In this episode, we examine changes to the Covid-19 virus that has altered the world over the past year. Dr Richard Lessells, infectious diseases specialist at Krisp, the KwaZulu-Natal Research and Innovation Sequencing Platform, part of the University of KwaZulu-Natal, helps us make sense of the latest developments in the spread of Covid-19 in South Africa. He provides an update on genomic surveillance of the disease and warns that the pandemic is still at an early stage. In this episode, we also hear insights from Johns Hopkins Bloomberg Public School of Health Vice Dean Josh Sharfstein about the evolution of the virus. Also coming up, an update from Dr Keith Cloete, head of the Western Cape health department, who cautions that hospitals are buckling under the pressure of a rapidly rising rate of Covid-19 in the province that attracts huge numbers of holidaymakers at this time of the year. – Jackie Cameron & Jarryd Neves

Inside Covid-19 headlines

  • More than 78m people have tested positive for Covid-19 and more than 1,7m people have died of the disease around the world. That’s according to the Johns Hopkins Coronavirus Resource Centre, which lists the US as the worst affected country. It has reported more than 322,000 deaths.
  • South Africa is the hardest-hit country in Africa. It is number 18 on the list of the countries with the highest rates of Covid-19, with just under 1m cases and about 25,000 reported deaths. South Africa is also experiencing a sharp uptick in the number of cases.
  • The new Covid-19 strain that emerged in the UK is possibly already in the US, Germany, France and Switzerland, officials in those countries said. Ireland imposed new restrictions to stem an “extraordinary growth” in cases, and said the nation should act on the assumption that the new variant has arrived, reports Bloomberg.
  • South Africa’s new strain of Covid-19 has appeared in the UK, sparking strict restrictions in Great Britain on individuals with recent ties to contacts who have been in South Africa. For more on that, see: Britain locks down South Africans as mutant Covid-19 SA strain enters UK
  • Pfizer’s partner BioNTech SE is exploring options to boost vaccine production, and its chief executive officer said its shot will probably work against the new virus strain. Taiwan reported the first locally transmitted infection since April, ending what was the world’s longest stretch without a domestic case. Source: Bloomberg
  • New Jersey and Arizona reported the highest number of deaths from Covid-19 since June and July, respectively. Deaths are up in New York City as well. Meanwhile, Anthony Fauci, the U.S. government’s top infectious-disease doctor, received Moderna Inc.’s vaccine, part of an effort by health officials to build confidence in the shots, says Bloomberg.
  • Denmark says another variant has been detected, says Bloomberg. Denmark’s health authorities said that about 10% the country’s positive test results are now of the N439K mutation of the virus, calling the rate “concerning.” The mutation, which was first discovered in Romania in May, is different from the one spreading in the U.K. and also from the one that infected the Danish mink farms earlier this year, authorities said.
  • The Covid-19 infection rate in U.S. counties dependent on meatpacking jobs was as high as 10 times the average level of rural counties last spring, according to a U.S. Department of Agriculture report. The report examined the spread of Covid in the 57 mostly rural US counties in which meatpacking accounts for at least 20% of employment, reports Bloomberg. Beginning in mid-April, confirmed Covid cases in those counties outpaced the rest of the country and remained “much higher” than in other U.S. counties through mid-July, the USDA’s Economic Research Service found. Meat-processing plants quickly became epicenters of the virus in the U.S. in the spring as mostly immigrant employees continued to work, sometimes shoulder to shoulder, in cramped, cold, damp facilities, often without protective gear.
  • Sweden plans to enact new pandemic laws on Jan. 15 that will give it the right to shutter businesses and public transport to help tackle a spike in cases, says Bloomberg. Despite a resurgence of infections, Sweden has so far stopped short of a full lockdown partly because it lacked the legal framework to do more.
  • Nicola Sturgeon has been caught flouting Covid rules by speaking to pensioners in a pub without wearing a mask, reports The Week. “The Scottish first minister has had to apologise for her lapse after months of advocating draconian regulations. The SNP leader, 50, was photographed chatting to three women at a wake last week in Edinburgh. Rules drawn up by her Scottish devolved government state customers in hospitality settings must wear a face covering unless seated at a table.”
  • NHS bosses have raised concerns about the rollout of the coronavirus vaccine and asked the government to speed up distribution, says The Week. With more than half of hospital trusts and two-thirds of GPs yet to receive supplies, Dr Richard Vautrey, the chair of the British Medical Association’s GP committee, is quoted as saying: “We need millions of doses to be made available as soon as possible – urgently.” Government sources have also warned that there is a “high chance” of a full national lockdown in the New Year. Yesterday, Britain recorded 691 coronavirus deaths – the second highest daily toll since last May and a jump of a fifth in one week.
  • A mass coronavirus testing programme for lorry drivers will relieve congestion at British ports following an agreement to reopen the border between France and the UK, reports The Week. Rail, air and sea services from Britain will resume this morning after Paris agreed to ease the ban imposed after the discovery of a new strain of Covid. “I am pleased we have made this important progress with our French counterparts this evening,”  Transport Secretary Grant Shapps is quoted as saying.
  • The National Department of Health and the Solidarity Fund have jointly announced that the down payment of just over US$19m (amounted to R283m at the exchange rate at time of payment) has been made to GAVI (the Vaccine Alliance) to secure South Africa’s entry into the Covax facility. The payment was made in line with the Fund’s previous allocation of funds and commitment to support Government’s efforts to accelerate the roll-out of vaccines in South Africa, they said. The down payment represents 15% of the total cost of securing access to vaccines for 10% (roughly 6 million) of the population. The country’s membership in the Covax facility ensures that South Africa receives its equitable share of the vaccine once it becomes available. “There can be no doubt that a Covid-19 vaccine will play an important role in helping South Africa manage the virus,” says Gloria Serobe, Chairman of the Solidarity Fund.
  • South African private hospital operators have warned that they are facing severe capacity constraints due to a resurgence in coronavirus cases, reports Bloomberg. The Covid-19 pandemic first peaked in Africa’s most industrialised economy in late July before infections tailed off. The country is in the midst of a second wave of the disease that began shortly before the festive season — which sees millions of people traverse the country to holiday destinations and home towns and villages, says the news agency. Netcare, Life Healthcare Group Holdings and Mediclinic International, the country’s three biggest private hospital groups, which had spare capacity in most areas during the initial surge, all said they were confronting bed shortages. State hospitals have also reported a rise in coronavirus cases. In four of South Africa’s most populous provinces, “we have noted a substantial resurgence in Covid-19 patients and the health-care system is under significant pressure,” Charl van Loggerenberg, Life Healthcare’s general manager of emergency medicine, told Bloomberg. Intensive care and high-care units are “particularly under severe strain” in the KwaZulu-Natal, Western Cape and Eastern Cape regions, he said. Besides admitting more Covid-19 patients, the hospitals are also having to administer additional treatment. “We are seeing a significantly higher demand for oxygenation of sick patients versus the first wave,” Netcare’s Chief Executive Officer Richard Friedland said in an emailed response to questions. “We have seen more cases in both the Eastern Cape and Western Cape, and expect to exceed the number of cases seen in the first wave in KwaZulu-Natal this week.”
  • Case numbers in South Africa’s economic hub of Gauteng, which was already on the rise, is expected to spike when holidaymakers return in early January, Friedland is quoted as saying. All three companies are recruiting more nurses, temporarily relocating staff to hotspot areas and making contingency plans to convert additional wards to accommodate Covid-19 patients. Non-essential surgical cases are largely being postponed. South Africa has reported a spread of a new SARS-CoV-2 lineage with multiple spike mutations, which may be driving new infections. At this stage, treatment guidelines haven’t changed, according Gerrit de Villiers, a group general manager at Mediclinic.
  • The new lineage has become dominant in the Western Cape, and has probably spread across most of the country, according to Keith Cloete, head of the province’s health department. It has spread faster than other variants, with smaller amounts of this strain needed to infect people, he said. The province is considering whether further restrictions are needed, including curtailing Christmas church services, says Bloomberg. In Cape Town, hospitals are expected “to come under even more pressure,” Cloete is reported as saying. “That’s why we need a radical intervention to safeguard the public and private healthcare system over the festive season, he said.

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