Responses to COVID-19 in South Asian Association for Regional Cooperation (SAARC) countries in 2020, a data analysis during a world of crises.

Coronavirus disease (COVID-19) caused by SARS-CoV-2 was notified from Wuhan city, Hubei province, China in the mid of December 2019. The disease is showing dynamic change in the pattern of confirmed cases and death toll in these low and middle-income countries (LMICs). In this study, exponential growth (EG) method was used to calculate the real-time reproductive number (Rt) for initial and later stage of epidemic in South Asian Association for Regional Cooperation (SAARC) member countries (April 2020 - December 2020). Time dependent (TD) method was used to calculate the weekly real -time reproduction number (Rt). We also presented the observations on COVID-19 epidemiology in relation with the health expenditure, poverty, BCG vaccination, literacy population density and Rt for understanding the current scenario, trends, and expected outcome of the disease in SAARC countries. A significant positive correlation was noticed between COVID-19 deaths and health expenditure (% GDP) (r = 0.58, P < 0.05). The other factors such as population density/sq km, literacy %, adult population %, and poverty % were not significantly correlated with number of COVID-19 cases and deaths. Among SAARC countries, the highest Rt was observed in India (Rt = 2.10; 95% CI 2.04-2.17) followed by Bangladesh (Rt = 1.62; 95% CI 1.59-1.64) in initial state of epidemic. A continuous monitoring is necessitated in all countries looking at the medical facilities, available infrastructure and healthcare manpower, constraints which may appear with increased number of critically ill patients if the situation persists longer.

Particularly vulnerable tribal groups of Tamil Nadu, India: A sociocultural anthropological review.

"Adivasi" is the collective term for tribes, an indigenous population, and ethnic minorities of India. In general, tribal populations live in harmony with nature and resources within their habitat and largely reside in segregates in an unpolluted and natural environment away from modern civilization. As per the 2011 census, India contains 705 scheduled tribes (STs) and subtribes and 75 primitive tribal clusters. The ST population of Tamil Nadu, India, was found to be 794,697 and broadly spread in 38 districts constituting 36 tribes, among which 6 tribes were grouped as "particularly vulnerable tribal groups" (PVTGs), namely (1) Todas, (2) Kotas, (3) Kurumbas, (4) Irulas, (5) Paniyas, and (6) Kattunayakas, as the number of population in these tribal communities is either declining or remaining static. The state government is offering lots of benefit schemes for the STs, but they have not reached the tribal groups. Health problems of tribal communities have been profoundly influenced by different factors such as social, cultural, educational, economic, and political practices. The tribal peoples are exceedingly disease prone as they do not have access to basic health-care facilities. Therefore, concerned policymakers should focus on the changing health needs of tribal communities. In this regard, the current review article has been focused on the complete details (language, occupation, worship or deity, subdivisions or other names, etc.) of these six PVTGs and also to concentrate on the kind of problems they face while living in the societies. Therefore, the government and nongovernmental organizations need to find a way to improve their livelihoods and health status.

Leptospirosis: a neglected tropical zoonotic infection of public health importance-an updated review.

Leptospirosis is a zoonotic and waterborne disease worldwide. It is a neglected, reemerging disease of global public health importance with respect to morbidity and mortality both in humans and animals. Due to negligence, rapid, unplanned urbanization, and poor sanitation, leptospirosis emerges as a leading cause of acute febrile illness in many of the developing countries. Every individual has a risk of getting infected as domestic and wild animals carry leptospires; the at-risk population varies from the healthcare professionals, animal caretakers, farmers and agricultural workers, fishermen, rodent catchers, water sports people, National Disaster Response Force (NDRF) personnel, people who volunteer rescue operations in flood-affected areas, sanitary workers, sewage workers, etc. The clinical manifestations of leptospirosis range from flu-like illness to acute kidney failure (AKF), pneumonia, jaundice, pulmonary hemorrhages, etc. But many rare and uncommon clinical manifestations are being reported worldwide. This review will cover all possible updates in leptospirosis from occurrence, transmission, rare clinical manifestations, diagnosis, treatment, and prophylactic measures that are currently available, their advantages and the future perspectives, elaborately. There are less or very few reviews on leptospirosis in recent years. Thus, this work will serve as background knowledge for the current understanding of leptospirosis for researchers. This will provide a detailed analysis of leptospirosis and also help in finding research gaps and areas to focus on regarding future research perspectives.

Factors associated with human immunodeficiency virus infection and self-assessed risk to human immunodeficiency virus among injecting drug users in Manipur, India.

BACKGROUND: The proximity of Northeast India to the Golden Triangle facilitates easy accessibility to illicit drugs, resulting in a higher proportion of injecting drug users (IDUs) in the states of Northeast India. The estimated human immunodeficiency virus (HIV) prevalence among IDU in Manipur which is 1.43% is higher than that of the national figure. OBJECTIVES: The objectives of the study were to find the factors associated with HIV infection and correlate the association between HIV status and self-assessed risk to HIV among IDUs in Manipur. METHODS: National Integrated Biological and Behavioral Surveillance (2014-2015) data were used for the study; all analyses done were weighted. In Manipur, information was collected from 1594 IDUs during the surveillance between 2014 and 2015 across four domains, namely Chandel (396), Imphal East (397), Thoubal (401), and Senapati (400). Chi-square test was performed to test the association between the independent and dependent variables. Multivariable logistic regression was performed to identify risk factors associated with HIV positivity. RESULTS: Higher age, unsafe injecting practice, low education status, and low-income status were significantly (P < 0.05) associated with HIV infection among IDUs in Manipur. Self-assessed risk of HIV infection by IDU was significantly associated with HIV positivity. CONCLUSION: Interventions among IDUs in Manipur should focus on emphasizing safe injecting practices along with creating awareness on HIV prevention and management.

Genome sequencing identifies genetic and antigenic divergence of porcine picobirnaviruses.

The full-length genome sequence of a porcine picobirnavirus (PBV) detected in Italy in 2004 was determined. The smaller (S) genome segment was 1730 nt, coding for a putative RNA-dependent RNA polymerase. Two distinct subpopulations of larger (L) genome segment (LA and LB) were identified in the sample, with the sizes ranging from 2351 to 2666 nt. The ORF1, coding for a protein of unknown function, contained a variable number of repetitions of the ExxRxNxxxE motif. The capsid protein-coding ORF2 spanned nt 810-2447 in the LB variants and started at nt 734 in the LA variants. However, a termination codon was present only in one of all the LA segment variants. Three-dimensional modelling of the porcine PBV capsids suggested structural differences in the protruding domain, tentatively involved as antigens in the humoral immune response. Altogether, these findings suggest the simultaneous presence of two different PBV strains sharing the same S segment but displaying genetically diverse L segments. In addition, the sample probably contained a mixture of PBVs with aberrant RNA replication products. Altered structure in the L segments could be tolerated and retained in the presence of functionally integer-cognate genes and represents a mechanism of virus diversification.

Genogroup I avian picobirnavirus detected in Brazilian broiler chickens: a molecular epidemiology study.

Picobirnavirus (PBV) belongs to the family Picobirnaviridae. Picobirnaviruses contain a bisegmented dsRNA genome that is non-enveloped. A total of 85 pooled faecal samples were collected from the poultry of 37 farms from the Metropolitan Mesoregion of Belém (MMB), Pará state, Brazil. The viral RNA from each sample was analysed by PAGE and reverse transcriptase PCR (RT-PCR). For each county affected, at least one positive sample was selected, cloned and sequenced. The samples showed a positivity of 15.3 % (13/85) by PAGE and 49.4 % (42/85) by RT-PCR. Sequencing of these strains demonstrated a considerable RdRp gene heterogeneity that ranged from 56.1 to 100 % at the nucleotide level compared with prototypes of different species and water sewage, and from 50.3 to 100 % among themselves. Avian picobirnavirus (AvPBV) was detected in MMB broiler farms and showed a heterogeneous relationship with the prototypes used. This report includes what is believed to be the first gene sequencing of AvPBV in Brazilian broiler chickens.

Analysis of the ORF2 of human astroviruses reveals lineage diversification, recombination and rearrangement and provides the basis for a novel sub-classification system.

Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5' or 3' end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.

Prevalence of hemoglobinopathies among Malayali tribes of Jawadhu hills, Tiruvannamalai district, Tamil Nadu, India: a community-based cross-sectional study.

BACKGROUND: Hemoglobin (Hb), a red pigment of red blood cells (RBCs), carries oxygen from the lungs to different organs of the body and transports carbon dioxide back to the lungs. Any fault present in the Hb structure leads to undesirable functional effects of the RBCs, such as sickle cell anemia (SCA), thalassemia, etc. Hemoglobinopathies affect around 7% of people in both developed and developing countries globally. The aim of the present study was to determine the prevalence and carrier frequencies of hemoglobinopathies including SCA, thalassemia, and other abnormal Hb variants among Malayali tribes in the Jawadhu hills of Tiruvannamalai district, Tamil Nadu, India. METHODS: A community-based cross-sectional study was carried out among 443 Malayali tribes inhabiting the Jawadhu hills of Tiruvannamalai district from July 2022 to September 2022. The RBC indices were analyzed using an automated 5-part hematology analyzer (Mindray, BC-5150) and hemoglobin fractions were done using the HPLC system (Bio-Rad, D-10) following standard protocols. FINDINGS: A total of 443 participants were screened, out of whom 14.67% had an abnormal Hb fraction, 83.30% were identified as normal, and 2.03% were borderline. Notably, the study revealed a prevalence of 0.68% for the α-thalassemia trait and 13.99% for the ß-thalassemia trait. INTERPRETATION: Haemoglobinopathies, specifically the ß-thalassemia trait, were most prevalent among the Malayali tribal population of Tamil Nadu residing in the Jawadhu hills of Tiruvannamalai district. Hence, we need special attention for creating awareness, increasing hemoglobinopathies screening programs, and improving the importance of tribal health conditions by the government and non-governmental organizations (NGOs) for the betterment of the ethnic tribes.

Picobirnavirus infections: viral persistence and zoonotic potential.

Picobirnaviruses (PBVs) are small, non-enveloped, bisegmented double-stranded RNA genomic viruses of vertebrate hosts. Since their discovery in the late 1980s in clinical specimens from outbreaks of acute gastroenteritis in children, significant efforts have been made to investigate the role of PBV in diarrheic diseases. PBV has been detected in sporadic episodes of diarrhea as sole pathogen or coinfection as well as in outbreaks of acute gastroenteritis and in immunocompromised patients with diarrhea. However, PBV is frequently detected in non-diarrheic healthy hosts, and prolonged shedding has been observed in some individuals. Of interest, similar patterns of PBV infection have also been observed in pigs and other animal hosts. The increasing amount of PBV sequence data gathered from molecular epidemiological studies has evidenced a great sequence diversity of PBVs in various hosts and environmental samples. Importantly, evidence has been found for genetic relatedness between human and animal PBV strains, suggesting extant crossing points in the ecology and evolution of heterologous PBV strains. At present, no cell culture and animal model exists for PBVs. Well-structured epidemiological studies are still the only alternative to demonstrate the potential etiological role of PBVs in acute gastroenteritis or other diseases. This review aims to analyze the public health aspects of PBV infection, especially its possible association with zoonosis.

Socio-demographic and behavioural determinants of HIV prevalence among homosexual and bisexual men having sex with men (MSM) in India: Integrated bio-behavioural surveillance.

Background: HIV prevalence among men who have sex with men (MSM) is 16.5 times higher than adult HIV prevalence. With a socio-cultural context that demands marriage, a considerable proportion of MSM in India have female sexual partners and act as a bridge population. Stratified analysis of HIV risk factors among homosexual and bisexual MSM will be instrumental in identifying the high-risk MSM. We aim to identify the socio-demographic and behavioural factors associated with HIV risk among homosexual and bisexual MSM. Methods: Overall, 23081 MSM were enrolled in the IBBS conducted across India between October 2014 and November 2015. Data and blood samples were collected. Chi-square test, univariate and multivariable logistic regression methods were used in data analysis. Results: HIV prevalence was significantly higher among homosexual MSM than bisexual MSM. Older age, lesser education, being a sex worker, being married, living with a male or hijra partner, younger age at initiation of MSM behaviour, duration, injecting drugs, and having STI symptoms were associated with higher prevalence. The prevalence of new homosexual MSM was 11.4%. Nearly 75% of the bisexual MSM reported inconsistent condom usage with female partners. Conclusion: Interventions for early identification of new MSM and advocacy for safe sex with alternative preventive techniques are recommended.

Clinical characteristics and novel mutations of omicron subvariant XBB in Tamil Nadu, India - a cohort study.

Background: Despite the continued vaccination efforts, there had been a surge in breakthrough infections, and the emergence of the B.1.1.529 omicron variant of SARS-CoV-2 in India. There is a paucity of information globally on the role of newer XBB variants in community transmission. Here, we investigated the mutational patterns among hospitalised patients infected with the XBB omicron sub-variant, and checked if there was any association between the rise in the number of COVID-19 cases and the observed novel mutations in Tamil Nadu, India. Methods: Nasopharyngeal and oropharyngeal swabs, collected from symptomatic and asymptomatic COVID-19 patients were subjected to real-time PCR followed by Next Generation Sequencing (NGS) to rule out the ambiguity of mutations in viruses isolated from the patients (n = 98). Using the phylogenetic association, the mutational patterns were used to corroborate clinico-demographic characteristics and disease severity among the patients. Findings: Overall, we identified 43 mutations in the S gene across 98 sequences, of which two were novel mutations (A27S and T747I) that have not been reported previously with XBB sub-variants in the available literature. Additionally, the XBB sequences from our cohort had more mutations than omicron B.1.1.529. The phylogenetic analysis comprising six major branches clearly showed convergent evolution of XBB. Our data suggests that age, and underlying conditions (e.g., diabetes, hypertension, and cardiovascular disease) or secondary complications confers increased susceptibility to infection rather than vaccination status or prior exposure. Many vaccinated individuals showed evidence of a breakthrough infection, with XBB.3 being the predominant variant identified in the study population. Interpretation: Our study indicates that the XBB variant is highly evasive from available vaccines and may be more transmissible, and potentially could emerge as the 'next' predominant variant, which likely could overwhelm the existing variants of SARS-CoV-2 omicron variants. Funding: National Health Mission (India), SIDASARC, VINNMER (Sweden), ORIP/NIH (USA).

Establishment and maintenance of persistent infection by picobirnavirus in greater rhea (Rhea Americana).

A study aimed to determine the infection model that picobirnavirus (PBV) established in birds was conducted in a farm of greater rheas in Córdoba, Argentina. Analysis of stools collected during a longitudinal study involving seven birds provided evidence that PBV is acquired very early in life and establishes a persistent infection in the host, which is characterized by intermingled periods of high, low and silent viral activity. Genomic analysis indicated that the rheas excreted virus with nucleotide sequence identity between 90.5-100 % and that more than one PBV strain with different electropherotype profiles could be involve in the infection. This report provides the first evidence of persistent infection of PBV in birds. The natural history of PBV infection has begun to be understood, and it appears that asymptomatic PBV-infected mammals and birds could persistently excrete the virus in stool samples, contributing to wide circulation of the virus in the environment.

Sickle cell anemia/sickle cell disease and pregnancy outcomes among ethnic tribes in India: an integrative mini-review.

Objective: To evaluate the studies which have reported the prevalence of maternal complications and outcomes for women with SCA/SCD. Healthy populations make a healthy community and improve the future for mankind. Pregnant women are an essential segment of humanity as they bear the fetus and supply nutrition for their development throughout the gestational period. Their health status and disease conditions also play a vital role in deciding the future of the offspring.Materials and methods: The Mesh terms: "Haemoglobinopathies" + "Sickle cell anemia" + "Sickle cell disease" + "Ethnic tribes" + "Pregnancy outcomes" + "India" were used to search the literature available from public databases such as "PubMed", "PubMed Central" "Google Scholar", "Science Direct" and "Scopus" and the same is checked for removing repetitions. The data was extracted and collected literature was thoroughly analysed. SCD/SCA is a commonly prevalent hereditary hemoglobinopathy disease and is related to augmented risk factors and premature mortality.Results: SCD severely affects pregnancy, which leads to the elevated occurrence of perinatal and maternal outcomes such as pre-eclampsia, eclampsia, abortions, intrauterine growth retardation (IUGR), etc., and sufficient care during the pregnancy guarantees an improved outcome. Due to the best health care conveniences, availability of drugs such as hydroxyurea, antibiotic prophylaxis, and vaccination, the life expectancy of SCD patients has greatly improved in recent times though directly related to the access and services available at the healthcare facilities for the needy and poor. Moreover, the latest innovations in the fields of prenatal screening and preimplantation genetic diagnosis (PGD), facilitate partners suffering from SCA/SCD to have a healthy child. There are no available studies on the prevalence of SCA/SCD in pregnant women among ethnic tribal populations from India.Conclusion: This review article is focused on the effects of SCA/SCD on pregnancy outcomes, the consistent follow-up, routine check-ups and successful management of complications throughout pregnancy, the various diagnostic methods toward preventive methods, curative and management therapeutic strategies and also defines the perinatal and maternal outcomes in the ethnic tribal populations of India.

Sub-regional Trend of HIV Infection Among Antenatal Clinic Attendees in Andhra Pradesh (2003-2019).

INTRODUCTION: The analyses of local risks at sub-national levels and tailored interventions are being emphasized for effective HIV management. Andhra Pradesh (AP) is a high HIV prevalence state in India, with the second-highest number of People with HIV (PWH) and a consistent decline in HIV prevalence at the state level. Probing further into the region and district-wise levels and trends of HIV prevalence will provide critical insights into sub-regional epidemic patterns. Hence, this paper analyzes the regional and district-level trends of HIV prevalence among pregnant women attending antenatal clinics (ANC) from 2003 to 2019 in AP, South India. METHODS: HIV prevalence data collected from pregnant women in AP during HIV Sentinel Surveillance (HSS) between 2003 and 2019 was used for trend analysis. The consistent sites were grouped into three regions (Coastal Andhra, Rayalaseema and Uttar Andhra), totaling 39 sites, including 21 rural and 18 urban sites. Regional and district-level HIV prevalence was analyzed using the Chisquare trend test, and spatial analysis was done using QGIS software. For the last three HSS rounds, HIV prevalence based on sociodemographic variables was calculated to understand the factors contributing to HIV positivity in each region. RESULTS: In total, 143,211 pregnant women were recruited. HIV prevalence in AP was 0.30% (95% CI: 0.22 - 0.39) in 2019. The prevalence was 0.31%, 0.35% and 0.22% in Coastal Andhra, Rayalaseema and Uttar Andhra, respectively. HIV prevalence had significantly (P < 0.05) declined in all regions. The overall trend indicated that the HIV prevalence was higher among older pregnant women and in urban regions. However, recent trends consistently report HIV positivity among young and new pregnant mothers, illiterates, and rural regions. CONCLUSION: The overall trend indicated that the HIV prevalence was higher among older pregnant women and in urban regions. However, recent trends consistently report HIV positivity among young and new pregnant mothers, illiterates, and rural regions. Identifying the contextual risk patterns associated with HIV transmission will further improve HIV preventive and management programs among the general population.

Diagnosis of Human Leptospirosis: Comparison of Microscopic Agglutination Test with Recombinant LigA/B Antigen-Based In-House IgM Dot ELISA Dipstick Test and Latex Agglutination Test Using Bayesian Latent Class Model and MAT as Gold Standard.

Leptospirosis is a spirochaetal infection that possesses a broad host range affecting almost all mammals. In the present study, the microscopic agglutination test (MAT) was compared with recombinant LigA/B antigen-based point-of-care diagnostics such as the in-house IgM dot ELISA dipstick test (IgM- DEDT) and the latex agglutination test (LAT) for the serodiagnosis of human leptospirosis. The comparison of the MAT with these two point-of-care diagnostics was performed using the MAT as the gold standard test and using Bayesian latent class modelling (BLCM), which considers all diagnostic tests as imperfect. The N-terminal conserved region of the LigA/B protein spanning the first to fifth big tandem repeat domains (rLigA/BCon1-5) was employed as a serodiagnostic marker in both of the bedside assays. A total of 340 serum samples collected from humans involved in high risk occupations were screened using the MAT, IgM DEDT and LAT. During the early phase of leptospirosis, BLCM analysis showed that the IgM DEDT and LAT had similar sensitivities (99.6 (96.0-100)) and (99.5 (95.2-100)), respectively, while the single acute phase MAT had the lowest sensitivity (83.3 (72.8-91.3)). Both the IgM DEDT and the LAT may be superior to the single acute phase MAT in terms of sensitivity during the early phase of infection and may be suitable for the early diagnosis of leptospirosis. However, BLCM analysis revealed that the use of both acute and convalescent samples substantially increased the sensitivity of the final MAT (98.2% (93.0-99.8%)) as a test to diagnose human leptospirosis. Both the IgM DEDT and LAT can be employed as bedside spot tests in remote locations where the MAT is not easily accessible.

Genogroup I picobirnavirus in diarrhoeic foals: can the horse serve as a natural reservoir for human infection?

Picobirnaviruses (PBV) are small, non-enveloped viruses with a bisegmented double-stranded RNA genome. In this study a PBV strain, PBV/Horse/India/BG-Eq-3/2010, was identified in the faeces of a 10 month old weaned female foal with diarrhoea in January 2010 from Kolkata, India. Surprisingly, sequence comparison and phylogenetic analysis of a short stretch of the RNA dependent RNA polymerase gene revealed close genetic relatedness (> 98% nucleotide identity) to a human genogroup I PBV strain (Hu/GPBV1) detected earlier from the same part of India. Our observations together with earlier findings on genetic relatedness between human and animal PBV warrant further studies on zoonotic potential.

Whole genome sequence analysis of multi drug resistant community associated methicillin resistant Staphylococcus aureus from food fish: detection of clonal lineage ST 28 and its antimicrobial resistance and virulence genes.

Methicillin-resistant staphylococcus aureus (MRSA) sequence type 28 (ST 28) and spa type t021 is a CC30, prototype of ST-30, Community Associated-MRSA (CA-MRSA) (lukS-lukF +). It is a multi-drug resistant strain harbouring staphylococcal endotoxins, haemolysins, ureolysin, serine protease, and antimicrobial resistance genes. In this study, we report the draft genome sequence of this MRSA isolated from the most commonly used food fish, ribbon fish (Trichiurus lepturus). The total number of assembled paired-end high-quality reads was 7,731,542 with a total length of  2.8Mb of 2797 predicted genes. The unique ST28/ t021 CA- MRSA in fish is the first report from India, and in addition to antibiotic resistance is known to co-harbour virulence genes, haemolysins, aureolysins and endotoxins. Comprehensive comparative genomic analysis of CA-MRSA strain7 can help further understand their diversity, genetic structure, diversity and a high degree of virulence to aid in fisheries management.

Epidemiology and pathobiology of SARS-CoV-2 (COVID-19) in comparison with SARS, MERS: An updated overview of current knowledge and future perspectives.

Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the causative etiology of 'Corona Virus Disease-2019' (COVID-19); formerly referred as 'novel-Coronavirus-2019'. It was originated in Wuhan city, Hubei province, China in early December 2019. The World Health Organization (WHO) declared it as 'Public Health Emergency of International Concern' due to their rapid transmission and causing public and health-care-related casualties worldwide. This review provides an updated overview of COVID-19 (SARS-CoV-2), in comparison with the etiologies of the same group viz. SARS and MERS and also its future perspectives for planning appropriate strategies for prevention, control and treatment modalities to avert similar catastrophe in near future.

Immunoinformatic Study of Recombinant LigA/BCon1-5 Antigen and Evaluation of Its Diagnostic Potential in Primary and Secondary Binding Tests for Serodiagnosis of Porcine Leptospirosis.

Leptospirosis is responsible for hampering the productivity of swine husbandry worldwide. The aim of this study was to assess the efficacy of bioinformatics tools in predicting the three-dimensional structure and immunogenicity of recombinant LigBCon1-5 (rLigBCon1-5) antigen. A battery of bioinformatics tools such as I-TASSER, ProSA and SAVES v6.0 were used for the prediction and assessment of the predicted structure of rLigBCon1-5 antigen. Bepipred-2.0, DiscoTope v2.0 and ElliPro servers were used to predict linear and conformational epitopes while T-cell epitopes were predicted using NetMHCpan 4.1 and IEDB recommended 2.22 method for MHC Class I and II peptides respectively. The results obtained using various in silico methods were then compared with wet lab experiments comprising of both primary (IgG Dot ELISA Dipstick test) and secondary-binding assays (Latex Agglutination Test [LAT]) to screen 1153 porcine serum samples. The three-dimensional structure of rLigA/BCon1-5 protein as predicted by I-TASSER was found to be reliable by Ramachandran Plot and ProSA. The ElliPro server suggested 10 and three potential linear and conformational B-cell-epitopes, respectively, on the peptide backbone of the rLigA/BCon1-5 protein. The DiscoTope prediction server suggested 47 amino acid residues to be part of B-cell antigen. Ten of the most efficient peptides for MHC-I and II grooves were predicted by NetMHCpan 4.1 and IEDB recommended 2.22 method, respectively. Of these, three peptides can serve dual functions as it can fit both MHC I and II grooves, thereby eliciting both humoral-and cell-mediated immune responses. The prediction of these computational approaches proved to be reliable since rLigBCon1-5 antigen-based IgG Dot ELISA Dipstick test and LAT gave results in concordance to gold standard test, the Microscopic Agglutination Test (MAT), for serodiagnosis of leptospirosis. Both the IgG Dot ELISA Dipstick test and LAT were serodiagnostic assays ideally suited for peripheral level of animal health care system as "point of care" tests for the detection of porcine leptospirosis.

SARS-CoV-2 Spike Protein Extrapolation for COVID Diagnosis and Vaccine Development.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) led to coronavirus disease 2019 (COVID-19) pandemic affecting nearly 71.2 million humans in more than 191 countries, with more than 1.6 million mortalities as of 12 December, 2020. The spike glycoprotein (S-protein), anchored onto the virus envelope, is the trimer of S-protein comprised of S1 and S2 domains which interacts with host cell receptors and facilitates virus-cell membrane fusion. The S1 domain comprises of a receptor binding domain (RBD) possessing an N-terminal domain and two subdomains (SD1 and SD2). Certain regions of S-protein of SARS-CoV-2 such as S2 domain and fragment of the RBD remain conserved despite the high selection pressure. These conserved regions of the S-protein are extrapolated as the potential target for developing molecular diagnostic techniques. Further, the S-protein acts as an antigenic target for different serological assay platforms for the diagnosis of COVID-19. Virus-specific IgM and IgG antibodies can be used to detect viral proteins in ELISA and lateral flow immunoassays. The S-protein of SARS-CoV-2 has very high sequence similarity to SARS-CoV-1, and the monoclonal antibodies (mAbs) against SARS-CoV-1 cross-react with S-protein of SARS-CoV-2 and neutralize its activity. Furthermore, in vitro studies have demonstrated that polyclonal antibodies targeted against the RBD of S-protein of SARS-CoV-1 can neutralize SARS-CoV-2 thus inhibiting its infectivity in permissive cell lines. Research on coronaviral S-proteins paves the way for the development of vaccines that may prevent SARS-CoV-2 infection and alleviate the current global coronavirus pandemic. However, specific neutralizing mAbs against SARS-CoV-2 are in clinical development. Therefore, neutralizing antibodies targeting SARS-CoV-2 S-protein are promising specific antiviral therapeutics for pre-and post-exposure prophylaxis and treatment of SARS-CoV-2 infection. We hereby review the approaches taken by researchers across the world to use spike gene and S-glycoprotein for the development of effective diagnostics, vaccines and therapeutics against SARA-CoV-2 infection the COVID-19 pandemic.