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Article ; Online: Development of a Real-Time Reverse Transcription-PCR Assay To Detect and Quantify Group A Rotavirus Equine-Like G3 Strains.

Katz, Eric M / Esona, Mathew D / Gautam, Rashi / Bowen, Michael D

2021 Volume 59, Issue 11, Page(s) e0260220

Abstract: Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant "equine-like G3" strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step ... ...

Abstract	Since 2013, group A rotavirus strains characterized as novel DS-1-like intergenogroup reassortant "equine-like G3" strains have emerged and spread across 5 continents among human populations in at least 14 countries. Here, we report a novel one-step TaqMan quantitative real-time reverse transcription-PCR assay developed to genotype and quantify the viral load for samples containing rotavirus equine-like G3 strains. Using a universal G forward primer and a newly designed reverse primer and TaqMan probe, we developed and validated an assay with a linear dynamic range of 227 to 2.3 × 10
MeSH term(s)	Animals ; Feces ; Genotype ; Horses ; Humans ; Phylogeny ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction ; Reverse Transcription ; Rotavirus/genetics ; Rotavirus Infections/diagnosis ; Rotavirus Infections/veterinary
Chemical Substances	RNA, Viral
Language	English
Publishing date	2021-08-25
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.02602-20
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Article ; Online: Genetic diversity of G9, G3, G8 and G1 rotavirus group A strains circulating among children with acute gastroenteritis in Vietnam from 2016 to 2021.

Le, Ly K T / Chu, Mai N T / Tate, Jacqueline E / Jiang, Baoming / Bowen, Michael D / Esona, Mathew D / Gautam, Rashi / Jaimes, Jose / Pham, Thao P T / Huong, Nguyen T / Anh, Dang D / Trang, Nguyen V / Parashar, Umesh

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2024 Volume 118, Page(s) 105566

Abstract: Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 2021, we conducted ... ...

Abstract	Rotavirus group A (RVA) is the most common cause of severe childhood diarrhea worldwide. The introduction of rotavirus vaccination programs has contributed to a reduction in hospitalizations and mortality caused by RVA. From 2016 to 2021, we conducted surveillance to monitor RVA prevalence and genotype distribution in Nam Dinh and Thua Thien Hue (TT Hue) provinces where a pilot Rotavin-M1 vaccine (Vietnam) implementation took place from 2017 to 2020. Out of 6626 stool samples, RVA was detected in 2164 (32.6%) by ELISA. RT-PCR using type-specific primers were used to determine the G and P genotypes of RVA-positive specimens. Whole genome sequences of a subset of 52 specimens randomly selected from 2016 to 2021 were mapped using next-generation sequencing. From 2016 to 2021, the G9, G3 and G8 strains dominated, with detected frequencies of 39%, 23%, and 19%, respectively; of which, the most common genotypes identified were G9P[8], G3P[8] and G8P[8]. G1 strains re-emerged in Nam Dinh and TT Hue (29.5% and 11.9%, respectively) from 2020 to 2021. G3 prevalence decreased from 74% to 20% in TT Hue and from 21% to 13% in Nam Dinh province between 2017 and 2021. The G3 strains consisted of 52% human typical G3 (hG3) and 47% equine-like G3 (eG3). Full genome analysis showed substantial diversity among the circulating G3 strains with different backgrounds relating to equine and feline viruses. G9 prevalence decreased sharply from 2016 to 2021 in both provinces. G8 strains peaked during 2019-2020 in Nam Dinh and TT Hue provinces (68% and 46%, respectively). Most G8 and G9 strains had no genetic differences over the surveillance period with very high nucleotide similarities of 99.2-99.9% and 99.1-99.7%, respectively. The G1 strains were not derived from the RVA vaccine. Changes in the genotype distribution and substantial diversity among circulating strains were detected throughout the surveillance period and differed between the two provinces. Determining vaccine effectiveness against circulating strains over time will be important to ensure that observed changes are due to natural secular variation and not from vaccine pressure.
MeSH term(s)	Child ; Animals ; Humans ; Cats ; Horses/genetics ; Rotavirus/genetics ; Rotavirus Infections ; Vietnam/epidemiology ; Genome, Viral ; Phylogeny ; Gastroenteritis/epidemiology ; Diarrhea/epidemiology ; Genotype ; Vaccines ; Genetic Variation ; Feces
Chemical Substances	Vaccines
Language	English
Publishing date	2024-02-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2024.105566
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Zs.A 5645: Show issues

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Article ; Online: Low fecal rotavirus vaccine virus shedding is significantly associated with non-secretor histo-blood group antigen phenotype among infants in northern Pretoria, South Africa.

Magwira, Cliff A / Kgosana, Lerato P / Esona, Mathew D / Seheri, Mapaseka L

Vaccine

2020 Volume 38, Issue 52, Page(s) 8260–8263

Abstract: Histo-blood group antigens are recognized by rotaviruses in a P- genotype dependent manner and their frequency in a population can influence fecal virus shedding. This study investigated the rate of fecal shedding of Rotarix vaccine and its association ... ...

Abstract	Histo-blood group antigens are recognized by rotaviruses in a P- genotype dependent manner and their frequency in a population can influence fecal virus shedding. This study investigated the rate of fecal shedding of Rotarix vaccine and its association with HBGA phenotype distribution in South Africa. Stool and saliva specimens were collected from 150 infants attending immunization on the day of both first and second doses and 7 days later. Virus shedding was detected by real-time qPCR while HBGA phenotypes in saliva were determined by enzyme linked immunosorbent assay. Vaccine virus shedding was higher (23.6%) after the first dose than the second dose (4.7%). About 77% of virus-shedding infants were secretors (OR = 129; 95% CI, 6.088 - 2733), compared with none of non-virus shedding infants. Non-secretor status was significantly associated with low vaccine virus shedding while the likelihood of shedding was significantly higher in secretors.
MeSH term(s)	Blood Group Antigens ; Feces ; Humans ; Infant ; Phenotype ; Rotavirus/genetics ; Rotavirus Infections/prevention & control ; Rotavirus Vaccines ; South Africa ; Virus Shedding
Chemical Substances	Blood Group Antigens ; Rotavirus Vaccines
Language	English
Publishing date	2020-11-16
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2020.11.025
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Zs.A 1930: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 458: Show issues

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Article ; Online: Rotavirus.

Esona, Mathew D / Gautam, Rashi

Clinics in laboratory medicine

2015 Volume 35, Issue 2, Page(s) 363–391

Abstract: Group A rotavirus (RVA) is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live, attenuated rotavirus vaccines, Rotarix® and RotaTeq®, has dramatically reduced RVA-associated AGE and mortality. High- ... ...

Abstract	Group A rotavirus (RVA) is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live, attenuated rotavirus vaccines, Rotarix® and RotaTeq®, has dramatically reduced RVA-associated AGE and mortality. High-throughput, sensitive and specific techniques are required to rapidly diagnose and characterize rotavirus strains in stool samples for proper patient treatment and to monitor circulating vaccine and wild-type rotavirus strains. New molecular assays are rapidly developed that are more sensitive and specific than the conventional assays for detection, genotyping and full genome characterization of circulating rotavirus wild-type and vaccine (Rotarix® and RotaTeq®) strains causing AGE.
MeSH term(s)	Agglutination Tests ; Gastroenteritis/diagnosis ; Gastroenteritis/epidemiology ; Gastroenteritis/virology ; Genotyping Techniques ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoenzyme Techniques ; Real-Time Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Rotavirus/classification ; Rotavirus/isolation & purification ; Rotavirus/physiology ; Rotavirus Infections/diagnosis ; Rotavirus Infections/epidemiology ; Rotavirus Infections/virology ; Sequence Analysis, RNA ; Virus Cultivation/methods
Language	English
Publishing date	2015-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	604580-7
ISSN	1557-9832 ; 0272-2712
ISSN (online)	1557-9832
ISSN	0272-2712
DOI	10.1016/j.cll.2015.02.012
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Zs.A 1695: Show issues

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Article: Low fecal rotavirus vaccine virus shedding is significantly associated with non-secretor histo-blood group antigen phenotype among infants in northern Pretoria, South Africa

Magwira, Cliff A / Kgosana, Lerato P / Esona, Mathew D / Seheri, Mapaseka L

Vaccine. 2020 Dec. 14, v. 38, no. 52

2020

Abstract	Histo-blood group antigens are recognized by rotaviruses in a P- genotype dependent manner and their frequency in a population can influence fecal virus shedding. This study investigated the rate of fecal shedding of Rotarix vaccine and its association with HBGA phenotype distribution in South Africa. Stool and saliva specimens were collected from 150 infants attending immunization on the day of both first and second doses and 7 days later. Virus shedding was detected by real-time qPCR while HBGA phenotypes in saliva were determined by enzyme linked immunosorbent assay. Vaccine virus shedding was higher (23.6%) after the first dose than the second dose (4.7%). About 77% of virus-shedding infants were secretors (OR = 129; 95% CI, 6.088 – 2733), compared with none of non-virus shedding infants. Non-secretor status was significantly associated with low vaccine virus shedding while the likelihood of shedding was significantly higher in secretors.
Keywords	Rotavirus ; antigens ; enzymes ; genotype ; immunization ; phenotype ; saliva ; vaccines ; viruses ; South Africa
Language	English
Dates of publication	2020-1214
Size	p. 8260-8263.
Publishing place	Elsevier Ltd
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2020.11.025
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Zs.A 1930: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Correlates of Rotavirus Vaccine Shedding and Seroconversion in a U.S. Cohort of Healthy Infants.

Burke, Rachel M / Payne, Daniel C / McNeal, Monica / Conrey, Shannon C / Burrell, Allison R / Mattison, Claire P / Casey-Moore, Mary C / Mijatovic-Rustempasic, Slavica / Gautam, Rashi / Esona, Mathew D / Thorman, Alexander W / Bowen, Michael D / Parashar, Umesh D / Tate, Jacqueline E / Morrow, Ardythe L / Staat, Mary A

The Journal of infectious diseases

2024

Abstract: Background: Rotavirus is a leading cause of severe pediatric gastroenteritis; two highly effective vaccines are used in the US. We aimed to identify correlates of immune response to rotavirus vaccination in a US cohort.: Methods: PREVAIL is a birth ... ...

Abstract	Background: Rotavirus is a leading cause of severe pediatric gastroenteritis; two highly effective vaccines are used in the US. We aimed to identify correlates of immune response to rotavirus vaccination in a US cohort. Methods: PREVAIL is a birth cohort of 245 mother-child pairs enrolled 2017-2018 and followed for 2 years. Infant stool samples and symptom information were collected weekly. Shedding was defined as RT-PCR detection of rotavirus vaccine virus in stools collected 4-28 days after dose one. Seroconversion was defined as a threefold rise in IgA between the six-week and six-month blood draws. Correlates were analyzed using generalized estimating equations and logistic regression. Results: Pre-vaccination IgG (OR=0.84, 95% CI [0.75-0.94] per 100-unit increase) was negatively associated with shedding. Shedding was also less likely among infants with a single-nucleotide polymorphism inactivating FUT2 antigen secretion ("non-secretors") with non-secretor mothers, versus all other combinations (OR 0.37 [0.16-0.83]). Of 141 infants with data, 105 (74%) seroconverted; 78 (77%) had shed vaccine virus following dose one. Pre-vaccination IgG and secretor status were significantly associated with seroconversion. Neither shedding nor seroconversion significantly differed by vaccine product. Discussion: In this US cohort, pre-vaccination IgG and maternal and infant secretor status were associated with rotavirus vaccine response.
Language	English
Publishing date	2024-02-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiae055
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Uh II Zs.50: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
Zs.MO 445: Show issues

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Article: Next-generation sequencing of human respiratory syncytial virus subgroups A and B genomes

Wang, Lijuan / Ng, Terry Fei Fan / Castro, Christina J. / Marine, Rachel L. / Magaña, Laura C. / Esona, Mathew / Peret, Teresa C.T. / Thornburg, Natalie J.

Journal of virological methods. 2022 Jan., v. 299

2022

Abstract: Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic ... ...

Abstract	Human respiratory syncytial virus (HRSV) is a leading cause of acute respiratory illness in young children worldwide. Whole genome sequencing of HRSV offers enhanced resolution of strain variability for epidemiological surveillance and provides genomic information essential for antiviral and vaccine development. A 10-amplicon one-step RT-PCR assay and a 20-amplicon nested RT-PCR assay with enhanced sensitivity were developed to amplify whole HRSV genomes from samples containing high and low viral loads, respectively. Ninety-six HRSV-positive samples comprised of 58 clinical specimens and 38 virus isolates with Cₜ values ≤ 24 were amplified successfully using the 10-amplicon one-step RT-PCR method and multiplexed in a single MiSeq run. Genome coverage exceeded 99.3% for all 96 samples. The 20-amplicon nested RT-PCR NGS method was used to generate >99.6% HRSV full-length genome for 72 clinical specimens with Cₜ values ranging from 24 to 33. Phylogenetic analysis of the genome sequences obtained from the 130 clinical specimens revealed a wide diversity of HRSV genotypes demonstrating methodologic robustness.
Keywords	Human orthopneumovirus ; genome ; genomics ; monitoring ; phylogeny ; respiratory tract diseases ; strain differences ; vaccine development ; viruses
Language	English
Dates of publication	2022-01
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114335
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Article ; Online: Using genomics to improve preparedness and response of future epidemics or pandemics in Africa.

Chaguza, Chrispin / Nyaga, Martin M / Mwenda, Jason M / Esona, Mathew D / Jere, Khuzwayo C

The Lancet. Microbe

2020 Volume 1, Issue 7, Page(s) e275–e276

MeSH term(s)	Africa/epidemiology ; Forecasting ; Genomics ; Pandemics/prevention & control
Language	English
Publishing date	2020-12-17
Publishing country	England
Document type	Journal Article
ISSN	2666-5247
ISSN (online)	2666-5247
DOI	10.1016/S2666-5247(20)30169-5
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Article: The Evolution of Post-Vaccine G8P[4] Group a Rotavirus Strains in Rwanda; Notable Variance at the Neutralization Epitope Sites.

Mwangi, Peter N / Potgieter, Robyn-Lee / Uwimana, Jeannine / Mutesa, Leon / Muganga, Narcisse / Murenzi, Didier / Tusiyenge, Lisine / Mwenda, Jason M / Mogotsi, Milton T / Rakau, Kebareng / Esona, Mathew D / Steele, A Duncan / Seheri, Mapaseka L / Nyaga, Martin M

Pathogens (Basel, Switzerland)

2023 Volume 12, Issue 5

Abstract: Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in ... ...

Abstract	Africa has a high level of genetic diversity of rotavirus strains, which is suggested to be a possible reason contributing to the suboptimal effectiveness of rotavirus vaccines in this region. One strain that contributes to this rotavirus diversity in Africa is the G8P[4]. This study aimed to elucidate the entire genome and evolution of Rwandan G8P[4] strains. Illumina sequencing was performed for twenty-one Rwandan G8P[4] rotavirus strains. Twenty of the Rwandan G8P[4] strains had a pure DS-1-like genotype constellation, and one strain had a reassortant genotype constellation. Notable radical amino acid differences were observed at the neutralization sites when compared with cognate regions in vaccine strains potentially playing a role in neutralization escape. Phylogenetic analysis revealed that the closest relationship was with East African human group A rotavirus (RVA) strains for five of the genome segments. Two genome sequences of the NSP4 genome segment were closely related to bovine members of the DS-1-like family. Fourteen VP1 and eleven VP3 sequences had the closest relationships with the RotaTeq™ vaccine WC3 bovine genes. These findings suggest that the evolution of VP1 and VP3 might have resulted from reassortment events with RotaTeq™ vaccine WC3 bovine genes. The close phylogenetic relationship with East African G8P[4] strains from Kenya and Uganda suggests co-circulation in these countries. These findings highlight the need for continued whole-genomic surveillance to elucidate the evolution of G8P[4] strains, especially after the introduction of rotavirus vaccination.
Language	English
Publishing date	2023-04-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens12050658
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Article ; Online: Genomic Analysis of G2P[4] Group A Rotaviruses in Zambia Reveals Positive Selection in Amino Acid Site 7 of Viral Protein 3.

Mwangi, Peter N / Potgieter, Robyn-Lee / Simwaka, Julia / Mpabalwani, Evans M / Mwenda, Jason M / Mogotsi, Milton T / Magagula, Nonkululeko / Esona, Mathew D / Steele, A Duncan / Seheri, Mapaseka L / Nyaga, Martin M

Viruses

2023 Volume 15, Issue 2

Abstract: The G2P[4] genotype is among the rotavirus strains that circulate commonly in humans. Several countries have reported its immediate upsurge after the introduction of rotavirus vaccination, raising concern about sub-optimal vaccine effectiveness against ... ...

Abstract	The G2P[4] genotype is among the rotavirus strains that circulate commonly in humans. Several countries have reported its immediate upsurge after the introduction of rotavirus vaccination, raising concern about sub-optimal vaccine effectiveness against this genotype in the long term. This study aimed to gain insight into the evolution of post-vaccine Zambian G2P[4] group A rotavirus (RVA) strains and their overall genetic make-up by analysis of sequence alignments at the amino acid (AA) level. Twenty-nine Zambian G2P[4] rotavirus strains were subjected to whole-genome sequencing using the Illumina MiSeq
MeSH term(s)	Humans ; Amino Acids ; Genomics ; Phylogeny ; Rotavirus/genetics ; Zambia/epidemiology ; Viral Proteins/genetics
Chemical Substances	Amino Acids ; Viral Proteins
Language	English
Publishing date	2023-02-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15020501
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