Viral load analysis of wastewater suggests that KwaZulu-Natal may already have entered the third wave of COVID infections, according to research by DUT.
The Institute for Water and Wastewater Technology, based at DUT, has been monitoring viral loads of wastewater at the central treatment plant in eThekwini since July 2020, and found a clear correlation between clinical cases and viral loads detected in wastewater.
While clinical cases were reported to be on the increase in KZN since April 20 this year, they had found an increase in wastewater viral load some three weeks earlier.
The Institute for Water and Wastewater noted that the peak of the COVID second wave in South Africa occurred in January with an average of 40 000 cases in KwaZulu-Natal.
Over this period, the researchers measured average viral loads of 4.72 log copies per 100 millilitres at the central wastewater treatment plant. However, over the last four weeks, viral loads have averaged 5.57 log copies per 100 millilitres.
This has led the institute to suggest that there are far more cases than have been reported clinically, with a significant presence of asymptomatic individuals.
A report [PDF] on the third wave by the National Institute for Communicable Diseases indicated that there was a seroprevalence for SARS-CoV-2, a proxy for previous infection, of 30% to 40% after the third wave. This indicates that COVID infections were already widespread, and lends credence to the institute’s notion of extremely widespread asymptomatic cases. Projections for KZN showed a much lower peak for hospital admissions.
The B1617 variant, is becoming increasingly dominant around the world and could worsen the pandemic – especially in countries where low vaccination rates are low. This warning comes from experts in Singapore, who added that there will be more virus mutations to come.
Professor Teo Yik Ying, dean of the National University of Singapore’s (NUS) Saw Swee Hock School of Public Health, said to The Straits Times: “What is frightening is the speed at which this variant is able to spread and circulate widely within the community, often surpassing the capability of contact-tracing units to track and isolate exposed contacts to break the transmission chains.
“It has the potential to unleash a bigger pandemic storm than the world has previously seen.”
Delta has mutated to be more transmissible, and may slightly weaken the protection conferred by vaccines as well as natural infection, experts said. The variant, which was first detected in India in October 2020, is now found around the world.
WHO chief scientist Soumya Swaminathan said that B1617 is 1.5 times to two times more transmissible than the strain that first appeared in Wuhan 18 months ago.
It is now present in more than 50 countries and is surpassing other strains causing infections in India, such as B117 (now ‘Alpha’, commonly known as the UK variant).
“On clinical severity, it’s a little less clear because there have not been controlled studies which look at patients that you control for multiple factors, and then look at the impact of the strain on the clinical profile,” Dr Soumya said at a recent webinar.
Dr Soumya added that anecdotal evidence seems to indicate that more young people in India had been infected and developed serious illness.
In India, more than 27 million people have been infected with COVID, with over 325 000 deaths.
There are three versions of B1617 – B16171 (Kappa), B16172 (Delta) and B16173. The second version is the most relevant as it has appeared to overtake B1671/Kappa as reported globally. The third version, B16173, is rare and has not yet been given a Greek letter designation by the WHO.
On May 8, the National Institute for Communicable Diseases announced that it had detected five cases of the Delta variant in South Africa; three in Gauteng and two in KwaZulu–Natal. Presently, it is unclear if B1617 causes more severe illness or a higher mortality rate.
The best weapon remains widespread vaccination, Prof Teo said. Vaccinated individuals have less chance of being infected, and are much less likely to develop severe symptoms even if infected, Prof Teo added.
Preliminary US research showed that the Pfizer and Moderna vaccines should still be effective against B1617.
A study by Public Health England also showed that the vaccines by Pfizer-BioNTech and AstraZeneca work against Delta, which has become the dominant strain in the UK.
The study found that the Pfizer-BioNTech shot was 88% effective against the Delta variant two weeks after the second dose, with a 60% effectiveness for the AstraZeneca vaccine.
The pressure is to keep up with the rapidly mutating virus and immunise populations to control it. Unfortunately, most countries’s vaccination programmes are far behind.
On Friday, WHO European director Hans Kluge warned that the pandemic will not be over until at least 70% of people are vaccinated. He deplored the roll-out in Europe, saying that while it was better it was still “too slow”.
The European Centre for Disease Prevention and Control said about 43% of adults in the European Union and European Economic Area have received at least one dose of a COVID vaccine as of Saturday, 29 May.
“Time is against us,” Dr Kluge warned, stressing the need to accelerate the immunisation campaign.
South Africa’s long-delayed vaccination programme is in full swing, but so far only about 1% of the population have received a jab, which is currently being administered to healthcare workers and those over 60.
Globally, the outlook does not seem good. The New York Times reported that more than 1.81 billion vaccine doses had been administered worldwide as at Friday (May 28), but a stark divide remains between countries’ vaccination programmes, with some not even reporting a single dose given.
Global inequity in vaccine supplies and distribution persists, and the opportunity for widespread vaccination remains a privilege for advanced economies, Prof Teo said.
Professor Dale Fisher, chair of the WHO’s Global Outbreak Alert and Response Network, said this means a higher chance of B1617 creeping into countries that had been virtually untouched by COVID.
“These countries, such as Thailand, Cambodia, Laos and Vietnam, are more vulnerable due to the low vaccination rates, leaving them more susceptible to severe disease,” Prof Fisher added.
He urged wealthier nations to lend more support to the WHO-backed Covax programme, a global project to secure and distribute vaccines to poorer countries.
A study of healthcare workers has shown their likelihood of being infected with COVID during the pandemic was three times higher compared to the general population, with about one in five of those infected workers being asymptomatic and unaware they had COVID.
The study also shows that it was not only frontline staff who faced the higher risk, suggesting that there was transmission between staff and within the wider community. The results are published in ERJ Open Research.
However, health care workers who had been infected were very unlikely to contract COVID a second time in the following six months.
The research was led by Professor James Chalmers, a consultant respiratory physician from the University of Dundee.
“We have always believed that front line health workers face a high risk of contracting COVID and that’s why we’ve tried to ensure they have the PPE needed to protect themselves,” said Prof Chalmers. “But many questions remain about the level of this risk and what other measures we can take to protect staff and reduce transmission of the disease.”
The study recruited 2063 staff working in a wide variety of healthcare roles in the East of Scotland. Between May and September 2020, the participants had blood tests for COVID antibodies, a very accurate indication of prior COVID infection. The researchers also recorded whether any participants developed an infection in subsequent months.
The health care workers results were compared with a randomly selected control group of blood samples taken by local GPs during the same time period.
These blood tests showed that 300 (14.5%) of the healthcare workers had been infected, a rate more than triple the proportion of people infected in the local population. The highest rates of infections among the workers were found in dentistry (26%), health care assistants (23.3%) and hospital porters (22.2%). The rate among admin staff was the same as that of doctors (21.1%).
Rates among people working in areas of the hospital where COVID patients were being treated were somewhat higher than those working in non-COVID areas (17.4% vs 13.5%). However, the majority of infections were in staff who were not working directly with COVID patients, suggesting there was transmission between staff or infections acquired in the community.
Out of the 300 healthcare workers testing positive, 56 (18.7%) did not think that they had ever caught COVID and were totally asymptomatic. This is an important finding, according to the researchers, since people without symptoms are likely to go to work, potentially infecting others.
In the months following their blood tests, 39 workers developed a symptomatic COVID infection, but only one of these was a worker who had previously tested positive. This equates to an 85% risk reduction, similar to the level of protection provided by COVID vaccines.
Prof Chalmers said: “A lot of attention during the pandemic has been around PPE for doctors and nurses but we found that dentists, healthcare assistants and porters were the staff most likely to test positive.
“We continued to monitor staff for up to seven months and found that having a positive antibody test gave 85% protection against a future infection. This is really good news for people who have already had COVID-19, as it means the chances of a second infection are very low.”
The team hopes to continue the research to see how long immunity persists and how vaccination affects infections among healthcare workers.
Professor Anita Simonds, President of the European Respiratory Society and Consultant in Respiratory and Sleep Medicine at Royal Brompton Hospital, UK, was not involved in the research, offered comments.
She said: “This research shows the high levels of COVID infection among all healthcare workers, with the highest evidence of infection in dentists, healthcare assistants and porters. Staff working in critical care, who are likely to have been protected by using personal protective equipment at all times, were not disproportionately affected.
“It should be noted that among administrative staff, 21.1% were found to have been infected with COVID, indicating that all those working directly with patients, and those working in other hospital roles are at risk, and vaccination and risk assessment for appropriate levels of PPE in all these frontline groups are crucial.”
Following a steep rise in COVID cases in three provinces, The National Institute for Communicable Diseases (NICD) is working with teams in those areas to monitor the situation.
Increases in the Northern Cape, North West and Free State have been observed by the NICD. The Northern Cape has over 3000 active cases, the North West over 2600 and the Free State over 2200.
The NICD said that it was working with provinces to ascertain whether the rise in cases could be attributed to cluster outbreaks and has recommend increased testing and contact tracing to contain the situation.
Acting executive director of the NICD, Professor Adrian Puren, said: “We want to reassure South Africans that we are actively monitoring the situation in these provinces and will keep the community informed of any new developments.”
The NICD said that with the April school holiday season soon starting and many people making plans for travel and social gatherings, it was still vital to continue to comply with COVID preventative health measures.
Earlier this month, Discovery Health described possible scenarios for COVID in South Africa. Poor social distancing and masking behaviours, superspreader events and a lack of early vaccinations, a third wave could claim as many as 76 000 lives, the insurance company estimated. However, by maintaining good nonpharmaceutical interventions and engaging in a prompt vaccination rollout, deaths would fall to 9000 by the end of the year.
The NICD monitors the number of confirmed COVID-19 cases and tests performed on a daily basis and associated resurgence metrics.
Researchers have found evidence suggesting that the P.1 COVID variant could be twice as transmissible as prior strains. The findings were published in the Journal Science.
The P.1 SARS-CoV-2 variant was first detected in four travellers from Brazil during a routine screening at Haneda airport, Tokyo. Manaus, the capital of the state of Amazonas in Brazil was the origin of the variant. According to preliminary investigations, the virus emerged late in 2020, beginning to spread in November and then quickly became the dominant strain. This prompted many to believe that it could reinfect those infected with the initial strain.
Some 70% of the residents in the city were believed to have been infected during the initial infection period. After variant infections rose in Manaus, the P.1 variant soon spread throughout Brazil, and then to other countries—thus far, it has been detected in at least 37 countries.
The researchers used molecular clock analysis to determine that the virus had 17 identifiable mutations and that three spike protein mutations (N501Y, E484K and K417T) allowed the virus to bind more effectively to host cells. These also may help in evading antibodies, and the researchers also found that P.1 can evade immunity granted by prior strains.
In simulations, P.1 was 1.7 to 2.4 times more transmissible than the prior virus baseline, but whether this was due to longer persistence in the body or increased viral load could not be determined. Additionally, it could not be established if it increased disease severity or raised mortality rates. Though people inffected with the variant were 1.2 to 1.9 times as likely to die, this could have been a result of the severe strain the overburdened healthcare systems were experiencing in the city.
More work is needed to find out whether the P.1 strain can infect those infected with prior strains or have been vaccinated, the researchers said.
Journal information: Nuno R. Faria et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil, Science (2021). DOI: 10.1126/science.abh2644
A US study uploaded onto the bioRxiv preprint server showed that pets with SARS-CoV-2 likely acquired the virus from humans.
This suggests that human-animal infection may actually occur much more frequently than previously thought – implying that infected individuals should limit their contact with animals. The paper is currently available on the bioRxiv* preprint server.
Both natural and experimental infections with SARS-CoV-2 have been demonstrated in various species of pets, which includes dogs, cats, hamsters, rabbits, and ferrets. Hamsters, cats and ferrets have been shown to transmit the virus to each other, and dogs are still weakly susceptible to the virus. However, natural infections of pets have almost always resulted from contact with a COVID-infected person.
Since pets share so much space with humans, this is a good use of the One Health approach, a transdisciplinary collaboration aiming for health outcomes through awareness of the interconnectedness between people, animals, plants and their mutual environment.
As part of a COVID household transmission investigation, researchers in the US conducted a One Health appraisal of SARS-CoV-2 infection in pet cohabitants as one of the earliest research endeavours in assessing risk and behavioral factors shared between people and pets.
The study was conducted between April and May of 2020, and mammalian pets from households with at least one individual with confirmed COVID were eligible for inclusion. Detailed descriptions of each animal’s residence were made.
Demographic and exposure information was obtained from all household members. At the same time, the pets were tested with the use of real-time reverse transcription-polymerase chain reaction (rRT-PCR) and neutralisation assays from oropharyngeal, nasal, rectal, fur, faecal, and blood samples.
The small sample size of this study made it difficult to analyse prevention measures in the home, so additional investigations are needed in order to determine the best methods to prevent human-pet COVID transmission.
All oropharyngeal, nasal, and rectal swabs from the tested animals tested negative when rRT-PCR was conducted; however, fur swabs from the one dog tested positive with the use of this molecular method at the first animal sampling. This is actually the first study to detect RNA of a virus from an animal’s fur.
Furthermore, in households where owners withs COVID lived with their pets, 20% had pets with serological evidence of prior SARS-CoV-2 infection, implying some secondary viral transmission. Four dogs and four cats from six households were found to have detectable neutralising antibodies against the virus.
In households with higher rates of human COVID infections, SARS-CoV-2 was more likely to be seen in pets, while much less common when owners limited interactions with their pets after they had developed COVID symptoms.
The authors stressed that it is still important for decision-makers to understand the role of animals in the epidemiology of the pandemic
“Our findings add to the growing body of evidence demonstrating SARS-CoV-2 transmission can occur between people and pets – most often from people to pets – and suggest this transmission may occur more frequently than previously recognized”, wrote the authors of the bioRxiv paper.
Representatives from the liquor industry have said that the South African government must consider data from a new report that shows little alcohol ban effectiveness on trauma cases. However, other studies show negative effects of alcohol during lockdown, and a surge in violent trauma in Cape Town after alcohol bans were lifted.
In a statement on Thursday, the South African Liquor Brand owners Association (Salba) referenced a new report showing that, compared to other countries, South Africa saw similar trauma cases with its lockdown and alcohol ban to those that only had a lockdown.
The report had financial support from Distell, led by independent data expert Ian McGorian of Silver Fox Consulting, in collaboration with professor Mike Murray from the University of KwaZulu-Natal.
The report found that trauma cases in South Africa under lockdown dropped 60%. But other countries also saw the same drop with no alcohol ban, including the UK (57%), Ireland (62%), Italy (56.6%) and the USA (54%), casting doubt over the effectiveness of alcohol bans in curbing trauma. The researchers also commented that curfews may have explained more of a reduction in trauma cases than alcohol bans.
While members of the liquor industry recognised the impact of alcohol on South African society, they said that government needs to be more objective with its lockdown regulations.
Salba chairperson Sibani Mngadi said the alcohol ban over Easter Weekend, while simultaneously allowing larger gatherings, made even less sense in reducing COVID transmission. This suggests that government was not considering science in its decision making, he said.
However, a multicentre study from Colorado, USA showed that even while trauma cases during lockdown fell by 33%, alcohol screens increased from 34% to 37%, and alcohol positive patients rose from 32% to 39%.
A study of Cape Town trauma admissionssaw a dramatic drop of 53% in trauma admissions during the hard lockdown and an immediate rebound coinciding with the resumption of alcohol sales, with a 107% increase in gunshots wounds compared to pre-lockdown conditions.
The researchers noted that in South Africa the trauma demographic is much younger, with much higher rates of violence, with about half of homicide victims in SA testing positive for alcohol.
Distell chief executive Richard Rushton said the industry was merely asking that the data should be viewed objectively to improve dialogue with decision makers.
“We are all on the same side, and we want to help find solutions. We are very clear that alcohol abuse is unacceptable and causes harm. Our view is that the focus must be on finding ways to deal with high-risk drinkers, rather than using blunt instruments that penalise all South Africans.
“Any proposed new regulations need to be evidence-based, rational and target problem areas,” he said.
Business Leadership SA chief executive Busisiwe Mavuso said that lockdown could have been better managed, as 220 000 jobs had been lost along billions of rands in tax to the fiscus, while uncertainty still plagued alcohol producers.
“The decisions made to confront the health crisis should not have unintended consequences for the economy, and that is exactly what has happened with the bans on alcohol,” she said.
Mr Mavuso added that, since the start of the pandemic, business has been a willing partner to government and “needs to be part of the solution to ensure we fight this pandemic with the least possible damage to the economy”.
“The data analysis by the alcohol industry is an important intervention and must be taken seriously as we move forward.”
According to a new study which used mobility tracking of cell phone data, a greater movement of people is a strong predictor of increased COVID cases rates.
Until people are widely vaccinated against SARS-CoV-2, the array of nonpharmaceutical public health interventions such as physical distancing and limiting travel and social contacts will remain the most effective means of controlling COVID. Capturing the interrelationship between human behaviour and infectious diseases is one of the hardest problems in epidemiology.
“Mobility measures capturing human activity through anonymized tracking of smartphones are believed to be reasonable proxies of contact rates outside of one’s own home; these measures can provide more timely and reliable sources of information on contact rates compared with time-use surveys or contact tracing,” the authors wrote.
Researchers looked at anonymised smartphone mobility data from nearly 12 months from March 2020 to March 2021, both at a national and provincial level, while controlling for date and temperature. A 10% increase in the mobility of Canadians outside their homes was found to be associated with a 25% increase in subsequent SARS-CoV-2 weekly growth rates. They investigated at the mobility threshold (the level needed to control the virus) and the mobility gap (the difference between the threshold and actual movement).
“The mobility threshold and mobility gap can be used by public health officials and governments to estimate the level of restrictions needed to control the spread of SARS-CoV-2 and guide, in real-time, the implementation and intensity of nonpharmaceutical public health interventions to control the COVID-19 pandemic,” wrote the authors.
Journal information: Brown, K. A., et al. (2021) The mobility gap: estimating mobility thresholds required to control SARS-CoV-2 in Canada. Canadian Medical Association Journal. doi.org/10.1503/cmaj.210132.
A study of SARS-CoV-2 genomes and epidemic case data has shown that COVID outbreaks emerge with new variants.
“As variants emerge, you’re going to get new outbreaks,” said Bart Weimer, professor of population health and reproduction at the UC Davis School of Veterinary Medicine. The study combined classical epidemiology with genomics, providing a tool for public health authorities to predict the course of pandemics.
SARS-CoV-2 only has 15 genes, but is mutating constantly. The majority of these changes have little impact, but occasionally they result in the virus becoming more or less transmissible.
Together with graduate student DJ Darwin R Bandoy, Prof Weimer at first analysed the genomes of 150 SARS-CoV-2 strains, mostly from outbreaks in Asia prior to March 1, 2020, along with epidemiology and transmission information on those outbreaks.
The classified outbreaks by stage: index (no outbreak), takeoff, exponential growth and decline. Virus transmissibility is set by the value R, or reproductive number, where R is the average number of new infections caused by each infected person.
They combined all this information into a metric called GENI, for pathogen genome identity. Comparing GENI scores with epidemic phases showed that an increase in genetic variation immediately preceded exponential growth in cases, for example in South Korea in late February. In Singapore, however, bursts of variation were associated with smaller outbreaks that were quickly brought under control.
Prof Weimer and Bandoy then looked at 20 000 sequences of SARS-CoV-2 viruses collected over February to April 2020 in the United Kingdom, and compared them with COVID cases data.
They found that the GENI variation score rose steadily with the number of cases. When a national lockdown was imposed in late March, the number of new cases stabilised but the GENI score continued to rise. This shows that control measures such as banning gatherings, mask mandates and social distancing are effective in controlling spread of disease in the face of rapid virus evolution.
It could also help explain “superspreader” events when large numbers of infections result from relaxed precautions at an event.
Prof Weimer said he hopes that health authorities will adopt this method of measuring virus variation and linking it to the local transmission rate, R.
“In this way you can get a very early warning of when a new outbreak is coming,” he said. “Here’s a recipe for how to go about it.”
A new model suggests that as lockdowns ease, other control measures such as mask use must be enhanced in order to prevent additional COVID outbreaks.
The mathematical model, developed by scientists at the Universities of Cambridge and Liverpool, provides general insights about how COVID will spread under different potential control scenarios.
They considered ‘non spatial’ control measures involving facemasks, handwashing and metre-scale social distancing can all limit the number of virus particles being spread between people. The other, ‘spatial’ control measures included lockdown and travel restrictions, which reduce how far virus particles can spread. Different combinations of COVID control measures showed that non-spatial control needs to be ramped up as lockdown is lifted.
“More effective use of control measures like facemasks and handwashing would help us to stop the pandemic faster, or to get better results in halting transmission through the vaccination programme. This also means we could avoid another potential lockdown,” said Dr. Yevhen Suprunenko, a Research Associate in the University of Cambridge’s Department of Plant Sciences and first author of the paper. The authors stress that their predictions rely on such non-spatial control measures being implemented effectively.
Their model took into account the socio-economic impact of the measures. The costs of spatial measures of lockdown increased over time, while costs for non-spatial measures decreased due to falling prices and greater availability of items such as masks, and usage becoming a habit.
“Measures such as lockdowns that limit how far potentially infected people move can have a stronger impact on controlling the spread of disease, but methods that reduce the risk of transmission whenever people mix provide an inexpensive way to supplement them,” explained co-author Dr Stephen Cornell at the University of Liverpool.
The model was derived from identifying control strategies for plant diseases threatening staple crops. Instead of the usual computer simulation model, mathematical approach allowed the authors to identify insights on how to control newly emerging infectious diseases of plants and animals.
“Our new model will help us study how different infectious diseases can spread and become endemic. This will enable us to find better control strategies, and stop future epidemics faster and more efficiently,” said co-author Professor Chris Gilligan in the University of Cambridge’s Department of Plant Sciences.
Journal information: Analytical approximation for invasion and endemic thresholds, and the optimal control of epidemics in spatially explicit individual-based models, Journal of the Royal Society Interface,rsif.royalsocietypublishing.or … .1098/rsif.2020.0966
