ABSTRACT
Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks. One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.
ABSTRACT
The progression of the SARS-CoV-2 pandemic in Africa has so far been heterogeneous and the full impact is not yet well understood. Here, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations, predominantly from Europe, which diminished following the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1 and C.1.1. Although distorted by low sampling numbers and blind-spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a breeding ground for new variants.
ABSTRACT
The COVID-19 vaccination efficacy depends on serum production level of the neutralizing IgG antibody (NA) specific to the receptor binding domain of SARS-Cov-2 spike protein. Therefore, a high-throughput rapid assay to measure the total SARS-CoV-2 NA level is urgently needed for COVID-19 serodiagnosis, convalescent plasma therapy, vaccine development, and assessment. Here, we developed a nanoplasmonic immunosorbent assay (NanoPISA) platform for one-step rapid quantification of SARS-CoV-2 NAs in clinical serum samples for high-throughput evaluation of COVID-19 vaccine effectiveness. The NanoPISA platform enhanced by the use of nanoporous hollow gold nanoparticle coupling was able to detect SARS-CoV-2 NAs with a limit of detection of 0.1 ng/mL within 15 min. The one-step NanoPISA for SARS-CoV-2 NA detection in clinical specimens yielded good results, comparable to those obtained in the gold standard seroneutralization test and the surrogate virus neutralizing ELISA. Collectively, our findings indicate that the one-step NanoPISA may offer a rapid and high-throughput NA quantification platform for evaluating the effectiveness of COVID-19 vaccines.
ABSTRACT
Picobirnavirus (PBV) is recognized as a putative cause of diarrhea and respiratory illnesses. Although PBV has been reported in several mammalian (including humans) and avian host species, data pertaining to its presence in small ruminants are limited. We report, here, PBV infection in small ruminants (ovine and caprine), in India. From January 2015 to December 2017, 400 samples were tested for the presence of PBV, using an RT-PCR assay specific for the genome segment-2. The overall rate of PBV infection was 35.75% (143/400), being higher in caprines (42.35%, 83/196) than in ovines (29.42%, 60/204). Viral genogrouping showed the predominance of PBV genogroup I (GG-I; 53.15%, 76/173), the detection of genogroup II (GG-II; 3.49%, 5/143), a concomitant infection with GG-I and GG-II (38.47%, 55/143), and un-typeable strains (4.9%, 7/143). Of note, these PBV strains exhibit low sequence identity (11.2% to 70.7%) to other reported PBV isolates from humans and other animals. By phylogenetic analysis, camel PBV isolates from the United Arab Emirates (UAE) and the reference human GG-I strain (1-CHN-97) from China were found to be the nearest neighbors of PBV strains. Furthermore, sequence analysis revealed the possible appearance of a new genogroup/genetic cluster and the existence of high genetic heterogeneity in the circulating PBV strains. Although much remains to be understood about the epidemiology and impact of PBV, the present study demonstrates the high prevalence of GG-I, the detection of GG-II, and the possible emergence of new genogroup/genetic cluster in small ruminant populations in India.
Subject(s)
Goat Diseases/virology , Picobirnavirus/genetics , RNA Virus Infections/veterinary , Sheep Diseases/virology , Animals , Goat Diseases/epidemiology , Goats , India/epidemiology , Phylogeny , RNA Virus Infections/epidemiology , RNA Virus Infections/virology , Sheep , Sheep Diseases/epidemiologyABSTRACT
All over the world, children and adults are severely affected by acute gastroenteritis, caused by one of the emerging enteric pathogens, rotavirus C (RVC). At present, no extensive surveillance program is running for RVC in India, and its prevalence is largely unknown except cases of local outbreaks. Here, we intended to detect the presence of RVC in diarrheic children visiting or admitted to hospitals in Haldwani (state of Uttarakhand, India), a city located in the foothills of the Himalayas. During 2010-2013, we screened 119 samples for RVC by an RVC VP6 gene-specific RT-PCR. Of these, 38 (31.93%) were found positive, which is higher than the incidence rates reported so far from India. The phylogenetic analysis of the derived nucleotide sequences from one of the human RVC (HuRVC) isolates, designated as HuRVC/H28/2013/India, showed that the study isolate belongs to genotype I2, P2 and E2 for RVC structural genes 6 and 4 (VP6, and VP4) and non-structural gene 4 (NSP4), respectively. Furthermore, the VP6 gene of HuRVC/H28/2013/India shows the highest similarity to a recently-reported human-like porcine RVC (PoRVC/ASM140/2013/India, KT932963) from India suggesting zoonotic transmission. We also report a full-length NSP4 gene sequence of human RVC from India. Under the One-health platforms there is a need to launch combined human and animal RVC surveillance programs for a better understanding of the epidemiology of RVC infections and for implementing control strategies.Reoviridae, possess 11 double-stranded segments of RNA that encode six structural viral proteins (VP1, VP2, VP3, VP4, VP6, VP7) and five/six non-structural proteins (NSP1-NSP5/6) [7]. Based on the antigenic properties of the major inner capsid protein (VP6), RVs are subdivided into eight well-characterized species (A-H) and two putative species viz. I and J [8-10]. Humans and other mammalian species are affected by species A, B, C and H rotaviruses and birds by species D, F and G, and species E has been reported exclusively in pigs [7,8,11-17]. The newly-proposed species I is reported in dogs [18] and cats [19], whereas species J is found in bats [10].
ABSTRACT
BACKGROUND/AIMS: There is increasing evidence for the effect of rs12979860 IL28B polymorphism in response to the standard treatment PEG-IFN/RBV (i.e. combination of pegylated interferon and ribavirin) in chronic hepatitis C virus (HCV) infection. The present study aimed to determine the impact of IL28B associations in interferon responsiveness in 187 Moroccan patients with chronic HCV infection. METHODS: HCV RNA levels were measured with a real-time RT-PCR assay and treatment efficacy was assessed by sustained virological response (SVR) and patients were classified as responders or non-responders. IL28B rs12979860 polymorphism genotyping was achieved by PCR-HRM technique. RESULTS: The results demonstrated that SVR was achieved in 102 patients (55%); while 69 were non-responders (37%) and 16 relapsed (8%). Genotype 1 was the predominant HCV genotype detected in 112 patients followed by genotype 2 in 56 patients. The genotype CC was observed in 42 cases (25%); CT in 69 (41%) and TT in 57 (34%) demonstrating a C allele frequency of 46%. The SVR was observed in 32 patients with genotype CC accounting for 76%. The frequencies of rs12979860 CC type in infected individuals with HCV genotype 1 were 47% and 12% respectively in SVR and non-SVR groups. A highly statistically significant association between this SNP and SVR was found (p<0.001). Using multivariate logistic regression analysis, CC genotype was an independent factor for SVR. In the group of patients infected with genotype 2, SVR rate was 79%. The frequency of rs12979860 CC type in SVR group (n=4) was 9% and rs12979860 non-CC genotype was highly associated with SVR (p=0.001). CONCLUSION: This finding adds evidence that genotyping for the IL-28B rs12979860 SNP can be a good parameter for the prediction of treatment success in patients with chronic hepatitis C before initiation of antiviral therapy in Morocco.
