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Coinfections have a potential role in increased morbidity and mortality rates during pandemics. Our investigation is aimed at evaluating the viral coinfection prevalence in COVID-19 patients. Rapid diagnostic tests are tools with a paramount impact both on improving patient care. Particularly in the case of respiratory infections, it is of great importance to quickly confirm/exclude the involvement of pathogens. The COVID-19 pandemic has been associated with changes in respiratory virus infections worldwide, which have differed between virus types. In this paper, we systematically searched the percentage of coinfection of various respiratory viruses in COVID-19-positive samples. We included patients of all ages, in all settings. The main outcome was the proportion of patients with viral coinfection. By describing the differences in changes between viral species across different geographies over the course of the COVID-19 pandemic, we may better understand the complex factors involved in the community cocirculation of respiratory viruses.

The SARS-CoV-2 B.1.617 variant emerged in the Indian state of Maharashtra in late 2020. There have been fears that 2 key mutations seen in the receptor-binding domain, L452R and E484Q, would have additive effects on evasion of neutralizing antibodies. We report that spike bearing L452R and E484Q confers modestly reduced sensitivity to BNT162b2 mRNA vaccine-elicited antibodies following either first or second dose. The effect is similar in magnitude to the loss of sensitivity conferred by L452R or E484Q alone. These data demonstrate reduced sensitivity to vaccine-elicited neutralizing antibodies by L452R and E484Q but lack of synergistic loss of sensitivity.

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying variants of concern (VOC). Viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host single nucleotide variations (iSNVs). Analysing 1347 samples collected till June 2020, we recorded 16 410 iSNV sites throughout the SARS-CoV-2 genome. We found ∼42% of the iSNV sites to be reported as SNVs by 30 September 2020 in consensus sequences submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1774 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) lineage-defining variations appeared as iSNVs before getting fixed in the population. Besides, mutations in RdRp as well as RNA-editing by APOBEC and ADAR deaminases seem to contribute to the differential prevalence of iSNVs in hosts. We also observe hyper-variability at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.

In April 2021, after successfully enduring three waves of the SARS-CoV2 pandemic in 2020, and having reached population seropositivity of about 50%, Delhi, the national capital of India was overwhelmed by the fourth wave. Here, we trace viral, host, and social factors contributing to the scale and exponent of the fourth wave, when compared to preceding waves, in an epidemiological context. Genomic surveillance data from Delhi and surrounding states shows an early phase of the upsurge driven by the entry of the more transmissible B.1.1.7 variant of concern (VOC) into the region in January, with at least one B.1.1.7 super spreader event in February 2021, relatable to known mass gatherings over this period. This was followed by seeding of the B.1.617 VOC, which too is highly transmissible, with rapid expansion of B.1.617.2 sub-lineage outpacing all other lineages. This unprecedented growth of cases occurred in the background of high seropositivity, but with low median neutralizing antibody levels, in a serially sampled cohort. Vaccination breakthrough cases over this period were noted, disproportionately related to VOC in sequenced cases, but usually mild. We find that this surge of SARS-CoV2 infections in Delhi is best explained by the introduction of a new highly transmissible VOC, B.1.617.2, with likely immune-evasion properties; insufficient neutralizing immunity, despite high seropositivity; and social behavior that promoted transmission.

Global Navigation Satellite System (GNSS) is becoming increasingly popular for its various advantages and potential for use in myriads of applications. Agriculture is one of the areas where GNSS is...

Global Navigation Satellite System (GNSS) currently consists of many global and regional satellite constellations developed by various countries. As a result of presence of multiple constellations,...

The SARS-CoV-2 B.1.617.2 (Delta) variant was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha). In vitro, B.1.617.2 is 6-fold less sensitive to serum neutralising antibodies from recovered individuals, and 8-fold less sensitive to vaccine-elicited antibodies as compared to wild type Wuhan-1 bearing D614G. Serum neutralising titres against B.1.617.2 were lower in ChAdOx-1 versus BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies against the receptor binding domain (RBD) and N-terminal domain (NTD), in particular to the clinically approved bamlavinimab and imdevimab monoclonal antibodies. B.1.617.2 demonstrated higher replication efficiency in both airway organoid and human airway epithelial systems as compared to B.1.1.7, associated with B.1.617.2 spike being in a predominantly cleaved state compared to B.1.1.7. Additionally we observed that B.1.617.2 had higher replication and spike mediated entry as compared to B.1.617.1, potentially explaining B.1.617.2 dominance. In an analysis of over 130 SARS-CoV-2 infected healthcare workers across three centres in India during a period of mixed lineage circulation, we observed substantially reduced ChAdOx-1 vaccine efficacy against B.1.617.2 relative to non-B.1.617.2. Compromised vaccine efficacy against the highly fit and immune evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.

As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being constantly used to investigate its transmissions and evolution. In the backdrop of the global emergence of “variants of concern” (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches was undertaken to identify possible new variants and gauge the fitness of current circulating strains.Phylogenetic analysis revealed that the predominant clade in circulation was a distinct newly identified lineage B.1.617 possessing common signature mutations D111D, G142D, L452R, E484Q, D614G and P681R, in the spike protein including within the receptor binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R and E484Q along with P681R in the furin cleavage site, revealed that these may possibly result in increased ACE2 binding and rate of S1-S2 cleavage resulting in better transmissibility. The same two RBD mutations indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Experimental validation against a wider panel of mAbs, sera from vaccinees and those that recovered from natural infection needs to be studied.The emergence of such local variants through the accumulation of convergent mutations during the COVID-19 second wave needs to be further investigated for their public health impact in the rest of the country and its possibility of becoming a VOC.

Supplementary data of the variant analysis

Delhi, the national capital of India, experienced multiple severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks in 2020 and reached population seropositivity of >50% by 2021. During April 2021, the city became overwhelmed by COVID-19 cases and fatalities, as a new variant, B.1.617.2 (Delta), replaced B.1.1.7 (Alpha). A Bayesian model explains the growth advantage of Delta through a combination of increased transmissibility and reduced sensitivity to immune responses generated against earlier variants (median estimates: 1.5-fold greater transmissibility and 20% reduction in sensitivity). Seropositivity of an employee and family cohort increased from 42% to 87.5% between March and July 2021, with 27% reinfections, as judged by increased antibody concentration after a previous decline. The likely high transmissibility and partial evasion of immunity by the Delta variant contributed to an overwhelming surge in Delhi.

Supplementary data of the variant analysis

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying Variants Of Concern (VOC). Besides, viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host Single Nucleotide Variations (iSNVs). Analysing 1, 347 samples collected till June 2020, we recorded 18, 146 iSNV sites throughout the SARS-CoV-2 genome. Both, mutations in RdRp as well as APOBEC and ADAR mediated RNA editing seem to contribute to the differential prevalence of iSNVs in hosts. Noteworthy, 41% of all unique iSNVs were reported as SNVs by 30th September 2020 in samples submitted to GISAID, which increased to ∼80% by 30th June 2021. Following this, analysis of another set of 1, 798 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) variations appeared as iSNVs before getting fixed in the population. We also observe hyper-editing events at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions.GRAPHICAL ABSTRACT

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 minute gradient run with 100% specificity and 90.4 % sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2. Electronic supplementary material The online version of this article (10.1007/s42485-020-00044-9) contains supplementary material, which is available to authorized users.

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

Global Navigation Satellite Systems are being increasingly used for myriads of applications. Along with many global systems, various regional systems are also deployed to exploit commercial potential, for strategic point of views and self-reliance. IRNSS/ NavIC is one of such regional systems developed by ISRO. NavIC enabled, costly, geodetic receivers are available in market and at the same time, few NavIC enabled chipsets also are being offered by manufacturers. These NavIC chips are low cost but the associated receiver board costs are much higher in comparison to the chipsets. Compact, cost-effective NavIC receiver boards are essential for NavIC based application development, popularization and effective utilization of the system. This manuscript presents an effort towards development of a compact, cost-effective NavIC receiver board and the results on the solution accuracy obtained from it. The power-efficient board operates in L5 band and is of 8 cm  10 cm size. The module is working properly both in static and dynamic operation and can provide meter level 2-dimensional precision; the altitude variation is found to be higher in comparison. Final cost of the prototype board is less than US$ 60 which may be reduced during bulk production. The board can be used with Raspberry Pi (RPi) or other controller boards for ASCII NMEA data reception, display and recording. The board has the potential for using it as a stand-alone receiver, for integration with other systems towards application development or as a geolocation sensor in IoT applications enhancing the possibility of deployment of multiple sensors because of cost, power and size efficiency.

Supplementary data of the variant analysis

Background: Healthcare workers (HCWs) deliver their duties at greater risk of occupationally acquired viral infections such as HIV, hepatitis B and hepatitis C, which transmit by direct exposure either with the infected sharps or the body fluids. However, most of such incidents remains unreported and hence pose a high risk to HCWs life. Aim: The timely investigation and interventions can change the fate of infection. In the present study, the knowledge, approach, awareness, and actions need to be taken post exposure were assessed among different categories of HCWs. Methods and materials: A cross sectional self-structured and responsive questionnaire was provided to HCWs and who furnished all information were included in analysis. Results and conclusions: Out of 138 questionnaires evaluated who acquired injury, 61 were resident doctors, 42 interns, 27 nursing staff, 8 were other paramedical staff. Only 19.6% HCWs have completed hepatitis B vaccination and maximum (93.5%) have post exposure prophylaxis for less than 24 h. Post exposure, only 42% HCWs reported to HIV screening center. After injury, spirit application and squeezing was done by 44.2% HCWs. 24% HCWs did not followed the universal precautions at work and 38.4% showed ignorance towards standard precautions. The results indicate ignorance and casual approach towards the universal precautions after occupational injuries which might be due to overworked or lack of resources/awareness. It necessitates the continuous education, monitoring, training, and disciplinary measures to control occupation infection hazards to HCWs.

Global navigation satellite systems (GNSSs) is currently used in myriads of applications and at the same time internet-based applications are also growing. In case of GNSS, stand-alone, single receiver-based position solution accuracy may not be enough in many applications like automated transporting service, unmanned air vehicle, Geodesy and agriculture etc and GNSS mass market needs low cost high accurate position solution. Carrier phase measurement-based position solution is more precise than code-based measurement, but phase ambiguity is a problem in carrier phase-based measurement. Real time Kinematic (RTK) technique is a method where precise position solution can be obtained using Network Transfer of RTCM message through IP (NTRIP) protocol; here multiple signal messages (MSM) are also sent from the GNSS base station to the rover and Carrier ambiguity can be resolved. This research work focuses on the RTK performance of geodetic, survey-grade receivers and low-cost receivers and analysis on their comparative performances. Geodetic receiver uses its own algorithm to calculate RTK solution and for the low-cost receivers, an open-source GNSS data processing software, RTKLib has been used. A static survey is made and found that low cost receivers can provide sub meter level precision in RTK operation which may help in GNSS mass market application and solution development.

Background and objective During past decades, fungal rhinosinusitis (FRS) has been diagnosed more frequently. Knowing the fungal flora and its prevalence in chronic rhinosinusitis (CRS) patients will allow a better understanding of this disease, diagnosis and treatment. We studied the prevalence of fungus in CRS patients in Delhi-NCR (National Capital Region) in a tertiary care hospital. Materials and methods In this prospective study, a total of 180 patients having CRS were enrolled in which functional endoscopic sinus surgery was done. In 173 (96.1%) patients, polyps/tissue/mass were collected during surgery. In seven (3.9%) cases, sinus secretions were obtained. All the collected samples were sent for microbiology and pathology examination. Diagnosis of FRS was confirmed by direct mycological (10% KOH) and/or culture and/or pathology analysis. Results Forty-eight cases were positive for fungus, out of these 180 patients of CRS. In patients of FRS, the most common presentation was nasal blockage followed by facial pain and facial fullness. The prevalence of FRS was found to be 26.6% in CRS and most common fungal pathogen isolated was Aspergillus flavus. Conclusion Delhi-NCR region falls under a moderate prevalence area for fungal infection in CRS patients as compared to other regions in India. Majority of cases were isolated in summer months, the dry and hot climate of the Delhi- NCR may be responsible for such prevalence. How to cite this article Garg S, Songara P, Sherwal BL, Agarwal S, Rakshit P, Kumar S. Fungal Rhinosinusitis in Delhi- National Capital Region. Clin Rhinol An Int J 2013;6(1): 28-31.

Polyvalent antivenom IgG s produced in equines against different snake venom are used for treatment in snakebite cases. For this, hyperimmune equine plasma is fractionated and purified before use. Hence, serum related side effects are common. To reduce it, search for more effective method with high yield and purity, is of concern. In the present study, a modified caprylic acid method for the fractionation of IgG, has been described. The method was also compared with routine method and previously described caprylic acid methods. The results indicated that modified caprylic acid method at concentration 1.5%, pH 4.8 with stirring for 60 minutes, was superior in terms of yield, and purity as compared to other methods (p

Background: Cross transmission of microorganisms by the hands of healthcare workers is the main route of spread of health care associated infections (HCAI) as they provide essential services to the patients. HCAI has increased the morbidity and mortality of hospitalized patients especially the ones admitted in Paediatric ICU and nursery. Objectives: The present study was undertaken to isolate bacteria from hands of resident doctors and nursing staff from Paediatric ICU and nursery and to correlate them with the patients sample isolates from same Paediatric ICU and Nursery during the same time period. Material and Methods: Fingertips of subjects were directly stabbed on MacConkey agar and Blood agar plates. Antibiogram of isolated pathogens was also determined by standard methods. Observations: Hands of 60% healthcare workers were culture positive. Predominant isolate were Coagulase negative Staphylococcus spp. (73.3%), followed by Staphylococcus aureus (10%), Enterococcus and Acinetobacter spp. (each 6.6%). Methicillin resistant Staphylococcus aureus (50%) were also observed. Conclusion: Implementation and improving the compliance to hand hygiene may result in order to reduce cross infection from health care workers to patients.