Summary SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2 1 , and is a major antibody target. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences over 23 time points spanning 101 days. Little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days. However, following convalescent plasma therapy we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro , the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type, possibly compensating for the reduced infectivity of D796H. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with evidence of reduced susceptibility to neutralising antibodies.

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Heterogeneity in host populations and communities can have large effects on the transmission and control of a pathogen. In extreme cases, a few individuals give rise to the majority of secondary infections, which have been termed super spreading events. Here, we show that transmission of West Nile virus (WNV) is dominated by extreme heterogeneity in the host community, resulting in highly inflated reproductive ratios. A single relatively uncommon avian species, American robin (Turdus migratorius), appeared to be responsible for the majority of WNV-infectious mosquitoes and acted as the species equivalent of a super spreader for this multi-host pathogen. Crows were also highly preferred by mosquitoes at some sites, while house sparrows were significantly avoided. Nonetheless, due to their relative rarity, corvids (crows and jays) were relatively unimportant in WNV amplification. These results challenge current beliefs about the role of certain avian species in WNV amplification and demonstrate the importance of determining contact rates between vectors and host species to understand pathogen transmission dynamics.

West Nile virus (WNV) has caused repeated large-scale human epidemics in North America since it was first detected in 1999 and is now the dominant vector-borne disease in this continent. Understanding the factors that determine the intensity of the spillover of this zoonotic pathogen from birds to humans (via mosquitoes) is a prerequisite for predicting and preventing human epidemics. We integrated mosquito feeding behavior with data on the population dynamics and WNV epidemiology of mosquitoes, birds, and humans. We show that Culex pipiens, the dominant enzootic (bird-to-bird) and bridge (bird-to-human) vector of WNV in urbanized areas in the northeast and north-central United States, shifted its feeding preferences from birds to humans by 7-fold during late summer and early fall, coinciding with the dispersal of its preferred host (American robins, Turdus migratorius) and the rise in human WNV infections. We also show that feeding shifts in Cx. tarsalis amplify human WNV epidemics in Colorado and California and occur during periods of robin dispersal and migration. Our results provide a direct explanation for the timing and intensity of human WNV epidemics. Shifts in feeding from competent avian hosts early in an epidemic to incompetent humans after mosquito infection prevalences are high result in synergistic effects that greatly amplify the number of human infections of this and other pathogens. Our results underscore the dramatic effects of vector behavior in driving the transmission of zoonotic pathogens to humans.

AimsTo estimate the effectiveness of pregnancy smoking cessation support delivered by short message service (SMS) text message and key parameters needed to plan a definitive trial.DesignMulti‐centre, parallel‐group, single‐blinded, individual randomized controlled trial.SettingSixteen antenatal clinics in England.ParticipantsFour hundred and seven participants were randomized to the intervention (n = 203) or usual care (n = 204). Eligible women were < 25 weeks gestation, smoked at least one daily cigarette (> 5 pre‐pregnancy), were able to receive and understand English SMS texts and were not already using text‐based cessation support.InterventionAll participants received a smoking cessation leaflet; intervention participants also received a 12‐week programme of individually tailored, automated, interactive, self‐help smoking cessation text messages (MiQuit).Outcome measurementsSeven smoking outcomes, including validated continuous abstinence from 4 weeks post‐randomization until 36 weeks gestation, design parameters for a future trial and cost‐per‐quitter.FindingsUsing the validated, continuous abstinence outcome, 5.4% (11 of 203) of MiQuit participants were abstinent versus 2.0% (four of 204) of usual care participants [odds ratio (OR) = 2.7, 95% confidence interval (CI) = 0.93–9.35]. The Bayes factor for this outcome was 2.23. Completeness of follow‐up at 36 weeks gestation was similar in both groups; provision of self‐report smoking data was 64% (MiQuit) and 65% (usual care) and abstinence validation rates were 56% (MiQuit) and 61% (usual care). The incremental cost‐per‐quitter was £133.53 (95% CI = –£395.78 to 843.62).ConclusionsThere was some evidence, although not conclusive, that a text‐messaging programme may increase cessation rates in pregnant smokers when provided alongside routine NHS cessation care.

The COVID-19 pandemic has necessitated a multi-faceted rapid response by the scientific community, bringing researchers, health officials and industry together to address the ongoing public health emergency. To meet this challenge, participants need an informed approach for working safely with the etiological agent, the novel human coronavirus SARS-CoV-2. Work with infectious SARS-CoV-2 is currently restricted to high-containment laboratories, but material can be handled at a lower containment level after inactivation. Given the wide array of inactivation reagents that are being used in laboratories during this pandemic, it is vital that their effectiveness is thoroughly investigated. Here, we evaluated a total of 23 commercial reagents designed for clinical sample transportation, nucleic acid extraction and virus inactivation for their ability to inactivate SARS-CoV-2, as well as seven other common chemicals including detergents and fixatives. As part of this study, we have also tested five filtration matrices for their effectiveness at removing the cytotoxic elements of each reagent, permitting accurate determination of levels of infectious virus remaining following treatment. In addition to providing critical data informing inactivation methods and risk assessments for diagnostic and research laboratories working with SARS-CoV-2, these data provide a framework for other laboratories to validate their inactivation processes and to guide similar studies for other pathogens.

The feeding behavior of vectors influences the likelihood of pathogen invasion and the exposure of humans to vector-borne zoonotic pathogens. We used multilocus microsatellite genetic typing of an introduced mosquito vector and DNA sequencing of mosquito blood meals to determine the impact of hybrid ancestry on feeding behavior and the emergence of West Nile virus (WNV). The probability of ancestry of Culex pipiens mosquitoes from two bionomically divergent forms, form molestus and form pipiens, influenced the probability that they fed on humans but did not explain a late summer feeding shift from birds to humans. We used a simple model to show that the occurrence of pure form molestus mosquitoes would have decreased the likelihood of WNV invasion (R(0) in bird populations) 3- to 8-fold, whereas the occurrence of pure forms pipiens mosquitoes would have halved human exposure compared with the hybrids that are present. Data and modeling suggest that feeding preferences may be influenced by genetic ancestry and contribute to the emergence of vector-borne pathogens transmitted by introduced species, including malaria, and dengue, Chikungunya, yellow fever, and West Nile viruses.

Non-native common carp (Cyprinus carpio L.) are the most abundant large-bodied fish in the Murray–Darling Basin. The abundance of common carp larvae and young-of-the-year appears to increase after flooding, although the relative contribution of floodplain habitats compared to riverine areas remains unresolved. Larval nets were used monthly from September 2000 to January 2001 to identify common carp spawning and recruitment areas in the regulated Murray River and floodplain around the Barmah–Millewa forest. Five non-native and five native fish species comprising 136 111 individuals were collected, with common carp constituting 88% of the overall catch. Less than 1% of common carp, however, originated from the Murray River upstream of the Barmah–Millewa floodplain. Consequently, this floodplain appears to be a major source of common carp recruitment in the mid-Murray area. Conversely, eggs from large-bodied native fish were only present in the Murray River and not the Barmah floodplain. There are opportunities for common carp control in this area, to potentially reduce populations in a wider river reach. Implementation of common carp control measures in the Barmah–Millewa floodplain should be further investigated, particularly with regard to seasonal irrigation flows, obligatory migration routes and in the timing of future large-scale environmental water allocations.