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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18 19 1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few 20 large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification. 212) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. 22The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. 23Specimens were morphologically classified, following standardised protocols, to the lowest taxonomic level for which 24 identification was feasible in the routine national monitoring. 253) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded 26 a higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological 27 method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of 28 specimens per taxon (a proxy for biomass) were significantly correlated in each sample, although the adjusted R 2 were low. 29With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding 30 datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately as 31 expensive as morphology-based identification. 32 4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve comparable assessment 33 results to current protocols relying on morphological identification. Thus, metabarcoding represents a feasible and reliable 34 method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological 35 identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock 36 the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems 37 with current laboratory protocols and reference databases. 38 39 40

A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to assess the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques. Immune responses against SARS-CoV-2 are also similar in both species and equivalent to those reported in milder infections and convalescent human patients. This finding is reiterated by our transcriptional analysis of respiratory samples revealing the global response to infection. We describe a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the preferred study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of interventions against SARS-CoV-2. Importantly, accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks.

18 19 1) DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few 20 large-scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification. 212) We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. 22The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. 23Specimens were morphologically classified, following standardised protocols, to the lowest taxonomic level for which 24 identification was feasible in the routine national monitoring. 253) DNA metabarcoding identified more than twice the number of taxa than the morphology-based protocol, and also yielded 26 a higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological 27 method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of 28 specimens per taxon (a proxy for biomass) were significantly correlated in each sample, although the adjusted R 2 were low. 29With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding 30 datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately as 31 expensive as morphology-based identification. 32 4) Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve comparable assessment 33 results to current protocols relying on morphological identification. Thus, metabarcoding represents a feasible and reliable 34 method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological 35 identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock 36 the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems 37 with current laboratory protocols and reference databases. 38 39 40