a distinct division in mask wearing – the United States. Implementation of mask mandates in the US was down to local authorities, which provides a basis for comparison.

One US study, published in Health Affairs, found that, compared to nonmasking counties, masking counties saw a daily case incidence decline by 25% at four weeks, 35% at six weeks after introduction of masking mandates. The reductions were strongest in Republican-leaning counties, which is notable since Republican voters were less in favour of lockdowns and mask mandates.

Another study found a 16.9% drop in cases four weeks after counties introduced masking mandates. Real-world data also show mask use was effective in preventing infection. A case-and-control study done in California by the CDC showed a 29% drop for surgical mask/respirator use “some of the time” and a 56% drop for “all of the time”.

While a direct comparison between a wealthy country like the US and South Africa as a middle-income country is impossible, it is easy to believe that masking mandates reduced cases by a significant percentage, perhaps saving tens of thousands of lives especially against the country’s possible true COVID death toll of 300 000.

Chinese Study Finds Children More Likely to Spread COVID

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By gaining access to a high quality COVID transmission data from a northern Chinese city which enforced stringent lockdowns, scientists concluded that young people were most responsible for an increase in direct and secondary infections, and also determined that county-wide lockdowns proved effective in limiting the virus’s spread.

The research study, led by Professor of Sociology Zai Liang at University of Albany, was given rare access to patient profiles and contact tracing data from every case accompanying the outbreak of the virus in Shijiazhuang from January to February in 2021. “Because of universal testing and digital tracing, the data are of high quality,” said Prof Liang, who was assisted by Sociology PhD student and lecturer Han Liu. Liu is from Shijiazhuang and has connections with that city’s CDC research centre, which enabled them to get the data.

The two UAlbany researchers, joined by two colleagues from China, published their findings in the Journal of Urban Health.

Prof Liang wrote that while individual-level contact tracing studies on the virus’s transmission and mitigation efforts have been growing, “because of limited testing capacities and risks of infringing on privacy, surveillance data used in individual-level research usually have limited representativeness.” His Shijiazhuang study, whose analysis included 99.52 percent (1028 of 1133) of the transmitted cases in Shijiazhuang, is designed “to fill this gap in the literature.”

The research examined sociodemographic factors including age, gender and socioeconomic status, postulating that “certain sociodemographic characteristics may facilitate the spread of germs by exposing the host to more social contacts.” This would include children interacting in the classroom, females having more contact with their relatives than do males, and less affluent workers working or living in overcrowded settings.

Among the study’s results are:

  • Children 0–17 years old had fewer close contacts than adults, but these led to more secondary infections: 32.1% infected children, 67.9% adults
  • Close contacts of children were 81% more likely to be infected than the contacts of those 18–49
  • Peasant workers, compared to non-manual workers, had 40% more secondary cases from the same neighbourhoods.

Prof Liang wrote, “While children have a low probability of having severe symptoms after being infected by COVID, they can seed the spread in the larger society by infecting their household members and other adults living in their neighbourhoods. These adults can then transmit the disease to their own social contacts. Future studies on how to control within-school infections are therefore urgently needed.”

Another major conclusion of the Shijiazhuang study is that timely non-pharmaceutical interventions, including restrictions on gatherings and school closures, effectively contained further infections via contact reduction, especially when implemented in small areas with the highest caseloads. Liang acknowledged that school closures did have negative ramifications for children’s education and socialisation.

Serendipitous data collection

How did Prof Liang and colleagues obtain comprehensive data not yet publicly available to others? “We heard of this COVID outbreak in this part of northern China early last year, when I was working on a proposal to study COVID. I asked Han Liu if we had connections in that city. It turned out that he is originally from Shijiazhuang and has connections with that city’s CDC research centre.

“The two researchers who collected the data agreed to join us in this effort. I am lucky to ask the right question at the right time.”

Source: University at Albany

By Now, Nearly All South Africans Have COVID Antibodies

South African flag with COVID theme
Image by Quicknews

The latest COVID seroprevalence survey shows that nearly every adult in South Africa has either been vaccinated or had COVID. For many, it’s both.

The study analysed blood from over 3000 blood donors. It was conducted by the South African National Blood Service, which is responsible for blood donations in eight provinces, and the Western Cape Blood Service.

The researchers estimated that by March 2022, before the fifth wave which appears to have peaked in the last few weeks, 98% of adults had some detectable antibodies, whether from COVID or from vaccination. This means that only 2% had neither been vaccinated nor been infected.

Only 10% had been vaccinated but not infected by COVID.

Read the study

(Note: The study has been published as a preprint and has not been peer-reviewed.)

What the survey tested for

Blood samples were collected and tested from 3395 consenting donors from all provinces in mid-March 2022. While blood donors are not precisely representative of the population, the researchers have argued that the study is representative enough.

This is the first time the blood services researchers have been able to look for two types of antibodies.

One test indicates if a sample has antibodies to the nucleocapsid proteins (anti-nucleocapsid antibodies). These antibodies develop if someone is infected, but won’t develop after a person receives a vaccine only (at least not those vaccines currently available in South Africa).

The other test indicates if the sample has antibodies to the spike protein (anti-spike antibodies). These antibodies develop when someone has been infected or has been vaccinated (or both).

Using these two tests together, researchers can, for the first time, evaluate the proportion of the population that has been vaccinated and not infected.


After weighting the results to reflect national demographics, the researchers found that a mere 2% of the population had neither anti-spike nor anti-nucleocapsid antibodies. These are people who have likely never had COVID nor been vaccinated.

10% had only anti-spike antibodies. These are people who were likely vaccinated, but never infected.

The researchers noted that there is “an increasing incidence of reinfection” with the omicron wave.

Blood service survey is the best we have

The blood services have been regularly testing blood samples from donors throughout the pandemic, looking at the presence of anti-nucleocapsid antibodies.

While other surveys might be more representative of the population than the blood donor ones, these have been infrequently published or published long after the survey was conducted. By contrast the blood donor surveys are relatively affordable and quick to publish. Also, as far as we are aware, it is the only survey repeatedly testing the same group of people, so that comparisons across time are possible.

Past blood surveys

The blood services’ survey from samples taken in May 2021 estimated that 47% of the adult population had previously been infected.

The next survey of blood samples was taken in November 2021 after the delta wave. This was just before the omicron wave. The researchers estimated that about 70% of people had been infected.

The latest survey indicates that about 87% of people have been infected.

The previous surveys found that levels of infection differed by province. Now these differences have “largely disappeared as prevalence appears to have saturated”.

Differences across race

There are significant differences in rates of infection when different races are compared.

The November survey showed that about 80% of black donors and 40% of white donors had been infected with COVID.

In the latest survey the proportion of white and Asian donors that only have anti-spike antibodies (indicating vaccination but no infection) was higher than black and coloured donors.

The researchers suggest that “white donors are both unusually likely to avail themselves of vaccination, and they are unusually able to avoid exposure, for instance by working predominantly from home, [and] living in smaller family units.”

Article by By James Stent. Republished from GroundUp under a Creative Commons Attribution-NoDerivatives 4.0 International License.

Source: GroundUp

Natural Facial Asymmetry Affects Mask Fit

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In research published in Physics of Fluids, researchers used computer modelling investigate mask fit and found that face shape, especially natural facial asymmetry, influences the most ideal fit. The findings suggested that double masking with improperly fitted masks may not greatly improve mask efficiency and produces a false sense of security.

Using more layers results in a less porous face covering, leading to more flow forced out the sides, top, and bottom of masks with a less secure fit. Double layers increase filtering efficiency only with good mask fit, however they could also lead to difficulties in breathing.

The researchers modelled a moderate cough jet from a mouth of an adult male wearing a cloth mask over the nose and mouth with elastic bands wrapped around the ears. They calculated the maximum volume flow rates through the front of mask and peripheral gaps at different material porosity levels.

To create a more realistic 3D face shape and size, the researchers used head scan data for 100 adult male and 100 adult female heads.

Their model showed how the slight asymmetry typical in all facial structures can affect proper mask fitting. For example, a mask can have a tighter fit on the left side of the face than on the right side.

“Facial asymmetry is almost imperceivable to the eye but is made obvious by the cough flow through the mask,” explained co-author Tomas Solano, from Florida State University. “For this particular case, the only unfiltered leakage observed is through the top. However, for different face shapes, leakage through the bottom and sides of the mask is also possible.”

Producing individually customised ‘designer masks’ is not practical at large scales. Still, better masks can be designed for different populations by revealing general differences between male and female or child versus elderly facial structures and the associated air flow through masks.

Source: American Institute of Physics

Vigorous Exercise and Talking Produce Similar Levels of Aerosols

Old man jogging
Photo by Barbra Olsen on Pexels

Vigorous exercise produces a similar level of aerosol particles as speaking, but high-intensity exercise produces more, according to new research published in Communications Medicine. This is the first study to measure exhaled aerosols generated during exercise, to help inform the risk of airborne viral transmission of SARS-CoV-2 for gyms and indoor physical training.

Inhalation of infectious aerosol is considered to be the main route of SARS-CoV-2 transmission. In this study, researchers performed a series of experiments to measure the size and concentration of exhaled particles (up to 20µm diameter) which are generated in our respiratory tracts and breathed out, during vigorous and high-intensity exercise.

Using a cardiopulmonary exercise test, 25 healthy participants (13 male, 12 female) with a range of athletic abilities were recruited to undertake four different activities (breathing at rest, speaking at normal conversational volume, vigorous exercise and high-intensity exercise) on a cycle ergometer. Airflow and particles emitted were measured by particle counter. Experiments were carried out in an orthopaedic operating theatre — an environment with ‘zero aerosol background’, letting the researchers to unambiguously identify the aerosols generated by the participants.

The results showed that the size of airborne particles emitted during vigorous exercise was consistent with those emitted while breathing at rest. However, the rate of aerosol mass exhaled during vigorous exercise was found to be similar to speaking at a conversational volume.

Jonathan Reid, scientific lead on the paper, said: “COVID has profoundly impacted sports and exercise, and this study provides a comprehensive analysis of the mass emission rates of aerosol that can potentially carry infectious virus produced from an individual during exercise. Our research has shown that the likely amount of virus that someone can exhale in small aerosol particles when exercising is comparable to when someone speaks at a conversational volume.  The most effective way to reduce risk is to ensure spaces are appropriately ventilated to reduce the risk of airborne transmission.”

Source: University of Bristol

Kids are a Significant Source of COVID Spread in Households

COVID spreads extensively in households, with children being a significant source of that spread. These are the findings from an antibody surveillance study published in CMAJ Open, which also shows that about 50% of household members were infected from the first-infected individual during the study period.

Although kids were less likely to spread the virus compared to adults, children and adults were equally likely to become infected from the first-infected individual.

The antibody surveillance study included 695 participants from 180 households in the Canadian city of Ottawa in Ontario, between September 2020 and March 2021. Included households had at least one member having had a confirmed COVID infection and at least one child within their household.

“Our study was conducted when we were dealing with a less transmissible virus and pandemic restrictions were strongly in place, and we still had a 50% transmission rate within households. Flash forward to where we are today with an extremely transmissible variant of COVID and the majority of pandemic restrictions lifted; it’s safe to say transmission rates will be higher even though we have a high vaccination rate amongst those who are eligible,” said Dr Maala Bhatt, the study’s lead author. 

“I know many want to ‘live with COVID’ and abandon the layers of protection that were previously mandated, but it’s important to be aware of the high transmissibility of this virus in closed, indoor settings, such as schools,” she cautioned.  “Our most vulnerable and our youngest children who are not yet able to be vaccinated are still at risk for COVID infection.”

In the Canadian province of Eastern Ontario, where the study was done, COVID is on the rise once again. Three-quarters of all children admitted to CHEO with COVID have come during the Omicron wave. Since the beginning of January this year a third of the roughly 4900 monthly visits to the Emergency Department were for COVID-related symptoms.

The study hypothesised that children would act as “an even greater source of spread within households with the emergence of more infectious variants.” Children also have “considerable potential to spread” in settings such as school and daycare, where they congregate indoors for long periods, especially now when masking is not required in many jurisdictions.

“While we’re lucky hospitals aren’t currently overloaded, emergency departments are and positivity rates are on the rise, even amongst children,” said Dr Bhatt, paediatric emergency physician and Director of Emergency Medicine Research at CHEO and an Investigator at the CHEO Research Institute.

“We continue to learn more about COVID and its potential long-term health impacts, and we still aren’t clear about how long immunity lasts; these are all things researchers continue to study.”

Source: University of Ottawa

Little COVID Viral Contamination Risk in Hospital Rooms

Source: Martha Dominguez de Gouveia on Unsplash

A study found that hospital rooms where COVID patients were treated had little to no active virus contaminations on surfaces. The finding, published in Clinical Infectious Diseases, concluded that contaminated surfaces in the hospital environment are unlikely to be a source of indirect transmission of the virus, contrary to earlier views.

“Early on in the pandemic, there were studies that found that SARS-CoV-2 could be detected on surfaces for many days,” said the study’s senior author, Professor Deverick Anderson. “But this doesn’t mean the virus is viable. We found there is almost no live, infectious virus on the surfaces we tested.”

The researchers tested a variety of surfaces in the hospital rooms of 20 COVID patients at Duke University Hospital over several days of hospitalisation, including on days 1, 3, 6, 10 and 14.

Samples were collected from the patients’ bedrail, sink, medical prep area, room computer and exit door handle. A final sample was collected at the nursing station computer outside the patient room.

PCR testing found that 19 of 347 samples gathered were positive for the virus, including nine from bedrails, four from sinks, four from room computers, one from the medical prep area and one from the exit door handle. All nursing station computer samples were negative.

Of the 19 positive samples, most (16) were from the first or third day of hospitalisation.

All 19 positive samples were screened for infectious virus via cell culture with only one sample, obtained on day three from the bedrails of a symptomatic patient with diarrhoea and a fever, demonstrating the potential to be infectious.

“While hospital rooms are routinely cleaned, we know that there is no such thing as a sterile environment,” Prof Anderson said. “The question is whether small amounts of viral particles detected on surfaces are capable of causing infections. Our study shows that this is not a high-risk mode of transmission.”

Prof Anderson said the findings reinforce the understanding that SARS-CoV-2 primarily spreads through person-to-person encounters via respiratory droplets in the air. He noted that people should concentrate on known anti-infection strategies such as masking and socially distancing to mitigate exposures to airborne particles.

Source: Duke University

A Smaller Fourth Wave Predicted for South Africa as Flu Cases Spike

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A fourth wave of infections is likely for South Africa but its impact probably won’t be as severe as during earlier surges, as shown by new modelling, according to BusinessTech.

Factoring in sero-prevalence surveys and other data, it appears that an estimated 60% to 70% of the population has already contracted COVID, which along with vaccinations will provide protection from severe disease, the South African COVID-19 Modelling Consortium said in an online presentation on Wednesday.

Even in its worst-case scenario, deaths and hospitalisations during a fourth wave were projected to be substantially lower than during previous surges.

Though current caseload for the country is “incredibly low”, it is still “very hard to commit to say South Africa is over the worst” of the COVID pandemic, said Harry Moultrie, a senior epidemiologist at the National Institute for Communicable Diseases, which coordinated the modelling.

“It’s going to be a bumpy ride,” he said. “We don’t know where this virus is going to take us. We will still be seeing hospital admissions and deaths related to Covid for years to come.”

South Africa;s seven-day rolling average of new infections has fallen below 300, much reduced from a third-wave peak which hit nearly 20 000 in July.

To date, South Africa has had 2.93 million confirmed cases of COVID, with 89 504 deaths, although excess death numbers indicate the true toll may be much higher. About 34% of the nation’s 39.8 million adults have been fully vaccinated.

While some countries in the northern hemisphere such as Germany are seeing severe fourth and even fifth waves of infection driven by the spread of the delta variant, that’s not a good indicator South Africa will follow a similar path because the strain has already spread widely in the country, explained Gesine Meyer-Rath, a member of the modelling consortium.
“We have paid in a way with high deaths and a lot of destruction” during previous waves, Meyer-Rath said. “We don’t think we will have a super-fast case increase again” unless a highly transmissible new variant emerges, she said.

While the outlook for the fourth wave is brighter, the past few weeks has seen a sharp rise of influenza cases, the National Institute for Communicable Diseases (NICD) reported.

A high number of cases had been seen from the beginning of the month, including influenza-like illness and pneumonia hospitalised cases at surveillance sentinel sites.

The NICD added that there had been clusters of influenza cases reported in schools and workplaces.

The NICD’s Cheryl Cohen said: “The increase in influenza this summer, which is not the typical time for the influenza season in South Africa, is likely the result of the relaxation of non-pharmaceutical interventions to control COVID combined with other factors such as reduced immunity because flu has not circulated since 2020 and 2021.”

Sources: Eyewitness News; BusinessTech