Retrospective phylogenetic analysis of circulating BA genotype of human respiratory syncytial virus with 60 bp duplication from New Delhi, India during 2007-2010

Reclassification of respiratory syncytial virus genotypes in India

Respiratory syncytial virus (RSV) is known to be the major cause of lower respiratory tract infections in infants and in the elderly. RSV was recently reclassified and simplified into three genotypes of the RSV-A subgroup (GA1-GA3) and into seven genotypes of the RSV-B subgroup (GB1-GB7). This classification strategy was not implemented globally. This study intended to reclassify the sequences that were submitted in GenBank till September 2021 from India. The gene sequences of the ectodomain region, second hypervariable region (SHR), and the partial second hypervariable region (PSHR) of the G gene were selected for the analysis. 25 ectodomain, 36 s hypervariable, and 19 partial second hypervariable regions of the RSV-A subgroup and 42-ectodomain, 49-s hypervariable region and 11-partial second hypervariable region of RSV-B subgroup were used for phylogenetic analysis. P-distance was calculated to support the genotype determination done by phylogenetic analysis. Phylogenetic analysis revealed that GA2.3.1, GA2.3.3, GA2.3.4, GA2.3.5, and GA2.3.6b lineages of GA2 genotype for RSV-A; and GB5.0.1, GB5.0.2, GB5.0.3, GB5.0.4a, GB5.0.4c, GB5.0.5a, GB5.0.5c lineages of GB5 genotype and GB7 genotype for RSV-B were that circulated in India. This work has implication for RSV vaccine research, and also for strategies for the prevention and control of RSV infection in humans.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-022-00802-x.

ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia

Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.

Respiratory syncytial virus among children hospitalized with severe acute respiratory infection in Kashmir, a temperate region in northern India

Background

Severe acute respiratory infections (SARI) are a leading cause of hospitalizations in children, especially due to viral pathogens. We studied the prevalence of respiratory viruses among children aged <5 years hospitalized with severe acute respiratory infections (SARI) in Kashmir, India.

Methods

We conducted a prospective observational study in two tertiary care hospitals from October 2013 to September 2014, systematically enrolling two children aged <5 years with SARI per day. We defined SARI as history of fever or measured fever (≥38°C) and cough with onset in the last 7 days requiring hospitalization for children aged 3-59 months and as physician-diagnosed acute lower respiratory infection for children aged <3 months. Trained study staff screened children within 24 hours of hospitalization for SARI and collected clinical data and nasopharyngeal swabs from enrolled participants. We tested for respiratory syncytial virus (RSV) A and B, influenza viruses, rhinoviruses (HRV)/enteroviruses, adenovirus (AdV), bocavirus (BoV), human metapneumovirus (hMPV) A and B, coronaviruses (OC43, NL65, C229E), and parainfluenza viruses (PIV) 1, 2, 3 and 4 using standardized duplex real-time polymerase chain reaction.

Results

Among 4548 respiratory illness admissions screened from October 2013 to September 2014, 1026 met the SARI case definition, and 412 were enrolled (ages = 5 days to 58 months; median = 12 months). Among enrolees, 256 (62%) were positive for any virus; RSV was the most commonly detected (n = 118, 29%) followed by HRV/enteroviruses (n = 88, 21%), PIVs (n = 31, 8%), influenza viruses (n = 18, 4%), BoV (n = 15, 4%), coronaviruses (n = 16, 4%), AdV (n = 14, 3%), and hMPV (n = 9, 2%). Fifty-four children had evidence of virus co-detection. Influenza-associated SARI was more common among children aged 1-5 years (14/18, 78%) while most RSV detections occurred in children <12 months (83/118, 70%). Of the RSV viruses typed (n = 116), the majority were type B (94, 80%). Phylogenetic analysis of G gene of RSV showed circulation of the BA9 genotype with 60bp nucleotide duplication.

Conclusions

Respiratory viruses, especially RSV, contributed to a substantial proportion of SARI hospitalizations among children <5 years in north India. These data can help guide clinicians on appropriate treatment and prevention strategies.

Molecular epidemiology of respiratory syncytial virus among children and adults in India 2016 to 2018

Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections among children less than 5 years of age and the elderly. This study intended to determine the circulating genotypes of RSV among severe acute respiratory illness (SARI) cases during the period 2016–2018 in India, among hospitalized acute febrile illness cases of age ranging from 1 to 65 years. Throat/nasopharyngeal swab samples were subjected for testing RSV and subgroups by real-time reverse transcriptase polymerase chain reaction (RT-PCR), further sequencing and phylogenetic analysis were performed for the second hypervariable region of the G gene. RSV-A and B subtypes co-circulated during the years 2016, 2017, and 2018, with RSV-A as the dominant subtype in 2016, and RSV-B as the dominant subgroup in 2017 and 2018. Phylogenetic analysis revealed that the circulating genotypes of RSV were GA2 (16/16), of RSV-A, and GB5 (23/23) of RSV-B in the South, North, and Northeast region of India during the period between 2016 and 2018. Here we report the first study comprising the distribution of RSV-A and B genotypes in the different geographic regions of India among children and adults during the year 2016 to 2018. We also report GA2.3.7 lineage of GA2 genotype for the first time in India to the best of our knowledge.

COVID-19 Pandemic and Vaccines Update on Challenges and Resolutions

The coronavirus disease (COVID-19) is caused by a positive-stranded RNA virus called severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), belonging to the Coronaviridae family. This virus originated in Wuhan City, China, and became the cause of a multiwave pandemic that has killed 3.46 million people worldwide as of May 22, 2021. The havoc intensified with the emergence of SARS-CoV-2 variants (B.1.1.7; Alpha, B.1.351; Beta, P.1; Gamma, B.1.617; Delta, B.1.617.2; Delta-plus, B.1.525; Eta, and B.1.429; Epsilon etc.) due to mutations generated during replication. More variants may emerge to cause additional pandemic waves. The most promising approach for combating viruses and their emerging variants lies in prophylactic vaccines. Several vaccine candidates are being developed using various platforms, including nucleic acids, live attenuated virus, inactivated virus, viral vectors, and protein-based subunit vaccines. In this unprecedented time, 12 vaccines against SARS-CoV-2 have been phased in following WHO approval, 184 are in the preclinical stage, and 100 are in the clinical development process. Many of them are directed to elicit neutralizing antibodies against the viral spike protein (S) to inhibit viral entry through the ACE-2 receptor of host cells. Inactivated vaccines, to the contrary, provide a wide range of viral antigens for immune activation. Being an intracellular pathogen, the cytotoxic CD8+ T Cell (CTL) response remains crucial for all viruses, including SARS-CoV-2, and needs to be explored in detail. In this review, we try to describe and compare approved vaccines against SARS-CoV-2 that are currently being distributed either after phase III clinical trials or for emergency use. We discuss immune responses induced by various candidate vaccine formulations; their benefits, potential limitations, and effectiveness against variants; future challenges, such as antibody-dependent enhancement (ADE); and vaccine safety issues and their possible resolutions. Most of the current vaccines developed against SARS-CoV-2 are showing either promising or compromised efficacy against new variants. Multiple antigen-based vaccines (multivariant vaccines) should be developed on different platforms to tackle future variants. Alternatively, recombinant BCG, containing SARS-CoV-2 multiple antigens, as a live attenuated vaccine should be explored for long-term protection. Irrespective of their efficacy, all vaccines are efficient in providing protection from disease severity. We must insist on vaccine compliance for all age groups and work on vaccine hesitancy globally to achieve herd immunity and, eventually, to curb this pandemic.

Disease Burden Due to Respiratory Syncytial Virus in Indian Pediatric Population: A Literature Review

Respiratory syncytial virus (RSV) is one of the leading causes of lower respiratory tract infections in young children. Globally, there is huge disease burden, high treatment cost, and health impact beyond acute episodes due to RSV which necessitate development and implementation of preventive strategies for the control of RSV infection. The disease burden due to RSV in pediatric population across India is still not clearly understood so this literature review was therefore conducted to gather data on disease burden due to RSV in Indian pediatric population. Systematic literature search was performed using PubMed and Google search with different medical subject headings from 2007 to 2020. Studies performed in Indian pediatric population were selected for review. Literature review revealed that in India, epidemiology of RSV infection is well documented in young children (0-5 years) as compared to children from other age groups. The rates of RSV detection in various studies conducted in younger children (0-5 years) vary from 2.1% to 62.4% in India which is higher as compared to children from other age groups. In India, RSV mainly peaks around rainy to early winter season, that is, during months of June through October while smaller peak was noted during December, January, and February. In 2020, higher RSV-associated disease burden was reported among children (<5 years) in low-income and lower-middle-income countries. Considering significant disease burden due to RSV in young Indian children, availability of RSV vaccine would be crucial to prevent RSV infections in children and its spread in the community.

COVID-19 and SARS-CoV-2 Variants: Current Challenges and Health Concern

The ongoing coronavirus disease 2019 (COVID-19) outbreak in Wuhan, China, was triggered and unfolded quickly throughout the globe by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The new virus, transmitted primarily through inhalation or contact with infected droplets, seems very contagious and pathogenic, with an incubation period varying from 2 to 14 days. The epidemic is an ongoing public health problem that challenges the present global health system. A worldwide social and economic stress has been observed. The transitional source of origin and its transport to humans is unknown, but speedy human transportation has been accepted extensively. The typical clinical symptoms of COVID-19 are almost like colds. With case fatality rates varying from 2 to 3 percent, a small number of patients may experience serious health problems or even die. To date, there is a limited number of antiviral agents or vaccines for the treatment of COVID-19. The occurrence and pathogenicity of COVID-19 infection are outlined and comparatively analyzed, given the outbreak's urgency. The recent developments in diagnostics, treatment, and marketed vaccine are discussed to deal with this viral outbreak. Now the scientist is concerned about the appearance of several variants over the globe and the efficacy of the vaccine against these variants. There is a need for consistent monitoring of the virus epidemiology and surveillance of the ongoing variant and related disease severity.

Respiratory syncytial virus infections in India: Epidemiology and need for vaccine

Respiratory syncytial virus (RSV) has been identified as a leading cause of lower respiratory tract infections in young children and elderly. It is an enveloped negative-sense RNA virus belonging to Genus Orthopneumovirus. The clinical features of RSV infection range from mild upper-respiratory-tract illnesses or otitis media to severe lower-respiratory-tract illnesses. Current estimates show that about 33.1 million episodes of RSV-acute lower respiratory infection (ALRI) occurred in young children in 2015, of these majority that is, about 30 million RSV-ALRI episodes occurred in low-middle-income countries. In India, the rates of RSV detection in various hospital- and community-based studies mostly done in children vary from 5% to 54% and from 8% to 15%, respectively. Globally, RSV epidemics start in the South moving to the North. In India, RSV mainly peaks in winter in North India and some correlation with low temperature has been observed. Different genotypes of Group A (GA2, GA5, NA1 and ON1) and Group B (GB2, SAB4 and BA) have been described from India. The burden of RSV globally has kept it a high priority for vaccine development. After nearly 50 years of attempts, there is still no licensed vaccine and challenges to obtain a safe and effective vaccine is still facing the scientific community. The data in this review have been extracted from PubMed using the keywords RSV and Epidemiology and India. The data have been synthesised by the authors.

BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics

Respiratory syncytial virus (RSV) is an important pathogen of global significance. The BA9 is one of the most predominant lineages of the BA genotype of group B RSV that has acquired a 60bp duplication in its G protein gene. We describe the local and global evolutionary dynamics of the second hyper variable region in the C- terminal of the G protein gene of the BA9 lineage. A total of 418 sequences (including 31 study and 387 GenBank strains) from 29 different countries were used for phylogenetic analysis. This analysis showed that the study strains clustered with BA (BA9 and BA8) and SAB4 genotype of group B RSV. We performed time-scaled evolutionary clock analyses using Bayesian Markov chain Monte Carlo methods. We also carried out glycosylation, selection pressure, mutational, entropy and Network analyses of the BA9 lineage. The time to the most recent common ancestor (tMRCA) of the BA genotype and BA9 lineage were estimated to be the years 1995 (95% HPD; 1987–1997) and 2000 (95% HPD; 1998–2001), respectively. The nucleotide substitution rate of the BA genotype [(4.58×10⁻³ (95% HPD; 3.89–5.29×10⁻³) substitution/site/year] was slightly faster than the BA9 lineage [4.03×10⁻³ (95% HPD; 4.65–5.2492×10⁻³)]. The BA9 lineage was categorized into 3 sub lineages (I, II and III) based on the Bayesian and Network analyses. The local transmission pattern suggested that BA9 is the predominant lineage of BA viruses that has been circulating in India since 2002 though showing fluctuations in its effective population size. The BA9 lineage established its global distribution with report from 23 different countries over the past 16 years. The present study augments our understanding of RSV infection, its epidemiological dynamics warranting steps towards its overall global surveillance.

Molecular characterization of human respiratory syncytial virus detected from central India

Human Respiratory syncytial virus (hRSV) is the major cause of respiratory tract infection in both children and adults, virtually all children acquire infection with hRSV by the age of 3 years. Two subgroups of the virus, hRSV-A and hRSV-B based on sequence variability of G protein gene are divided into 11 and 17 genotypes, respectively. Very limited data regarding circulating genotypes is available from India. This study aimed to detect and characterize the circulating genotype of hRSV from central India. Throat swabs collected from patient's having influenza like illness (ILI) were subjected to RT-PCR for diagnosis, further sequencing and phylogenetic analysis was performed using primers specific for C-terminal end of G gene. Out of 526 tested samples 62 (12%) were found positive, 90% cases were from children under 3-year age children. Both hRSV-A and hRSV-B were detected in equal proportions. Sequence analysis of 15 samples revealed circulation of genotypes NA1, ON1 of hRSV-A, and BA9 of hRSV-B. We advocate molecular surveillance of hRSV for better patient management and epidemiological monitoring.

Co-Circulation of 72bp Duplication Group A and 60bp Duplication Group B Respiratory Syncytial Virus (RSV) Strains in Riyadh, Saudi Arabia during 2014

Respiratory syncytial virus (RSV) is an important viral pathogen of acute respiratory tract infection (ARI). Limited data are available on molecular epidemiology of RSV from Saudi Arabia. A total of 130 nasopharyngeal aspirates were collected from children less than 5 years of age with ARI symptoms attending the Emergency Department at King Khalid University Hospital and King Fahad Medical City, Riyadh, Saudi Arabia between October and December, 2014. RSV was identified in the 26% of the hospitalized children by reverse transcriptase PCR. Group A RSV (77%) predominated during the study as compared to group B RSV (23%). The phylogenetic analysis of 28 study strains clustered group A RSV in NA1 and ON1 genotypes and group B viruses in BA (BA9) genotype. Interestingly, 26% of the positive samples clustered in genotypes with duplication in the G protein gene (ON1 for group A and BA for group B). Both the genotypes showed enhanced O-linked glycosylation in the duplicated region, with 10 and 2 additional sites in ON1 and BA respectively. Selection pressure analysis revealed purifying selection in both the ON1 and BA genotypes. One codon each in the ON1 (position 274) and BA genotypes (position 219) were positively selected and had high entropy values indicating variations at these amino acid positions. This is the first report describing the presence of ON1 genotype and the first report on co-circulation of two different genotypes of RSV with duplication in the G protein gene from Saudi Arabia. The clinical implications of the simultaneous occurrence of genotypes with duplication in G protein gene in a given population especially in the concurrent infections should be investigated in future. Further, the ongoing surveillance of RSV in this region will reveal the evolutionary trajectory of these two genotypes with duplication in G protein gene from largest country in the Middle East.