• Global deaths from COVID-19 surpass four million. Source

• Africa marks its worst pandemic week to date, with 251,000 new cases. As new cases double every 18 days, Dr. Matshidiso Moeti, the WHO Regional Director, warned, “The end to this precipitous rise is still weeks away.” Source

Nature publishes a report from a large human genetic study of SARS-CoV-2 infection. Researchers swiftly set up a large international collaboration at the beginning of the pandemic, collecting data from over 49,000 people with COVID-19 across 46 studies. The study included people from six ancestry groups and 19 countries – as well as a control group of two million people, and information on known risk factors among participants.

The researchers looked at three categories of illness – people with self-reported or laboratory-confirmed COVID-19; people who were hospitalized with moderate-to-severe COVID-19, and people who became critically ill, required respiratory support or died, comparing frequencies of genetic variants among participants and uninfected controls.

Researchers found 13 locations (or loci) in the human genome that affect susceptibility to, and severity of COVID-19, and over 40 genes near these loci, many which are known to be involved in immune function or lung function. The authors noted that two previously unassociated loci were discovered only because individuals with East Asian ancestry were included in the analysis; they highlighted the value of including diverse populations in human genomics studies (however, 80% of the study participants were of European ancestry despite efforts to increase genetic diversity). The study could not address the combined effect of SARS-CoV-2 variants plus variants in the human genome on disease outcome, or fully control socio-demographic factors, such as healthcare access, which might bias some associations between genetic variants and disease outcome. Nonetheless, the authors note that genomic information can help to understand the biological mechanisms that underlie immune responses to specific infections, identify at-risk individuals and develop new drugs and vaccines for existing or emerging infections. Source

Nature publishes a report on the Delta variant’s reduced sensitivity to monoclonal antibodies, sera from unvaccinated people who recovered from COVID-19, and people who given a single vaccine dose. Notably, after two doses of the Pfizer/BioNTech vaccine, 81 to 100 percent of people were able to neutralize the Alpha, Beta, and Delta variants (although protection against Beta waned to 46 percent 16 weeks later). After a second dose of the AstraZeneca vaccine, 95 to 100 percent of people were able to neutralize all three variants. Source

• Uganda has made a three-year, $1.1 billion plan to vaccinate half of its 44 million residents before it fully re-opens; Finance Minister Matia Kasaija said that most of the money will go to the Ministry of Health and for provision of economic stimulus and social support through June of 2022. Uganda – which has received 1.14 million vaccine doses through COVAX and the Indian government, has made arrangements to procure two million doses of the J & J vaccine through the Africa Export-Import Bank, and is working to get additional vaccines from China, Cuba, Russia and the UK. The country is anticipating an additional 285,600 doses from COVAX in July and 688,800 in August as well as a donation of 300,000 doses of CoronaVac from Sinovac. Source

• Pfizer/BioNTech issue a press release to update their strategy for coronavirus boosters, noting that an ongoing trial of a third dose of their current vaccine increases immune responses against the Beta variant by five-to-ten-fold. The companies believe that a third dose of the current vaccine will also increase immune responses against the Delta variant, and are assessing this in trials. In addition, they are developing a new version of the vaccine which targets the Delta variant, with clinical trials beginning in August. Pfizer and BioNTech expect to publish their booster data in a peer-reviewed journal and submit it to the EMA, US FDA and other regulatory agencies in the coming weeks. Source

• The US CDC and the US FDA issue a statement contradicting Pfizer’s claim that coronavirus boosters will be needed within six to twelve months, saying, “Americans who have been fully vaccinated do not need a booster shot at this time. FDA, CDC, and NIH are engaged in a science-based, rigorous process to consider whether or when a booster might be necessary. This process takes into account laboratory data, clinical trial data, and cohort data – which can include data from specific pharmaceutical companies, but does not rely on those data exclusively. We continue to review any new data as it becomes available and will keep the public informed. We are prepared for booster doses if and when the science demonstrates that they are needed.” Source

• Argentina, which has given a single dose to 23.7 million of its 45 million residents, and fully vaccinated 4.9 million of them, announced that it has struck a deal with Moderna, but did not provide details on the number of doses, delivery dates or pricing. Source

• The coronavirus is spreading among anti-coup prisoners in Myanmar, as the country’s COVID-19 cases and deaths hit record-breaking highs. Source

• Zimbabwe has registered coronavirus vaccines from China, India and Russia. The country just received two million doses of Sinovac’s CoronaVac, bringing its total of purchased and donated doses to 4.2 million. By the end of July, Zimbabwe anticipates delivery of an additional 3.5 million doses, and it plans to purchase 1.5 million doses per month beginning in August. Source

• The US FDA announces a Class I recall – its most serious – of the Quidel Lyra SARS-CoV-2 Assay, a PCR test with significant risk of false negative results for people with relatively high amounts of SARS‐CoV‐2 virus. Source

• The NIH issues an update to its COVID-19 treatment guidelines, specifically for people who have been hospitalized. The panel recommends against use of dexamethasone or corticosteroids in people who do not require supplemental oxygen, while it recommends remdesivir for people who require minimal amounts of supplemental oxygen and remdesivir plus dexamethasone for people with increasing oxygen requirements or dexamethasone alone (when remdesiver cannot be used or is not available). For people who require high-flow oxygen or non-invasive ventilation, the panel recommends dexamethasone with or without remdesivir (and either baricitinib or tocilizumab for recently hospitalized patients with systemic inflammation and rapidly increasing oxygen needs). For patients who need ECMO or invasive mechanical ventilation, the panel recommends dexamethasone – and adding tocilizumab for those admitted to the ICU within 24 hours. Source

BMC Virology Journal publishes a retrospective cohort study among 403 patients with moderate COVID-19 pneumonia who were hospitalized in China between 11 January and 21 May, 2020. They were treated with arbidol or interferon alpha-1b or lopinavir–ritonavir and ribavirin to assess whether or which of these antivirals had an effect on disease progression and mortality. Arbidol was associated with faster recovery when administered within a week of symptom onset and a lower rate of disease severity (3.5 percent versus 30.5 percent among the control group) as was interferon alpha-1b (15.5 percent versus 29.3% among the control group), while there was no benefit associated with lopinavir/ritonavir plus ribavirin. The authors noted that overall mortality was too low to assess the impact of antiviral treatment on death risk; that different timing for initiation of antiviral treatments may have biased the results, as well as unmeasured confounding factors. Source

• In Bangladesh, where only 3 percent of residents are fully vaccinated, daily COVID-19 deaths reached a record-breaking total of 201 and cases have reached over 9.7 million. The country’s current lockdown has been extended by an additional week. Source

• In New Zealand, an outbreak of respiratory syncytial virus (RSV) among babies and young children has overwhelmed primary care centers and hospitals across the country. Although RSV is a normal winter illness, pandemic lockdowns and border closures have left children under age two with lower immunity. Dr Philip Moore said he had never seen so many sick children needing hospital care “in all my 28 years as a paediatrician in Hawke’s Bay.” Source