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The Delta variant of SARS-CoV-2: The current global scourge 

11 Oct 2021

By Suranjith L Seneviratne, Pamodh Yasawardene, Dineshani Hettiarachchi, Danuksha K. Amarasena, Widuranga Wijerathne, Buddhika Samaraweera, D.K.D. Mathew, and Visula Abeysuriya Introduction Coronavirus disease-2019 (Covid-19) has affected more than 210 million individuals worldwide and caused over 4.5 million deaths. Several vaccines and medications have been developed to prevent the infection and treat those affected. Even though it is primarily a respiratory infection, manifestations may develop in multiple vital organs. Human coronaviruses were discovered in the 1960s, and presently seven strains cause disease. Human coronavirus OC43 (HCoV-OC43), human coronavirus HKU1 (HCoV-HKU1), human coronavirus 229E (HCoV-229E) and human coronavirus NL63 (HCoV-NL63) are known to cause mild disease, whilst the severe acute respiratory syndrome coronavirus (SARS-CoV-1), Middle East respiratory syndrome-related coronavirus (MERS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may potentially cause severe disease. Outbreaks of SARS-CoV-1 and MERS-CoV infections occurred in 2002 and 2012 respectively. The current pandemic virus SARS-CoV-2 has a 70% and 40% genetic sequence similarity with SARS-CoV-1 and MERS-CoV respectively. Viruses multiply and spread from cell to cell and person to person. During the process of multiplication, changes may occur in the genetic make-up of the virus. Some RNA viruses, such as the flu viruses, change more often than others. Many of the changes are not of any consequence, whilst a very few may have specific and important follow-on clinical effects. The changes may affect one or more of the following: Transmission, disease severity, diagnostic testing aspects, effectiveness of medications, and vaccine effectiveness. A variant is designated as a variant of concern (VOC) when there is evidence of fulfilling at least one of several criteria: an increase in transmissibility, more severe disease (such as increased hospitalisations or deaths), significant reduction in neutralisation by antibodies that are produced during a previous SARS-CoV-2 infection or vaccination, failures with diagnostic testing, or reduced effectiveness of treatments or vaccines. The World Health Organisation (WHO) classification has identified four SARS-CoV-2 variants of concern: Alpha, Beta, Gamma, and Delta. Several studies have found the Alpha and Delta variants to increase disease transmission by significant levels, leading to rapid spread of the particular variant after it is introduced into a locality. In both laboratory and clinical studies, the Alpha variant was shown to increase disease severity while the Beta variant has shown a significant negative effect on viral neutralisation and vaccine efficacy. The currently authorised Covid-19 vaccines have been found to be efficacious and effective against the Alpha variant. At present, the Delta variant is causing significant infection outbreaks in several parts of the world. A frequent query is what is currently known about the effectiveness of the authorised Covid-19 vaccines against the Delta variant, and new data keeps emerging on this aspect virtually on a daily basis. In this article we would discuss what is currently known about the Delta variant and outline the effectiveness of Covid-19 vaccines against it, as at end August 2021.   What is the Delta variant? A variant of SARS-CoV-2 first discovered in India was named B.1.617 (this was before the WHO classification of SARS-CoV-2 variants was announced). This variant had 15 lineage-defining mutations when compared to the gene sequence of the initial SARS-CoV-2 virus. It has two critical mutations in the receptor binding domain of the virus spike protein (namely the E484Q and L452R mutations). One mutation, known as L452R, is also found in a variant first identified in California and has been associated with increased transmissibility. The change E484Q, is similar to the E484K mutation found in the Beta and Gamma variants. The initially described variant has three sub-lineages, lineage one is identified as the Kappa variant and lineage two as the Delta variant. The current distribution of the Delta variant The highly transmissible Delta variant has now spread to over 130 countries. It was first identified in the state of Maharashtra in late 2020 and then spread throughout India, displacing the Alpha variant and other pre-existing lineages. Currently, it is the predominant variant in the UK, the US, and several countries including Sri Lanka. By the end of July 2021, Delta was the cause of more than 80% of new Covid-19 cases in the US. During the past four weeks, over 90% of new cases in Israel have been caused by the Delta variant. In the UK, Delta variant increased fourfold in less than a month and it has become the predominant strain in much of Europe. It also accounts for more than half of Africa’s Covid-19 cases. The variant has been detected in 97% and 79% of samples, sequenced in Uganda and the Democratic Republic of the Congo, respectively. Transmission The Delta variant is 60% more transmissible than the Alpha variant (which is 50% more contagious than the original strain of SARS-CoV-2. The highest spread of the Delta variant with severe illness outcomes has been observed in places with low vaccination rates. Currently, most hospitalisations and almost all deaths in the US are among the unvaccinated. In an internal document, the US Centers for Disease Control and Prevention (CDC) described the Delta variant to be as contagious as chickenpox and more transmissible than the common cold and influenza, as well as the viruses that cause smallpox, MERS, SARS, and Ebola. A recent study showed that vaccinated people could also transmit the Delta variant.  Clinical findings  The Delta variant appears to be causing illness among young adults. For instance, a study from the UK found children and adults under 50 years to be 2.5 times more likely to be infected with the Delta variant than those older than 50 years. In Uganda, 66% of severe illness in people younger than 45 years, was attributed to the Delta variant. Some reports from the UK (where more than 90% of the cases are due to the Delta variant), point to differences in symptoms from that seen with the original SARS-CoV-2 virus strain. Cough and loss of smell appears to be less common and headache, sore throat, runny nose, nasal congestion and fever have been observed.  Disease severity Some studies have shown that the Delta variant may cause more severe disease among unvaccinated persons than previous strains. A study from Scotland found the Delta variant to be about twice as likely as the Alpha variant in causing hospitalisation. Similar findings were also observed in a Canadian study. A recent study from England, which focused largely on the unvaccinated or partially vaccinated populations, found that the Delta variant doubled the risk of Covid-19 hospitalisations compared to the Alpha variant. Here, healthcare data from over 40,000 Covid-19 cases in England between 29 March and 23 May 2021 were analysed. The study found that 24% had received one dose, while 74% were unvaccinated. The cumulative risk of hospitalisation due to the infection with the Delta variant was 2.26 fold higher when compared to the Alpha variant. Vaccine effectiveness  
  • Pfizer vaccine
  A study carried out by Public Health England (PHE) found the Pfizer vaccine to be 36% effective against symptomatic infection from the Delta variant after the first dose. Single dose effectiveness against the original strain was 79% and 48% against the Alpha variant. Two weeks after receiving the second Pfizer vaccine dose, effectiveness increased to 88% against the Delta variant (compared to 94% against the Alpha variant). A separate study from the UK showed only a mild reduction in effectiveness of the Pfizer vaccine (against all infections) after two doses from 80% in the Alpha-predominant period to 78% in the Delta-predominant period. A laboratory study found almost six times fewer antibodies protecting against the Delta variant, and that the antibody levels decreased with age and time. Another study reported an almost threefold reduction in neutralising antibody titres to the Delta variant as compared to the Alpha variant following two doses of the Pfizer vaccine. A single dose resulted in almost undetectable levels of neutralising antibodies against the Delta variant. A subsequent PHE analysis found the Pfizer vaccine to be 96% effective against hospitalisation after two doses. These levels are comparable with vaccine effectiveness against hospitalisation from the Alpha variant. The effectiveness of the Pfizer vaccine in preventing Covid-19 infections in Israel has reduced from 95% in May 2021 to 64% in June 2021, and reduced further to 39% in July. This change has been considered to be due to the rapid spread of the Delta variant. However, severe infections of Covid-19, hospitalisation rates, and deaths remain low, and the vaccine is still 93% effective at preventing serious illness and hospitalisation. Nearly half of new cases have been detected in fully-vaccinated patients and in children. With the predominant spread of the Delta variant, preliminary data from Israel has shown a third dose of the Pfizer vaccine to be 86% effective in preventing infection in people aged over 60 years. This is approximately four times higher compared to only two doses and approximately five to six times higher at preventing serious illness and hospitalisation. An assessment of effectiveness of the Pfizer vaccine in preventing Covid-19 infection among nursing home residents in the US has reported a decline in adjusted vaccine effectiveness of the Pfizer-mRNA vaccine from 74% in the pre-Delta period (March-May 2021) through 67% in the intermediate period (May-June 2021) to 52% in the Delta-predominant period (June-August 2021). Effectiveness of partial (single dose) vaccination with the Pfizer vaccine after ≥14 days against symptomatic infection reported from Canada is 56% for the Delta variant (vs. 66% for Alpha variant). Effectiveness of full (double dose) vaccination against symptomatic infection is 85% for the Delta variant (vs. 89% for Alpha variant). The effectiveness against infection by the Delta variant, as reported by a pre-print study in Qatar, was 64% following the second dose of the Pfizer vaccine. Effectiveness against severe, critical, or fatal infection by Delta variant was 90%.  
  • Moderna vaccine
  On 29 June 2021, Moderna announced results from in-vitro neutralisation studies using sera from persons vaccinated with the Moderna vaccine. The Moderna vaccine produced neutralising titres against all the variants that were tested. There was a modest reduction in neutralising titre against the Delta (2.1-fold), Gamma (3.2-fold), Kappa (3.3-3.4-fold) variants relative to titres against the original strain. The study conclusion was that the Moderna vaccine produced promising protection in a lab setting against the Delta variant. An assessment of effectiveness of the Moderna vaccine in preventing Covid-19 infection among nursing home residents in the US has reported a decline in adjusted vaccine effectiveness of the Moderna-mRNA vaccine from 75% in the pre-Delta period (March-May 2021), through 70% in the intermediate period (May-June 2021), to 51% in the Delta-predominant period (June-August 2021). Effectiveness of partial (single dose) vaccination with the Moderna vaccine after ≥14 days against symptomatic infection reported from Canada is 72% for the Delta variant (vs. 83% for Alpha variant). However, the study was unable to accurately determine the effectiveness following full (double dose) vaccination due to the absence of test-positive cases following full vaccination. The effectiveness against infection by the Delta variant, as reported by a pre-print study in Qatar, was 85% following the second dose of the Moderna vaccine.  
  • Oxford-AstraZeneca vaccine
  A PHE study published on 22 May 2021 found a single dose of the Oxford-AstraZeneca (Oxford-AZ) vaccine reduced a person’s risk of developing symptomatic Covid-19 by the Delta variant by 30% (compared to 49% for the Alpha variant). A second dose of the Oxford-AZ vaccine boosted protection against the Delta variant to 67% (compared to 75% against the Alpha variant). This shows that two doses of the Oxford-AZ vaccine are effective against the Delta variant, with similar levels of protection as seen against the Alpha variant. A separate study from the UK has shown a reduction in effectiveness against all infections following two doses of the Oxford-AZ vaccine from 79% in the Alpha-predominant period to 67% in the Delta-predominant period.  Additional real world data from the PHE also found that two doses of the Oxford-AZ vaccine to be 92% effective against hospitalisation due to the Delta variant, and there were no deaths among those vaccinated. The analysis included 14,019 cases of the SARS-CoV-2 Delta variant between 12 April and 4 June 2021, of whom 122 were hospitalised. The follow-up period was limited and this may affect the calculated level of effectiveness. Vaccine effectiveness after ≥14 days following a single dose of Oxford-AZ vaccine was reported as 67% for Delta variant (vs. 64% for Alpha variant) in a pre-print study from Canada. However, the study was unable to accurately determine the effectiveness following full (double dose) vaccination due to the absence of test-positive cases following full vaccination. A laboratory study investigated the ability of antibodies found in serum from Covid-19 recovered persons and those who were vaccinated with the Oxford-AZ vaccine to neutralise the Delta and Kappa variants. Neutralisation against the Delta and Kappa variants was comparable with that seen against the Alpha and Gamma variants. There was no evidence of widespread antibody escape as seen with the Beta variant. The “Delta variant emergence and vaccine breakthrough collaborative study” analysed vaccine breakthroughs in over 100 healthcare workers across three centres in India. They found the Delta variant to dominate vaccine breakthrough infections. In a laboratory setting, the Delta variant showed approximately eight-fold reduced sensitivity to vaccine-elicited antibodies compared to the wild type virus. The serum neutralising antibody levels against the Delta variant were significantly lower in those vaccinated with the Oxford-AZ vaccine as compared to the Pfizer vaccine.  
  • Johnson & Johnson vaccine
  A recent laboratory study tested if the antibody response from its vaccine was capable of neutralising the Delta variant. The analysis was done on blood samples obtained from a subset of participants in the Phase 3 ensemble study. The vaccine elicited neutralising antibody activity against the Delta variant at a higher level than against the Beta variant. Humoral and cellular immune responses generated by the vaccine had lasted for at least eight months (which was the length of time evaluated as of now). T-cell responses (including CD8+ T-cells) persisted over the eight-month timeframe.  Johnson & Johnson (J&J) have also reported that its vaccine is effective against the Delta variant. An initial study on the Delta variant found 71% and 95% effectiveness against hospitalisation and death. However, a more recent study found this vaccine to be less effective against the Delta variant and when considered the current surge in Delta variant cases in the US.   
  • Sputnik-V vaccine
  On 15 June 2021, one of the developers of the Sputnik-V vaccine claimed this vaccine was more efficient against the Delta variant when compared to other vaccines. The effectiveness of the vaccine was reported as 2.6 times lower against the Delta variant. In a study of nearly 14,000 individuals, two doses of the Sputnik-V vaccine were found to reduce the risk of hospitalisation with Covid-19 by 81%. The Sputnik-V vaccine had 76% effectiveness at protecting against severe lung injury (where more than 50% of the lung is visibly affected on a CT scan) from Covid-19. Though this study did not differentiate between vaccine types, as 96% of vaccine recipients in the region received the Sputnik-V vaccine, the authors speculate that the reported overall vaccine effectiveness would approximate that of the Sputnik-V vaccine.  
  • Bharat Biotech vaccine
  A recent study found the Covaxin vaccine to provide 65.2% protection against the Delta variant. In the Phase 3 trial, the overall efficacy of this vaccine was 77.8%, with 93.4% and 63.6% effectiveness against severe and asymptomatic Covid-19 respectively. The trial assessed 130 confirmed Covid-19 cases, with 24 observed in the vaccine group vs. 106 in the placebo group. A laboratory-based study, comparing the neutralisation of Delta and Beta variants with sera of recipients of Covaxin vaccine 28 days after the second dose reported well established, albeit reduced, neutralisation potential of the vaccine against the Delta and Beta variants. The geometric mean titre ratio of vaccine sera against prototype B.1 to Delta and Beta variants was 2.7 and 3.0 respectively. A pre-print study has also demonstrated a 1.3-fold reduction in neutralisation activity against Delta variant vs. prototype B.1 variant using sera of Covid-19 naïve individuals fully-vaccinated with Covaxin. Additionally, there was a 2.5-fold and 1.9-fold reduction of neutralisation activity against the Delta variant vs. the prototype B.1 in those who were fully vaccinated against Covid-19 following full recovery, and those who experienced breakthrough infections, respectively.  
  • Sinopharm and Sinovac vaccines
  There is little robust data on the effectiveness of the Sinopharm and Sinovac vaccines against the Delta variant. In a recent interview, a former director of the Chinese Center for Disease Control and Prevention (CDC) stated that antibodies produced by two of the Chinese inactivated-Covid-19 vaccines were less effective against the Delta variant as compared to the other variants. He mentioned that the vaccines still offered protection against severe Covid-19. A study from Sri Lanka found a 1.38-fold reduction in receptor-binding domain antibodies to the Delta variant in those who were fully-vaccinated with two doses of the Sinopharm vaccine when compared to the original serotype. A study of the Delta variant outbreak in Guangzhou, China, found a vaccine effectiveness of 59% against Covid-19 infection and 70.2% against moderate Covid-19 infection following two vaccine doses, and only 13.8% after a single dose. The study did not differentiate between the Sinopharm and Sinovac vaccines for effectiveness calculation. However, most participants in this study had received the Sinovac vaccine. Recently, 350 medical staff in Indonesia developed Covid-19 despite receiving both doses of the Sinovac (CoronaVac) vaccine. Most were asymptomatic and hence underwent self-isolation at home. This particular region in Indonesia has seen a surge in Covid-19, and health officials suspect this to be mainly due to the Delta variant. Cases of breakthrough infection due to the Delta variant Covid-19 that arises in a person who is fully-immunised (14 days after the second dose of the Pfizer, Moderna, Oxford-AZ, Sputnik-V, Covaxin, Sinopharm, or Sinovac vaccines) is known as a breakthrough infection. Despite the high level of protection conferred by immunisation, breakthrough cases of Covid-19 have been observed among the fully vaccinated (i.e. two weeks after receiving two vaccine doses). For instance, the outbreak in Provincetown, Massachusetts, attracted a lot of attention as the vast majority of those who got Covid-19 were vaccinated. It was observed that this cohort was exposed to a considerable degree of indoor activity with limited ventilation due to prevailing weather conditions. Additionally, it was also observed that the group had a mixture of people with different vaccination status. Those who suffer from a breakthrough infection have high amounts of viral particles in their nose and throat, and are able to spread the virus to others irrespective of them being asymptomatic. However, breakthrough infections are less frequent than infections in those who are unvaccinated. The greatest risk of transmission is among unvaccinated people who are much more likely to contract, and therefore transmit, the virus. Furthermore, those who are fully vaccinated appear to be infectious only for a short duration. Owing to the fact that breakthrough infections tend to be mild or asymptomatic, it is difficult to know the full extent of the problem as many cases go undetected. In the US, recent reports suggest at least 125,000 fully-vaccinated persons tested positive for SARS-CoV-2 and 1,400 of them had succumbed to the illness. This represents less than 0.08% of more than 164 million people who have been fully-vaccinated since January 2021. Therefore, deaths among the fully vaccinated are extremely low. Recently, the CDC has changed from monitoring all reported vaccine breakthrough cases to focus on identifying and investigating only hospitalised or fatal cases. Some contributing reasons for breakthrough infections include: None of the vaccines are 100% effective at preventing infection, the emergence of new SARS-CoV-2 viral variants such as the highly transmissible Delta variant, and the waning of long term vaccine immunity.     
  • None of the vaccines are 100% effective 
  The initial and landmark Pfizer Covid-19 vaccine clinical trial found 95% efficacy against infection from the strains of the virus circulating at the time. Even in this initial trial, there was a small proportion of individuals who were susceptible to infection and illness. As no vaccine is 100% effective, it is important for everyone to get vaccinated, as the fewer hosts available to a virus, the less likely it is to spread.  
  • Emergence of more transmissible SARS-CoV-2 variants 
  Breakthrough infections may occur with the more transmissible viral variants and may need booster vaccination programmes to be initiated.  
  • Waning of long term vaccine immunity
  Currently, we do not know how long vaccine-induced protective immunity lasts. This aspect would be particularly important among clinically vulnerable individuals and the elderly who were vaccinated early in the vaccine rollout process. If immunity wanes after a certain time period, a booster dose would need to be considered.  Would a Covid-19 vaccine booster be needed? Currently, there is intense discussion if a booster vaccine dose (either against the original virus or the Delta variant) would be needed by those who have been fully vaccinated. Israel became one of the first countries to start a Covid-19 vaccine booster programme. A third vaccine dose was given to its citizens aged 60 and over at the end of July 2021. Very recently, the FDA approved the use of the Pfizer and Moderna vaccines as a third dose for certain immuno-compromised persons. Face masks The WHO has encouraged mask-wearing even among vaccinated people. In July 2021, the CDC updated its guidelines and recommended that both vaccinated and unvaccinated individuals should wear masks in public indoor settings, in areas of high transmission. This was done with a view to reduce Delta’s rapid spread and to protect those who are immuno-compromised, at risk for severe disease, or unvaccinated. Universal indoor masking was also recommended for all teachers, and students. Currently, anyone who is unvaccinated and not practicing preventive strategies (such as wearing masks and following other social distancing measures) is considered to be at high risk of Delta variant infection. Conclusions The available data suggests the SARS-CoV-2 Delta variant is somewhat less responsive to the current Covid-19 vaccines and can cause breakthrough infections, especially among persons who have received only a single dose of a two dose vaccine. However, all the WHO “emergency use”-listed Covid-19 vaccines are considered to protect against persons developing severe disease, hospitalisation, and death due to the Delta variant. The importance of receiving both doses of a two dose vaccine regime has become very apparent. The WHO has warned that coronavirus variants are emerging and moving faster than the global vaccine rollout. Currently, around 40% of older persons and 30% of health care workers are still not protected. Governments across the world have been urged to increase the pace of vaccine roll outs or risk being overwhelmed by increased cases of Covid-19. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The full article was published in Sri Lankan Family Physician 2021, Vol 36: 17-25  

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