Viral infection and transmission in a large, well-traced outbreak caused by the SARS-CoV-2 Delta variant

Abstract

The SARS-CoV-2 Delta variant has spread rapidly worldwide. To provide data on its virological profile, we here report the first local transmission of Delta in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of quarantined individuals indicated that the viral loads of Delta infections, when they first become PCR-positive, were on average ~1000 times greater compared to lineage A/B infections during the first epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. The estimated transmission bottleneck size of the Delta variant was generally narrow, with 1-3 virions in 29 donor-recipient transmission pairs. However, the transmission of minor iSNVs resulted in at least 3 of the 34 substitutions that were identified in the outbreak, highlighting the contribution of intra-host variants to population-level viral diversity during rapid spread.

Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis

“…The viral load trajectories of individuals with infections due to the alpha and delta variants have also previously been estimated. 35 , 36 , 37 Although estimating how infectiousness varies during infection using viral load data might be possible, 38 the timing of realised transmissions depends on factors additional to inherent infectiousness, such as behaviour (eg, individuals might be less likely to transmit after developing symptoms and self-isolating) and the availability of susceptible individuals. Our approach explicitly accounts for changes in transmission risk following symptom onset, and the household generation time accounts for depletion of susceptible individuals within households.…”

Impact of the Sinopharm’s BBIBP-CorV vaccine in preventing hospital admissions and death in infected vaccinees: Results from a retrospective study in the emirate of Abu Dhabi, United Arab Emirates (UAE)

“…According to the Genetic Testing Registry (GTR), by June 27, 2021 the circulating variants in the UAE included the Beta variant at 39.2%, followed by the Delta variant at 33.9%, while the Alpha variant was present at 11.3%, revealing the infectious nature of the newer variants and the potential of the vaccine to prevent their spread [34] . The Delta variant is the most contagious variant so far that is steadily replacing the other variants [35] . This may be due in part to its higher replication rate, revealing viral loads at ∼ 1000 times higher in the upper respiratory tract than the original variants early in infection, possible escape from the vaccine-generated immune response, and duration of vaccine protection [32] , [35] .…”

“…The Delta variant is the most contagious variant so far that is steadily replacing the other variants [35] . This may be due in part to its higher replication rate, revealing viral loads at ∼ 1000 times higher in the upper respiratory tract than the original variants early in infection, possible escape from the vaccine-generated immune response, and duration of vaccine protection [32] , [35] . Thus, surveillance and analysis of post vaccine efficacy in vaccinated populations is critical in informing public health policy measures, especially in the midst of an ensuing pandemic where the rates of infection and vaccine availability may suddenly change, as is being observed in countries around the world.…”

Organoid Models of SARS-CoV-2 Infection: What Have We Learned about COVID-19?

“…The viral load in the upper respiratory tract is highest in the first 3 to 5 days of infection [67], and although the loads are higher in symptomatic individuals, both pre-symptomatic and symptomatic persons can shed high viral loads, readily transmit infection and be associated with high secondary attack rates [68]. The viral load and duration of infectious virus shedding are higher for both the Delta and Omicron variants [69,70]. COVID-19 is a multisystem disease (Figure 3) that starts in the upper respiratory tract and lungs but can also involve the heart, blood vessels, brain, liver, kidneys and intestine [71].…”