Regional Analysis of Intact and Defective HIV Proviruses in the Brain of Viremic and Virally Suppressed People with HIV.

Here, we provide the first regional analysis of intact and defective HIV reservoirs within the brain. Brain tissue from both viremic and virally suppressed people with HIV (PWH) harbored HIV pol DNA in all regions tested, with lower levels present in basal ganglia and cerebellum relative to frontal white matter. Intact proviruses were primarily found in the frontal white matter but also detected in other brain regions of PWH, demonstrating frontal white matter as a major brain reservoir of intact, potentially replication competent HIV DNA that persists despite antiretroviral therapy. ANN NEUROL 2023;94:798-802.

SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern.

BACKGROUND: Genetically distinct viral variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been recorded since January 2020. The introduction of global vaccine programs has contributed to lower COVID-19 hospitalisation and mortality rates, particularly in developed countries. In late 2021, Omicron BA.1 emerged, with substantially altered genetic differences and clinical effects from other variants of concern. Shortly after dominating global spread in early 2022, BA.1 was supplanted by the genetically distinct Omicron lineage BA.2. A sub-lineage of BA.2, designated BA.5, presently has an outgrowth advantage over BA.2 and other BA.2 sub-lineages. Here we study the neutralisation of Omicron BA.1, BA.2 and BA.5 and pre-Omicron variants using a range of vaccine and convalescent sera and therapeutic monoclonal antibodies using a live virus neutralisation assay. Using primary nasopharyngeal swabs, we also tested the relative fitness of BA.5 compared to pre-Omicron and Omicron viral lineages in their ability to use the ACE2-TMPRSS2 pathway. METHODS: Using low passage clinical isolates of Clade A.2.2, Beta, Delta, BA.1, BA.2 and BA.5, we determined humoral neutralisation in vitro in vaccinated and convalescent cohorts, using concentrated human IgG pooled from thousands of plasma donors, and licensed monoclonal antibody therapies. We then determined infectivity to particle ratios in primary nasopharyngeal samples and expanded low passage isolates in a genetically engineered ACE2/TMPRSS2 cell line in the presence and absence of the TMPRSS2 inhibitor Nafamostat. FINDINGS: Peak responses to 3 doses of BNT162b2 vaccine were associated with a 9-fold reduction in neutralisation for Omicron lineages BA.1, BA.2 and BA.5. Concentrated pooled human IgG from convalescent and vaccinated donors and BNT162b2 vaccination with BA.1 breakthrough infections were associated with greater breadth of neutralisation, although the potency was still reduced 7-fold across all Omicron lineages. Testing of clinical grade antibodies revealed a 14.3-fold reduction using Evusheld and 16.8-fold reduction using Sotrovimab for the BA.5. Whilst the infectivity of BA.1 and BA.2 was attenuated in ACE2/TMPRSS2 entry, BA.5 was observed to be equivalent to that of an early 2020 circulating clade and had greater sensitivity to the TMPRSS2 inhibitor Nafamostat. INTERPRETATION: Observations support all Omicron variants to significantly escape neutralising antibodies across a range of vaccination and/or convalescent responses. Potency of therapeutic monoclonal antibodies is also reduced and differs across Omicron lineages. The key difference of BA.5 from other Omicron sub-variants is the reversion in tropism back to using the well-known ACE2-TMPRSS2 pathway, utilised efficiently by pre-Omicron lineages. Monitoring if these changes influence transmission and/or disease severity will be key for ongoing tracking and management of Omicron waves globally. FUNDING: This work was primarily supported by Australian Medical Foundation research grants MRF2005760 (ST, GM & WDR), MRF2001684 (ADK and ST) and Medical Research Future Fund Antiviral Development Call grant (WDR), Medical Research Future Fund COVID-19 grant (MRFF2001684, ADK & SGT) and the New South Wales Health COVID-19 Research Grants Round 2 (SGT).

Intact HIV Proviruses Persist in the Brain Despite Viral Suppression with ART.

OBJECTIVE: Human immunodeficiency virus (HIV) persistence in blood and tissue reservoirs, including the brain, is a major barrier to HIV cure and possible cause of comorbid disease. However, the size and replication competent nature of the central nervous system (CNS) reservoir is unclear. Here, we used the intact proviral DNA assay (IPDA) to provide the first quantitative assessment of the intact and defective HIV reservoir in the brain of people with HIV (PWH). METHODS: Total, intact, and defective HIV proviruses were measured in autopsy frontal lobe tissue from viremic (n = 18) or virologically suppressed (n = 12) PWH. Total or intact/defective proviruses were measured by detection of HIV pol or the IPDA, respectively, through use of droplet digital polymerase chain reaction (ddPCR). HIV-seronegative individuals were included as controls (n = 6). RESULTS: Total HIV DNA was present at similar levels in brain tissues from untreated viremic and antiretroviral (ART)-suppressed individuals (median = 22.3 vs 26.2 HIV pol copies/106 cells), reflecting a stable CNS reservoir of HIV that persists despite therapy. Furthermore, 8 of 10 viremic and 6 of 9 virally suppressed PWH also harbored intact proviruses in the CNS (4.63 vs 12.7 intact copies/106 cells). Viral reservoirs in CNS and matched lymphoid tissue were similar in the composition of intact and/or defective proviruses, albeit at lower levels in the brain. Importantly, CNS resident CD68+ myeloid cells in virally suppressed individuals harbored HIV DNA, directly showing the presence of a CNS resident HIV reservoir. INTERPRETATION: Our results demonstrate the first evidence for an intact, potentially replication competent HIV reservoir in the CNS of virally suppressed PWH. ANN NEUROL 2022;92:532-544.

Impact of nitrogen fertilizer timing on nitrate loss and crop production in northwest Iowa.

In the U.S. Midwest, nitrate in subsurface tile drainage from corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] systems is detrimental to water quality at local and national scales. The objective of this replicated plot study in northwest Iowa, performed in 2015-2020, was to investigate the influence of nitrogen (N) fertilizer timing on crop production and NO3 load in subsurface (tile) drainage discharge. Four treatments applied to corn included fall anhydrous ammonia with a nitrification inhibitor (F), spring anhydrous ammonia (S), split-banded urea at planting and mid-vegetative growth (SS), and no N fertilizer (0N). Across crops and years, NO3 -N concentration in subsurface drainage discharge was the same at 11.7 mg L-1 for F and S applied anhydrous ammonia (AA). The NO3 -N concentration was statistically lower with SS urea (10 mg L-1 ) than F and S, and 0N was lower than SS at 8.3 mg L-1 . Average annual NO3 -N loads were not different between any treatments due to plot variability in drainage discharge. Corn responded to N application, with overall mean yield the same for F, S, and SS. There were no agronomic or water quality benefits for applying AA in spring compared with fall, where the F included a nitrification inhibitor and was applied to cold soils. Split-applied urea had a small positive water quality impact but no crop yield enhancement. This study shows that there were improvements to NO3 -N concentration in subsurface drainage discharge, but more nutrient reduction practices are needed than fertilizer N management alone to reduce nitrate load to surface water systems.

Influence of no-till and a winter rye cover crop on nitrate losses from tile-drained row-crop agriculture in Iowa.

Artificial subsurface drainage is necessary to maintain agricultural production in the soils and climate of north-central Iowa. However, it can result in adverse environmental impacts, because it intercepts and diverts some water and soluble NO3 -N directly to streams. We investigated the impact of no-till and a winter rye cover crop (Secale cereale L.) on seasonal and annual NO3 -N concentration and loading in leachate from a corn (Zea mays L.)-soybean [Glycine max (L.) Merr.] rotation. The eight treatments are chisel plow (CT), chisel plow with winter cereal rye (CTr), no-till (NT), and no-till with winter cereal rye (NTr), with "-C" indicating corn and "-S" indicating soybeans. Plots with artificial subsurface drainage were monitored for water quality from 2011 to 2015. The NT and CTr treatments consistently decreased NO3 -N loss on the seasonal and annual scales compared with CT. Compared with NT, NTr did not reduce NO3 -N loading nor concentration in leachate, probably because of low NO3 leaching potential from NT combined with low rye cover crop biomass throughout the study with NT. The 5-yr average annual NO3 -N concentrations were: 16.9 mg L-1 with CT-S, 16.7 mg L-1 with CT-C, 12.6 mg L-1 with NT-S, 12.0 mg L-1 with CTr-S, 11.8 mg L-1 with CTr-C, 11.4 mg L-1 with NTr-S and NTr-C, and 11.1 mg L-1 with NT-C. Overall, both no-till and a cover crop showed potential for improving N management for water quality.