Clinical presentation,viral kinetics,and management of human monkeypox cases from New Delhi,India 2022

We describe the clinical and demographic characteristics, virological follow-up, and management of five confirmed monkeypox cases from New Delhi, India without any international travel history. The viral load kinetics and viral clearance were estimated in oropharyngeal swabs (OPS), nasopharyngeal swabs (NPS), EDTA blood, serum, urine, and various lesion specimens on every fourth day of follow-up ranging from 5 to 24 post onset day (POD) of illness. All five cases presented with mild to moderate-grade intermittent fever, myalgia, and lesions on the genitals, groins, lower limb, trunk, and upper limb. Four cases had non-tender firm lymphadenopathy. No secondary complications or sexually transmitted infections were recorded in these cases except for the presence of viral hepatitis B infection marker hepatitis B virus surface antigen (HBsAg) in one case. All the cases were mild and had a good recovery. A higher viral load was detected in lesion fluid (POD 9), followed by lesion roof (POD 9), urine (POD 5), lesion base (POD 5), and OPS/NPS (POD 5). The monkeypox virus (MPXV) DNA was detected in clinical samples from 5th to 24th POD. These monkeypox cases without international travel history suggest the underdiagnosed monkeypox infection in the community. This emphasizes the need for active surveillance of MPXV in the high-risk population such as men having sex with men and female sex workers.     

Strong methane point sources contribute a disproportionate fraction of total emissions across multiple basins in the United States

Understanding, prioritizing, and mitigating methane (CH₄) emissions requires quantifying CH₄ budgets from facility scales to regional scales with the ability to differentiate between source sectors. We deployed a tiered observing system for multiple basins in the United States (San Joaquin Valley, Uinta, Denver-Julesburg, Permian, Marcellus). We quantify strong point source emissions (>10 kg CH₄ h⁻¹) using airborne imaging spectrometers, attribute them to sectors, and assess their intermittency with multiple revisits. We compare these point source emissions to total basin CH₄ fluxes derived from inversion of Sentinel-5p satellite CH₄ observations. Across basins, point sources make up on average 40% of the regional flux. We sampled some basins several times across multiple months and years and find a distinct bimodal structure to emission timescales: the total point source budget is split nearly in half by short-lasting and long-lasting emission events. With the increasing airborne and satellite observing capabilities planned for the near future, tiered observing systems will more fully quantify and attribute CH₄ emissions from facility to regional scales, which is needed to effectively and efficiently reduce methane emissions.

Due to its short atmospheric lifetime and strong contribution to global radiative forcing, methane (CH₄) has been a focus for near-term climate mitigation efforts (1). Robust, unbiased accounting systems are requisite to prioritizing and validating CH₄ mitigation, ideally from multiple independent data streams. Atmospheric observations of CH₄ can be key for mitigation, as observed CH₄ concentrations are used to quantify emission rates and attribute emissions to sources. Findings from many independent research efforts have shown that CH₄ emissions across multiple sectors follow heavy-tailed distributions (2–5), meaning that a small fraction of emission sources emits at disproportionately higher rates than the full population of emitters. CH₄ sources can be intermittent or persistent in duration, which may be associated with short-lasting process-driven releases or long-lasting emissions due to abnormal or otherwise avoidable operating conditions such as malfunctions or leaks (5). Isolating populations of large emitters at varying levels of intermittency while quantifying their contribution to regional budgets creates a clear direction for mitigation focus. This tiered observing system strategy can be deployed in data-rich regions where multiple independent layers of observations are jointly leveraged to quantify and isolate emissions, and then drive action.Advances in CH₄ remote sensing have enabled quantification of emissions from global to facility scales. Generally, these observing systems operate by measuring solar backscattered radiance in shortwave infrared regions where CH₄ is a known absorber. Global mapping satellite missions have been used to identify CH₄ hotspots and infer global- to regional-scale CH₄ emission fluxes (6–8). In particular, the TROPOspheric Monitoring Instrument [TROPOMI (9)] onboard the Sentinel-5p satellite has proven capable of quantifying fluxes at basin scales (10, 11). Due to the kilometer-scale resolution of measurements from these global mapping missions, further attribution to particular facilities or even emission sectors is often not feasible. Less precise, target-mode satellites [e.g., PRISMA (12), GHGSat (13)] have proven capable of quantifying very large emissions at an ∼30-m scale, allowing for direct emission attribution to facilities or even subfacility-level infrastructure. However, the current generation of CH₄ plume imaging satellites lack the spatial and temporal coverage to provide quantification completeness across multiple basins. For global mapping, high–spatial resolution multispectral satellites such as Sentinel-2 and Landsat are capable of CH₄ detection (14, 15), but only for large emission sources (e.g., 2+ t h⁻¹) over very bright surfaces.Airborne imaging spectrometers with shortwave infrared sensitivities and sufficient instrument signal-to-noise ratios can also quantify column CH₄ concentrations. These remote sensing platforms are capable of resolving CH₄ concentrations at high spatial resolution (∼3 to 5 m) depending on flight altitude, and can quantify point source emissions as low as 5 to 10 kg h⁻¹ (16, 17). These instruments are sensitive to concentrated point-source emissions, and less sensitive to diffuse emissions spread over large areas (e.g., wetlands). Given the heavy-tailed nature of anthropogenic emissions, point-source detections above an imaging spectrometer’s detection limit may constitute a sizable fraction of the total regional CH₄ flux, but independent measurements are needed to provide that context. Therefore, in this study, we flew a combination of the Global Airborne Observatory (GAO) and next-generation Airborne Visible/Infrared Imaging Spectrometer (AVIRIS-NG) over multiple CH₄ emitting regions between 2019 and 2021, including the southern San Joaquin Valley (SJV), the Permian, the Denver-Julesburg (DJ), the Unita, and the southwestern Pennsylvania portion of the Marcellus. We generally mapped each basin at least three times during each campaign to quantify persistence of emission sources. For the Permian, DJ, and SJV, we surveyed each region again after several months to assess trends and identify long-lasting emission sources. We also performed simultaneous regional CH₄ flux inversions based on TROPOMI CH₄ retrievals to quantify the total CH₄ flux for each survey and compared against the quantified airborne point source budgets. With this tiered approach, we are able to quantify the contribution of unique point sources by sector on the regional budget, therefore highlighting specific points of action for mitigation.     

Vaccination Decreases the Infectious Viral Load of Delta Variant SARS-CoV-2 in Asymptomatic Patients

The Delta variant of SARS-CoV-2 has caused many breakthrough infections in fully vaccinated individuals. While vaccine status did not generally impact the number of viral RNA genome copies in nasopharyngeal swabs of breakthrough patients, as measured by Ct values, it has been previously found to decrease the infectious viral load in symptomatic patients. We quantified the viral RNA, infectious virus, and anti-spike IgA in nasopharyngeal swabs collected from individuals asymptomatically infected with the Delta variant of SARS-CoV-2. Vaccination decreased the infectious viral load, but not the amount of viral RNA. Furthermore, vaccinees with asymptomatic infections had significantly higher levels of anti-spike IgA in their nasal secretions compared to unvaccinated individuals with asymptomatic infections. Thus, vaccination may decrease the transmission risk of Delta, and perhaps other variants, despite not affecting the amount of viral RNA measured in nasopharyngeal swabs.     

Utilizing the Retrograde Flow of Internal Mammary Vessels as a Donor Pedicle

Introduction  The aim of this study is to assess the results of retrograde flow of internal mammary artery and vein (IMA/V) as a donor vessel for free flap microvascular anastomosis (MVA). This need arises with bipedicle deep inferior epigastric perforator (DIEP) flaps, when all four zones with extra fat need to be harvested for unilateral breast reconstruction coupled with poor midline crossover of circulation naturally or because of midline scar. Large anterolateral thigh flaps for chest wall cover, with multiple perforators from separate pedicles, also need supercharging. This needs an additional source of donor vessels, antegrade IMA/V being the first one. Materials and Methods  Retrospective study of microvascular breast reconstruction using retrograde internal mammary donor vessels. Results  Out of 35 cases, 20 cases had distal IMA/V, with retrograde flow, as donor vessel for second set of arterial and venous anastomosis. In two cases, retrograde IMA/V was used for the solitary set of MVA. In remaining 13 cases, either retrograde IMA or V was utilized either as a principal or accessory donor. No flap was lost. Venous and arterial insufficiency happened in one case each, both were salvaged. Two cases developed partial necrosis, needing debridement and suturing. One case developed marginal necrosis. Only one case developed fat necrosis with superadded infection on follow-up. Conclusion  Distal end of IMA and IMV on retrograde flow is safe for MVA as an additional or sole pedicle. It is convenient to use being in the same field. It enables preservation of other including thoracodorsal pedicle and latissimus dorsi flap for use in case of a complication or recurrence.     

Prevalence of hereditary tubulointerstitial kidney diseases in the German Chronic Kidney Disease study

Hereditary chronic kidney disease (CKD) appears to be more frequent than the clinical perception. Exome sequencing (ES) studies in CKD cohorts could identify pathogenic variants in ~10% of individuals. Tubulointerstitial kidney diseases, showing no typical clinical/histologic finding but tubulointerstitial fibrosis, are particularly difficult to diagnose. We used a targeted panel (29 genes) and MUC1-SNaPshot to sequence 271 DNAs, selected in defined disease entities and age cutoffs from 5217 individuals in the German Chronic Kidney Disease cohort. We identified 33 pathogenic variants. Of these 27 (81.8%) were in COL4A3/4/5, the largest group being 15 COL4A5 variants with nine unrelated individuals carrying c.1871G>A, p.(Gly624Asp). We found three cysteine variants in UMOD, a novel missense and a novel splice variant in HNF1B and the homoplastic MTTF variant m.616T>C. Copy-number analysis identified a heterozygous COL4A5 deletion, and a HNF1B duplication/deletion, respectively. Overall, pathogenic variants were present in 12.5% (34/271) and variants of unknown significance in 9.6% (26/271) of selected individuals. Bioinformatic predictions paired with gold standard diagnostics for MUC1 (SNaPshot) could not identify the typical cytosine duplication (“c.428dupC”) in any individual, implying that ADTKD-MUC1 is rare. Our study shows that >10% of selected individuals carry disease-causing variants in genes partly associated with tubulointerstitial kidney diseases. COL4A3/4/5 genes constitute the largest fraction, implying they are regularly overlooked using clinical Alport syndrome criteria and displaying the existence of phenocopies. We identified variants easily missed by some ES pipelines. The clinical filtering criteria applied enriched for an underlying genetic disorder.Subject terms: End-stage renal disease, Genetics research, Alport syndrome, Nephrosclerosis     

QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis

The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif (ΔQTQTN). Here, we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated, and disruption of its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site—the FCS, loop length, and glycosylation—are required for efficient SARS-CoV-2 replication and pathogenesis.

SARS-CoV-2 emerged in late 2019 and has caused the largest pandemic since the 1918 influenza outbreak (1). An unusual feature of SARS-CoV-2 is the presence of a furin cleavage site (FCS) in its spike protein (2). The CoV spike is a trimer of spike proteins composed of the S1 and S2 subunits, responsible for receptor binding and membrane fusion, respectively (1). After receptor binding, the spike protein is proteolytically cleaved at the S1/S2 and S2′ sites to activate the fusion machinery. For SARS-CoV-2, the spike protein contains a novel cleavage motif recognized by the host cell furin protease (PRRAR) directly upstream of the S1/S2 cleavage site that facilitates cleavage prior to virion release from the producer cell. This FCS, not found in other group 2B CoVs, plays a key role in spike processing, infectivity, and pathogenesis as shown by our group and others (3, 4).Importantly, another novel amino acid motif, QTQTN, is found directly upstream of the FCS. This QTQTN motif, also absent in other group 2B CoVs, is often deleted and has been pervasive in cultured virus stocks of the alpha, beta, and delta variants (5–8). In addition, the QTQTN deletion has been observed in a small subset of patient samples as well (9–11). Because this deletion has been frequently identified, we set out to characterize it and determine whether it has consequences for viral replication and virulence. Using our infectious clone (12, 13), we demonstrated that the loss of this motif attenuates SARS-CoV-2 replication in respiratory cells in vitro and pathogenesis in hamsters. The QTQTN deletion results in reduced spike cleavage and diminished capacity to use serine proteases on the cell surface for entry. Importantly, mutations of glycosylation-enabling residues in the QTQTN motif results in similar replication attenuation despite intact spike processing. Together, our results highlight elements in the SARS-CoV-2 spike in addition to the FCS that contribute to increased replication and pathogenesis.