Response of Wastewater-Based Epidemiology Predictor for the Second Wave of COVID-19 in Ahmedabad, India: A Long-term Data Perspective (preprint)

Wastewater-based epidemiology (WBE) surveillance could play a key role in managing the COVID-19 pandemic by covering pre-symptomatic and asymptomatic cases in highly populated areas with limited clinical tests. In the present work, wastewater surveillance was introduced in Ahmedabad, India, after the successful containment of the first wave of COVID-19 to predict the resurge of the infection during the second wave of the pandemic. The increasing number of positive influent samples correlated with the number of confirmed clinical cases. It also showed clear evidence of early detection of the second wave of COVID-19 in Ahmedabad. We further put forward the wastewater surveillance-based city zonation for effective COVID-19 pandemic preparedness. An eight-month data of Surveillance of Wastewater for Early Epidemic Prediction (SWEEP) was generated for the Ahmedabad, Gujarat, India. Influent wastewater samples (n=287) were analyzed weekly to detect SARS-CoV-2 RNA from nine locations during September 2020 to April 2021. A total of 258 out of 287 samples were detected positive with at least two out of three SARS-CoV-2 genes (N, ORF 1ab, and S). Monthly variation represented a significant decline in all three gene copies in October compared to September 2020, followed by an abrupt increase in November 2020. A similar increment in the gene copies was observed in March 2021, which is an indicator of the second wave of COVID-19. Correspondingly, the descending order of average effective gene concentration was: November (1.1 x 104 copies/L)> April (7.5 x 103 copies/L)> March (4.5 x 103 copies/L)> September (3.0 x 103 copies/L)> December (1.8 x 103 copies/L)> January (1.6 x 103 copies/L)> February (4.7 x 102 copies/L) > October (4.5 x 102 copies/L). A lead of 1-2 weeks was observed in the percentage change in gene concentration with respect to the confirmed cases. Th study highlighted the effectiveness of wastewater surveillance as a tool to predict various waves of the pandemic, to identify the hotspots within the city, and to instigate better implementation of the management interventions.

Surveillance and molecular characterization of SARS-CoV-2 infection in non-human hosts in Gujarat, India. (preprint)

Since December 2019, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been spreading worldwide, triggering one of the most challenging pandemics in human population. In the light of reporting of this virus in domestic and wild animals from several parts of world, a systematic surveillance study was conceptualized to detect the SARS-CoV-2 among species of Veterinary importance. Nasal and/or rectal samples of 413 animals (Dog=195, cattle=64, horse=42, goat=41, buffalo=39, sheep=19, cat=6, camel=6 and monkey=1) were collected from different places of Gujarat state of India. RNA was extracted from samples and subjected to RT-qPCR based amplification of target sequences in viral nucleoprotein (N), spike (S) and ORF1ab genes. A total of 95 (23.79 %) animals were found positive, comprised of 67 (34.35 %) dogs, 15(23.43 %) cattle and 13(33.33 %) buffaloes. Overall, nasal samples (N=80/412, 19.41 %) gave more positive results than rectal samples (N=70/407, 17.19 %) in RT-qPCR. The whole SRAS-CoV-2 genome sequencing was done on one sample (ID-A4N; from dog) where 32 mutations, including 29 single nucleotide variation (SNV) and two deletions, were detected. Among them, 9 mutations were located in the receptor binding domain of the spike (S) protein. The consequent changes in amino acid sequence revealed that T19R, G142D, E156-, F157-, A222V, L452R, T478K, D614G, P681R mutation in S protein and D63G, R203M and D377Y in N protein. The lineage assigned to this SARS-CoV-1 sequence is B.1.617.2. Thus, the present study highlights the importance of SARS-CoV-2 surveillance in non-human host.

A simple and quick PCR based method for detection of Omicron variant of SARS-CoV-2 (preprint)

SARS-CoV-2 pandemic has changed the global landscape since last 2 years. Against many challenges posed by the COVID19 pandemic to the humanity, the pace of solutions created by mankind is exemplary; diagnostics, vaccines, alternate therapies to name a few. With a rapidly changing virus strain its early identification in the field can be a quick solution to trace the individuals and control the spread of new emerging variants of SARS-CoV-2. This paper describes PCR based quick method for differentiation of Omicron variant of SARS-CoV-2 from other variants. Timely identification of this new variant will enable better management of pandemic control in the population.

Nasopharyngeal Microbiome of COVID-19 Patients Using 16S Amplicon Analysis Revealed Distinct Bacterial Profile in Demised and Recovered Individuals (preprint)

Background: COVID-19 pandemic has shaken the entire world and the socio-economic life on the planet. The implications of the bacterial co-infections in SARS-CoV-2 patients remained the least explored subject of clinical manifestations among the COVID-19. Identification and association of the nasopharyngeal microbial community structure within SARS-CoV-2 infected patients could reveal microbiota dynamics that may determine and/or influence the disease outcome in the COVID-19 patients. Results Here, in this study, we present distinct nasopharyngeal microbiome in the demised (N=48) and recovered (N=29) COVID-19 patients as compared to the control group (N=33). The nasal microbiome composition in the three groups vary significantly (PERMANOVA, p-value <0.001), where demised patients showed higher species richness as compared to the recovered and control groups. Pathogenic genera including C orynebacterium (LAD score 5.51), Staphylococcus , Serratia , Klebsiella and their corresponding species were found as biomarkers (p-value <0.05, LDA cutoff 4.0) in the patients those who demised due to SARS-CoV-2 infection. Except for a few pathogenic species in the genera, Ochrobactrum (LDA score 5.79), and Burkholderia (LDA 5.29), the recovered group harbors ordinal bacteria (p-value <0.05, LDA-4.0) as biomarkers. Similarly, Pseudomonas (LDA score 6.19), and several healthy oral/nasal cavity commensal including Veillonella , and Porphyroonas , were biomarkers for the control individuals. Conclusions Dysbiosis in the commensal nasopharyngeal microbiota, especially due to infection of opportunistic pathogens could lead to more complex and severe COVID-19 disease dynamics. Whereas, healthy commensal bacteria may trigger the immune response and alter the viral infection susceptibility and thus, may help in preventing the viral infection and possible recovery which is yet to be explored. The findings in the present study provide key considerations and have significant implications for the COVID-19 treatment and control measures. However, further study is required to address the microbiome based therapeutic aspects.

Genomic epidemiology of early SARS-CoV-2 transmission dynamics in Gujarat, India (preprint)

Genomic surveillance of SARS-CoV-2 has played a decisive role in understanding the transmission and evolution of the virus during its emergence and continued circulation. However, limited genomic sampling in many high-incidence countries has impeded detailed studies of SARS-CoV-2 genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. To address this gap, we investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during its first epidemic wave and shed light on virus spread in one of the pandemics hardest-hit regions. By integrating regional case data and 434 whole virus genome sequences sampled across 20 districts from March to July 2020, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat, India. Our findings revealed that global and regional connectivity, along with population density, were significant drivers of the Gujarat SARS-CoV-2 outbreak. The three most populous districts in Gujarat accounted [~]84% of total cases during the first wave. Moreover, we detected over 100 virus lineage introductions, which were primarily associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations with low-population density. Our findings suggest SARS-CoV-2 transmission follows a gravity model in India, with urban centres contributing disproportionately to onward virus spread.

Defective ORF8 dimerization in delta variant of SARS CoV2 leads to abrogation of ORF8 MHC-I interaction and overcome suppression of adaptive immune response (preprint)

In India, the breakthrough infections during second wave of COVID-19 pandemic was due to SARS-COV-2 delta variant (B.1.617.2). It was reported that majority of the infections were caused by the delta variant and only 9.8% percent cases required hospitalization whereas, only 0.4% fatality was observed. Sudden dropdown in COVID-19 infections was observed within a short timeframe, suggesting better host adaptation with evolved delta variant. Down regulation of host immune response against SARS-CoV-2 by ORF8 induced MHC-I degradation has been reported earlier. The Delta variant carried mutations (deletion) at Asp119 and Phe120 amino acids which are critical for ORF8 dimerization. The deletions of amino acids Asp119 and Phe120 in ORF8 of delta variant results in structural instability of ORF8 dimer caused by disruption of hydrogen bonding and salt bridges as revealed by structural analysis and MD simulation studies of ORF8 dimer. Further, flexible docking of wild type and mutant ORF8 dimer revealed reduced interaction of mutant ORF8 dimer with MHC-I as compared to wild type ORF8 dimer with MHC-1, thus implicating its possible role in MHC-I expression and host immune response against SARS-CoV-2. We thus propose that mutant ORF8 may not hindering the MHC-I expression thereby resulting in better immune response against SARS-CoV-2 delta variant, which partly explains the sudden drop of SARS-CoV-2 infection rate in the second wave of SARS-CoV-2 predominated by delta variant in India Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/457457v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@751eeaorg.highwire.dtl.DTLVardef@140b5b5org.highwire.dtl.DTLVardef@159a3a5org.highwire.dtl.DTLVardef@6c206_HPS_FORMAT_FIGEXP M_FIG C_FIG

First detection of SARS-CoV-2 Delta variant (B.1.617.2) in the wastewater of (Ahmedabad), India (preprint)

Contrary to the conventional genomic surveillance based on clinical samples (symptomatic patients), the wastewater-based genomic surveillance can identify all the variants shed by the infected individuals in the population, as it does also include RNA fragmented shredded by clinically escaped asymptomatic patients. We analyzed four samples to detect key mutations in the SARS-CoV-2 genome and track circulating variants in Ahmedabad during the first wave (Sep/ Nov 2020) and before the second wave (in Feb 2021) of COVID-19 in India. The analysis showed a total of 35 mutations in the spike protein across four samples categorized into 23 types. We noticed the presence of spike protein mutations linked to the VOC-21APR-02; B.1.617.2 lineage (Delta variant) with 57% frequency in wastewater samples of Feb 2021. The key spike protein mutations were T19R, L452R, T478K, D614G, & P681R and deletions at 22029 (6 bp), 28248 (6 bp), & 28271 (1 bp). Interestingly, these mutations were not observed in the samples of Sep and Nov 2020 but appeared before the devastating second wave of COVID-19, which started in early April 2021 in India, caused rapid transmission and deaths all over India. We found the genetic traces of the B.1.617.2 in samples of early Feb 2021 i.e., more than a month before the first clinically confirmed case of the same variant in March 2021 in Ahmedabad, Gujarat. The present study tells about the circulating variants in Ahmedabad and suggests early prediction VOCs employing the wastewater genomic surveillance approach that must be exploited at a large scale for effective COVID-19 management.

The Spectre of SARS-CoV-2 in the Ambient Urban Natural Water in Ahmedabad and Guwahati: A Tale of Two Cities (preprint)

COVID-19 positive patients can egest live SARS-CoV-2 virus through fecal matter and urine, raising concerns about viral transmission through the fecal-oral route and/or contaminated aerosolized water. These worries are heightened in many low and middle-income nations, where raw sewage is often dumped into surface waterways and open defecation betide. In this manuscript we attempt to discern the presence of SARS-CoV-2 genetic material (ORF-1ab, N and S genes) in two urban cities of India viz., Ahmedabad, in western India with ~12 WWTPs and Guwahati, in the northeast of the country with no such plants. 100% and 20% of the surface water samples had detectable SARSCoV-2 RNA load in Ahmedabad and Gandhinagar, respectively. N-gene>S-gene>ORF-1ab-gene were readily detected in the surface water of Ahmedabad, whereas, no such significant trend was found in the case of Guwahati. The high concentration of gene (ORF-1ab 800 copies/L for Sabarmati river, Ahmedabad and S-gene 565 copies/L for Bharalu urban river, Guwahati) found in natural waters indicates low sanitation and have various health and ecological consequences that should be investigated further.

E156/G and Arg158, Phe-157/del mutation in NTD of spike protein in B.1.167.2 lineage of SARS-CoV-2 leads to immune evasion through antibody escape (preprint)

New emerging variants of SARS-CoV-2 remains a persistent threat with better immune escape mechanisms and higher transmissibility across the globe. B.1.617.2 (Delta) variant first emerged from Maharashtra, India in December, 2020. This variant is classified to be a major cause and concern of the recent peak of COVID-19 in India. Cellular entry of coronaviruses largely depends on binding of the viral spike (S) proteins to host receptors and priming by host cell proteases through the contact of the droplets containing pathogenic virus particles. Our research study, explore the genomic and structural basis of this variant through computational analysis, protein modelling and molecular dynamics simulations approach and identifies the mechanism through which it is probably more pathogenically evolved with higher transmissibility as compared to the wild-type. These findings reveal the significant difference in rigidity and reducing the flexibility within N-terminal domain (NTD) of the spike protein, hence prevailing case of antibody escape. The results of the present study demonstrate the fitness advantage to the new variant which further need to be critically examined though supportive experimental biology that might help devising better therapeutics and containment of SARS-CoV-2.

First comparison of conventional activated sludge versus root-zone treatment for SARS-CoV-2 RNA removal from wastewaters: statistical and temporal significance (preprint)

In the initial pandemic phase, effluents from wastewater treatment facilities were reported mostly free from Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) RNA, and thus conventional wastewater treatments were generally considered effective. However, there is a lack of first-hand data on i) comparative efficacy of various treatment processes for SARS-CoV-2 RNA removal; and ii) temporal variations in the removal efficacy of a given treatment process in the backdrop of active COVID-19 cases. This work provides a comparative account of the removal efficacy of conventional activated sludge (CAS) and root zone treatments (RZT) based on weekly wastewater surveillance data, consisting of forty-four samples, during a two-month period. The average genome concentration was higher in the inlets of CAS-based wastewater treatment plant in the Sargasan ward (1.25 x 103 copies/ L), than that of RZT plant (7.07 x 102 copies/ L) in an academic institution campus of Gandhinagar, Gujarat, India. ORF 1ab and S genes appeared to be more sensitive to treatment i.e., significantly reduced (p <0.05) than N genes (p>0.05). CAS treatment exhibited better RNA removal efficacy (p=0.014) than RZT (p=0.032). Multivariate analyses suggested that the effective genome concentration should be calculated based on the presence/absence of multiple genes. The present study stresses that treated effluents are not always free from SARS-CoV-2 RNA, and the removal efficacy of a given WWTPs is prone to exhibit temporal variability owing to variations in active COVID-19 cases in the vicinity and genetic material accumulation over time. Disinfection seems less effective than the adsorption and coagulation processes for SARS-CoV-2 removal. Results stress the need for further research on mechanistic insight on SARS-CoV-2 removal through various treatment processes taking solid-liquid partitioning into account. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/21256898v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@131f5cborg.highwire.dtl.DTLVardef@1001968org.highwire.dtl.DTLVardef@18409b7org.highwire.dtl.DTLVardef@19a079a_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWastewater treatments may not completely remove the SARS-CoV-2 RNA. C_LIO_LIThe activated sludge process exhibited better RNA removal efficacy than root-zone treatment. C_LIO_LIORF 1ab and S genes appeared more sensitive to treatment than N genes. C_LIO_LITemporal variability is observed in the removal efficacy of wastewater treatment plants. C_LI

Reflections of COVID-19 cases on the wastewater loading of SARS-CoV-2 RNA: A case of three major cities of Gujarat, India (preprint)

The scientific community has widely supported wastewater monitoring of SARS-CoV-2 due to the early and prolonged excretion of coronavirus in the faecal matter. In the present study, eighteen influent wastewater samples from different wastewater treatment plants and pumping stations (5 samples from Vadodara city, 4 from Gandhinagar, and nine from Ahmedabad city) were collected and analyzed for the occurrence of SARS-CoV-2 RNA in Gujarat province, India. The results showed the highest SARS-CoV-2 genome concentration in Vadodara (3078 copies/ L), followed by Ahmedabad (2968 copies/ L) and Gandhinagar (354 copies/ L). The comparison of genome concentration corresponded to the number of confirmed and active cases in all three cities. The study confirms the potential of the Surveillance of Wastewater for Early Epidemic Prediction (SWEEP) that can be used at a large scale around the globe for better dealing with the pandemic situation.

First wastewater surveillance-based city zonation for effective COVID-19 pandemic preparedness powered by early warning: A study of Ahmedabad, India (preprint)

Following the proven concept, capabilities, and limitations of detecting the RNA of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) in wastewater, it is pertinent to understand the utility of wastewater surveillance data on various scale. In the present work, we put forward the first wastewater surveillance-based city zonation for effective COVID-19 pandemic preparedness. A three-month data of Surveillance of Wastewater for Early Epidemic Prediction (SWEEP) was generated for the world heritage city of Ahmedabad, Gujarat, India. In this expedition, one hundred sixteen wastewater samples were analyzed to detect SARS-CoV-2 RNA, from September 3rd to November 26th, 2020. A total of 111 samples were detected with at least two out of three SARS-CoV-2 genes (N, ORF 1ab, and S). Monthly variation depicted a significant decline in all three gene copies in October compared to September 2020, followed by a sharp increment in November 2020. Correspondingly, the descending order of average genome concentration was: November ([~]10729 copies/ L) > September ([~]3047 copies/ L) > October ([~]454 copies/ L). Monthly variation of SARS-CoV-2 RNA in the wastewater samples may be ascribed to a decline of 19.3% in the total number of active cases in October 2020 and a rise of 1.82% in November 2020. Also, the monthly recovery rate of patients was 16.61, 19.31, and 15.58% in September, October, and November 2020, respectively. The percentage change in the genome concentration was observed in the lead of 1-2 weeks with respect to the provisional figures of confirmed cases. SWEEP data-based city zonation was matched with the heat map of the overall COVID-19 infected population in Ahmedabad city, and month-wise effective RNA concentration variations are shown on the map. The results expound on the potential of WBE surveillance of COVID-19 as a city zonation tool that can be meaningfully interpreted, predicted, and propagated for community preparedness through advance identification of COVID-19 hotspots within a given city. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/21253898v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@c1669org.highwire.dtl.DTLVardef@19358f5org.highwire.dtl.DTLVardef@b56189org.highwire.dtl.DTLVardef@167711_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights{blacksquare} Wastewater surveillance-based city zonation is effective for COVID-19 pandemic preparedness. {blacksquare}Three months variation of SARS-CoV-2 RNA in the wastewaters of Ahmedabad, India is presented. {blacksquare}Wastewater monitoring offers a lead of [~]2 weeks to realize and manage the pandemic situation. {blacksquare}Mapping powered by early warning can strengthen the preparedness of community. {blacksquare}WBE based COVID-19 surveillance is a high end technique for identifying hotspots on city scale.

Host Genetic Factors for COVID-19 Severity and Outcome in Western Indian Population (preprint)

Background: Different human populations across the globe responded in a different way against the SARS-CoV-2 infection. Therefore, it is anticipated that host genetic variants have straight association with the COVID-19. Genome Wide Association Study (GWAS) may help to understand this aspect.Methods: We carried out GWAS analysis with 571 SARS-CoV-2 infected patients from Gujarat state of India with different phases of COVID-19 severity. After quality filtering, total 94, 320 and 147, deceased, recovered (after admitting in intensive care unit), and asymptomatic, patients were included in the final analysis using three tools i.e. PLINK, OrdinalGWAS·jl and SAIGE.Findings: We identified total ten, thirteen, and ten unique genomic loci for deceased vs recovered, deceased vs asymptomatic and recovered vs asymptomatic groups, respectively. TNFSF4, LRRC56 and TUBD1 genes have shown an association in deceased vs recovered. Similarly, genomic markers where nearby genes are OR7C2, OR7A17, PAX5, etc. are significant for disease vs asymptomatic comparison. For recovered vs asymptomatic comparison, a strong signal at chromosome 6, locus 6p21·32 where HLA group of genes, which are key regulators of the immune system, is found. Unfavorable alleles in AX-11318356, AX-11403743, and AX-11509434 have shown the higher frequency in European compared to the South Asian population and it is reversed for AX-40266551, AX-40266553, AX-38975337, AX-11258333, and AX-30353919.Interpretation: Unfavorable alleles of the markers showing association with the disease severity and outcome can be used for risk prediction in the SARS-CoV-2 infections. GWAS study in other populations may help to further strengthen the outcome of this study.Funding: Department of Science and Technology, Government of Gujarat, India.Conflict of Interest: All the authors of this manuscript declare no competing interests.Ethical Approval: The present studies involving human participants were reviewed and approved by Institutional Ethical Committee of Gujarat Biotechnology Research Centre (GBRC), Gandhinagar, and B. J. Medical College and Civil hospital, Ahmedabad, reference No. EC/Approval/38/2020.

Unravelling the early warning capability of wastewater surveillance for COVID-19: A temporal study on SARS-CoV-2 RNA detection and need for the escalation (preprint)

ABSTRACT Wastewater-based Epidemiological (WBE) surveillance offers a promising approach to assess the pandemic situation covering pre-symptomatic and asymptomatic cases in highly populated area under limited clinical tests. In the present study, we analysed SARS-CoV-2 RNA in the influent wastewater samples ( n = 43) from four wastewater treatment plants (WWTPs) in Gandhinagar, India, during August 7 th to September 30 th , 2020. A total of 40 samples out of 43 were found positive i.e. having at least two genes of SARS-CoV-2. The average Ct values for S, N, and ORF 1ab genes were 32.66, 33.03, and 33.95, respectively. Monthly variation depicted a substantial rise in the average copies of N (∼120%) and ORF 1ab (∼38%) genes in the month of September as compared to August, while S-gene copies declined by 58% in September 2020. The SARS-CoV-2 genome concentration was higher in the month of September (∼924.5 copies/ L) than August (∼897.5 copies/ L), corresponding to a ∼ 2.2-fold rise in the number of confirmed cases during the study period. Further, the percentage change in genome concentration level on a particular date was found in the lead of 1-2 weeks of time with respect to the official confirmed cases registered based on clinical tests on a temporal scale. The results profoundly unravel the potential of WBE surveillance to predict the fluctuation of COVID-19 cases to provide an early warning. Our study explicitly suggests that it is the need of hour that the wastewater surveillance must be included as an integral part of COVID-19 pandemic monitoring which can not only help the water authorities to identify the hotspots within a city but can provide up to 2 weeks of time lead for better tuning the management interventions. HIGHLIGHTS □ Study unravels the early warning potential of wastewater based surveillance of COVID-19. □ Adequate SARS-CoV-2 RNA were detected despite of limited reported case in the vicinity. □ Up to 2 weeks of lead is possible from a regular wastewater based COVID-19 surveillance. □ SARS-CoV-2 RNA was higher in September than August in response to a ∼ 2.2-fold rise in COVID-19 active cases. Graphical Abstract

Publishing of COVID-19 Preprints in Peer-reviewed Journals, Preprinting Trends, Public Discussion and Quality Issues (preprint)

IntroductionCOVID-19-related (vs. non-related) articles appear to be more expeditiously processed and published in peer-reviewed journals. We aimed to evaluate: (i) whether COVID-19-related preprints were favoured for publication, (ii) preprinting trends and public discussion of the preprints and (iii) relationship between the publication topic (COVID-19-related or not) and quality issues. MethodsManuscripts deposited at bioRxiv and medRxiv between January 1 and October 21 were assessed for the probability of publishing in peer-reviewed journals, and those published were evaluated for submission-to-acceptance time. The extent of public discussion was assessed based on Altmetric and Disqus data. The Retraction Watch database and PubMed were used to explore the retraction of COVID-19 and non-COVID-19 articles and preprints. ResultsWith adjustment for the preprinting server and number of deposited versions, COVID-19-related preprints were more likely to be published within 120 days since the deposition of the first version (OR=1.99, 95%CI 1.76-2.25) as well as over the entire observed period (OR=1.49, 95%CI 1.36-1.62). Submission-to-acceptance was by 41.69 days (95%CI 46.56-36.80) shorter for COVID-19 articles. Public discussion of preprints was modest and COVID-19 articles were overrepresented in the pool of retracted articles in 2020. ConclusionCurrent data suggest a preference for publication of COVID-19-related preprints over the observed period.

In-Silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1 (preprint)

Novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has claimed more than 1.5 million lives worldwide and counting. As per the GISAID database, the genomics of SARS-CoV2 is extensively studied with more than 500 genome submissions per day. Out of several hotspot mutations within the SARS-CoV-2 genome, researchers have focused a lot on missense variants but the least work is done on the UTRs. One of the most frequent UTR variants in the SARS-CoV-2 genome is the C241T with a global frequency of more than 0.9. In the present study, the effect of the C241T mutation has been studied with respect to change in RNA structure and its interaction with the host replication factors MADP1 Zinc finger CCHC-type and RNA-binding motif 1 (hnRNP1). The results obtained from molecular docking and molecular dynamics simulation indicated weaker interaction of C241T mutant stem loops with host transcription factor MADP1 indicating reduced replication efficiency. The results are also correlated with increased recovery rates and decreased death rates of global SARS-CoV-2 cases.

Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology (preprint)

Humanity has seen numerous pandemics during its course of evolution. The list includes many such as measles, Ebola, SARS, MERS, etc. Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. As of 4th July 2020, COVID-19 has affected over 10 million people from 170+ countries, and 5,28,364 deaths. Genomic technologies have enabled us to understand the genomic constitution of the pathogens, their virulence, evolution, rate of mutations, etc. To date, more than 60,000 virus genomes have been deposited in the public depositories like GISAID and NCBI. While we are writing this, India is the 3rd most-affected country with COVID-19 with 0.6 million cases, and >18000 deaths. Gujarat is the fourth highest affected state with 5.44 percent death rate compared to national average of 2.8 percent. Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. The other significant deleterious variant found in diseased patients from Gujarat and the world is G25563T, which is located in Orf3a and has a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID.

The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2 (preprint)

we made the first-ever successful effort from India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of WBE surveillance in India. Sampling was carried out on 8 and 27 May 2020 from Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat with 106 million liters per day (MLD) capacity receiving effluent of Civil Hospital treating COVID-19 patient. All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents with no gene spotted in the effluent collected on 8 and 27 May 2020. Temporal difference between 8 and 27 May 2020 samples was of 10x in gene copy loading with a corresponding change of 2x in the number active COVID-19 patient in the city. Number of gene copies was found comparable to that reported in the untreated wastewaters of Australia, China, and Turkey and lower than that of the USA, France, and Spain. This study, being the first from India and probably among the first ten reports in the world of gene detection of SARS-CoV-2 in the environmental samples, aims to assist concerned authorities and policymakers to formulate and/or upgrade the COVID-19 surveillance to have an explicit picture of the phase of the pandemic. While infectious SARS-CoV-2 has yet to be identified in the aquatic environment, the virus potentially enters the wastewater stream from patient excretions and thus can be a great tool for pandemic monitoring.

Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype (preprint)

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), which was first reported in Wuhan, China in November 2019 has developed into a pandemic since March 2020, causing substantial human casualties and economic losses. Studies on SARS-CoV-2 are being carried out at an unprecedented rate to tackle this threat. Genomics studies, in particular, are indispensable to elucidate the dynamic nature of the RNA genome of SARS-CoV-2. RNA viruses are marked by their unique ability to undergo high rates of mutation in their genome, much more frequently than their hosts, which diversifies their strengths qualifying them to elude host immune response and amplify drug resistance. In this study, we sequenced and analyzed the genomic information of the SARS-CoV-2 isolates from two infected Indian patients and explored the possible implications of point mutations in its biology. In addition to multiple point mutations, we found a remarkable similarity between relatively common mutations of 36-nucleotide deletion in ORF8 of SARS-CoV-2. Our results corroborate with the earlier reported 29-nucleotide deletion in SARS, which was frequent during the early stage of human-to-human transmission. The results will be useful to understand the biology of SARS-CoV-2 and itsattenuation for vaccine development.