Diversity and transboundary mobility of serotype O foot-and-mouth disease virus in East Africa: Implications for vaccination policies

Foot-and-mouth disease (FMD) virus serotype O has been responsible for most reported outbreaks of the disease in East Africa. A sustained campaign for the past 40 years to control FMD mainly by vaccination, combined with quarantine and zoosanitary measures has been undertaken with limited success. We investigated the genetic relationships among serotype O strains in eastern Africa using complete VP1 coding region sequences obtained from 46 FMD virus isolates collected in Kenya in the years 1964–2008 and 8 Ugandan isolates collected between 1999 and 2006. In addition, 21 selected FMDV sequences from Genbank representing reference strains from eastern Africa and elsewhere were included in the Bayesian inference analyses and the detection of selection forces. The results confirmed previous observations that eastern Africa harbours four distinct topotypes (clades with >15% sequence divergence). All but one strain isolated post-2000 belonged to topotypes EA-2, EA-3 and EA-4, while all three vaccines have been based on strains in the EA-1 topotype. The estimated dN/dS ratios across the individual codons of the entire VP1 coding region revealed that purifying (negative) selection constituted the dominant evolutionary force. Cross-border disease transmission within the region has been suggested with probable incursions of topotypes EA-3 and EA-4 into Kenya and Uganda from neighboring Ethiopia and Sudan. We conclude that the vaccines have probably been effective in controlling EA-1, but less so for the other topotypes and propose a more comprehensive representation of topotypes in the development of new vaccines in recognition of the considerable diversity and transboundary nature of serotype O.     

Pandemic strain of foot-and-mouth disease virus serotype O

A particular genetic lineage of foot-and-mouth disease virus (FMDV) serotype O, which we have named the PanAsia strain, was responsible for an explosive pandemic in Asia and extended to parts of Africa and Europe from 1998 to 2001. In 2000 and 2001, this virus strain caused outbreaks in the Republic of Korea, Japan, Russia, Mongolia, South Africa, the United Kingdom, Republic of Ireland, France, and the Netherlands, countries which last experienced FMD outbreaks decades before (ranging from 1934 for Korea to 1984 for the Netherlands). Although the virus has been controlled in all of these normally FMD-free or sporadically infected countries, it appears to be established throughout much of southern Asia, with geographically separated lineages evolving independently. A pandemic such as this is a rare phenomenon but demonstrates the ability of newly emerging FMDV strains to spread rapidly throughout a wide region and invade countries previously free from the disease.     

Efficacy of a high-potency multivalent foot-and-mouth disease virus vaccine in cattle against heterologous challenge with a field virus from the emerging A/ASIA/G-VII lineage

In 2015, outbreaks of foot-and-mouth disease (FMD) in the Middle East were discovered to be caused by a viral lineage (A/ASIA/G-VII), which has recently emerged from the Indian sub-continent. In vitro vaccine matching data generated by the World Reference Laboratory (WRLFMD) indicated that A/ASIA/G-VII field viruses were poorly matched with vaccines (A-SAU-95, A22 IRQ and A-IRN-05) that are already used in the region. In order to assess the likely performance of one of these commercially available FMD vaccines, sixteen cattle were vaccinated with a polyvalent vaccine which contained two serotype A components (A-SAU-95 and A-IRN-05) with a homologous potency of at least 6PD₅₀, and two cattle were left unvaccinated as controls. Twenty-one days later, all 18 cattle were challenged by tongue inoculation with an FMDV field isolate A/IRN/22/2015 from the A/ASIA/G-VII lineage, in line with the European Pharmacopeia PPG test conditions. The two control animals developed generalised FMD, and 7/16 vaccinated animals developed at least one foot lesion, thus only 56.3% were defined as protected. For the vaccine components, there was a significant increase in the probability of protection with increasing serological titres for A-SAU-95 (p = 0.03), but not for A-IRN-05 (p = 0.42). Analysis of FMDV in blood and nasal swabs suggested that vaccination reduced shedding and potential onward spread of FMD virus even if the animal developed foot lesions. In summary, the results from this study suggest that whilst this vaccine would not be appropriate for use in an emergency situation (in previously FMD-free countries), it may be partially effective in the field in endemic countries where repeat prophylactic vaccination is practiced. For emergency reactive vaccination, the findings from this study support the idea that a new vaccine strain should be developed that is tailored to the A/ASIA/G-VII lineage.     

Genetic and antigenic relationship of foot–and–mouth disease virus serotype O isolates with the vaccine strain O1/BFS

Foot–and–mouth disease serotype O viruses (FMDV/O) are responsible for the most outbreaks in FMD endemic countries. O1/BFS is one of the recommended FMD/O vaccine strains by World Reference Laboratory for FMD. In the current study, FMDV/O1 BFS vaccine strain and serotype O field isolates (45) were analyzed phylogenetically and antigenically to gain more insight into the genetic and antigenic characteristics of the vaccine strain and field isolates.O1/BFS showed similarity with 89% of the field isolates using a virus neutralization test (VNT). The P1 region encoding the FMDV capsid was sequenced and analysed for 46 strains of FMDV/O. Phylogenetic analysis showed these viruses originated from five continents and covered eight of 11 reported topotypes. Five isolates that demonstrated low antigenic similarities with O1/BFS were analyzed for their antigenic variation at the known neutralizing antigenic sites. Three of the five isolates demonstrated unique amino acid substitutions at various antigenic sites. No unique amino acid substitutions were observed for the other two unmatched isolates. Positively selected residues were identified on the surface of the FMD virus capsid supporting that it is important to continuously monitor field isolates for their antigenic and phenotypic changes.In conclusion, the vaccine strain O1/BFS is likely to confer protection against 89% of the 45 FMDV/O isolates based on VNT. Thus O1/BFS vaccine strain is still suitable for use in global FMD serotype O outbreak control. Combining data from phylogenetic, molecular and antigenic analysis can provide improvements in the process of vaccine selection.     

Genetic and antigenic characterisation of serotype A FMD viruses from East Africa to select new vaccine strains

Vaccine strain selection for emerging foot-and-mouth disease virus (FMDV) outbreaks in enzootic countries can be addressed through antigenic and genetic characterisation of recently circulating viruses. A total of 56 serotype A FMDVs isolated between 1998 and 2012, from Central, East and North African countries were characterised antigenically by virus neutralisation test using antisera to three existing and four candidate vaccine strains and, genetically by characterising the full capsid sequence data. A Bayesian analysis of the capsid sequence data revealed the viruses to be of either African or Asian topotypes with subdivision of the African topotype viruses into four genotypes (Genotypes I, II, IV and VII). The existing vaccine strains were found to be least cross-reactive (good matches observed for only 5.4–46.4% of the sampled viruses). Three bovine antisera, raised against A-EA-2007, A-EA-1981 and A-EA-1984 viruses, exhibited broad cross-neutralisation, towards more than 85% of the circulating viruses. Of the three vaccines, A-EA-2007 was the best showing more than 90% in-vitro cross-protection, as well as being the most recent amongst the vaccine strains used in this study. It therefore appears antigenically suitable as a vaccine strain to be used in the region in FMD control programmes.     

Molecular characterization of serotype Asia-1 foot-and-mouth disease viruses in Pakistan and Afghanistan; emergence of a new genetic Group and evidence for a novel recombinant virus

Foot-and-mouth disease (FMD) is endemic in Pakistan and Afghanistan. The FMD virus serotypes O, A and Asia-1 are responsible for the outbreaks in these countries. Diverse strains of FMDV, even within the same serotype, co-circulate. Characterization of the viruses in circulation can facilitate appropriate vaccine selection and tracing of outbreaks. The present study characterized foot-and-mouth disease serotype Asia-1 viruses circulating in Pakistan and Afghanistan during the period 1998-2009. Phylogenetic analysis of FMDV type Asia-1 revealed that three different genetic Groups of serotype Asia-1 have circulated in Pakistan during this time. These are Group-II, -VI and, recently, a novel Group (designated here as Group-VII). This new Group has not been detected in neighbouring Afghanistan during the study period but viruses from Groups I and -II are in circulation there. Using near complete genome sequences, from FMD viruses of serotypes Asia-1 and A that are currently circulating in Pakistan, we have identified an interserotypic recombinant virus, which has the VP2-VP3-VP1-2A coding sequences derived from a Group-VII Asia-1 virus and the remainder of the genome from a serotype A virus of the A-Iran05(AFG-07) sub-lineage. The Asia-1 FMDVs currently circulating in Pakistan and Afghanistan are not efficiently neutralized by antisera raised against the Asia-1/Shamir vaccine strain. Thus, new Asia-1 vaccine strains may be required to block the spread of the current Asia-1 viruses.     

Development and serology based efficacy assessment of a trivalent foot-and-mouth disease vaccine

Foot-and-mouth disease (FMD) is a highly contagious disease of cloven-hoofed animals throughout the world. The endemicity of this disease in Bangladesh has been causing high economic loss and an impediment to the full potential surge of livestock industries. In Bangladesh, vaccination using imported or locally produced FMD vaccines is the existing practice of controlling the disease, although vaccine failure cases are very common. Hence, to address the problem, the present study was envisaged to develop an effective FMD vaccine tailored to the circulating indigenous foot-and-mouth disease virus (FMDV) strains. Three local circulating FMDVs O/BAN/TA/Dh-301/2016 (MK088170.1), A/BAN/CH/Sa-304/2016 (MK088171.1) and Asia1/BAN/DH/Sa-318/2018 (MH457186.1) isolates were selected as vaccine strains based on recent epidemiology, genetic and antigenic analyses. These serotype O, A and Asia1 vaccine strains showed strong antigenic relationship (r1 > 0.3) with 100% to 75% of the respective circulating viruses. The candidate viruses were successfully inactivated by 3.0 mM binary ethylenimine within 7–10 h after the onset of inactivation. Extrapolation of inactivation kinetics confirmed < 1 log₁₀ TCID₅₀ in a 10000-liter batch liquid preparation after 24 h inactivation cycle. The inactivated virus particles were significantly (p < 0.05) concentrated and the trivalent vaccine was formulated using 6 µg per dose per serotype antigen payload. The trivalent vaccine was administered in divided doses in different groups of cattle. All doses of the vaccine elicited significantly (p < 0.05) higher levels of antibodies as early as 14-day post-vaccination (dpv) and peak antibody titers were achieved in 28 dpv. The ‘full dose’ (6.0 µg per dose per serotype) vaccine elicited antibody titers expected to confer protection in 100% cattle of the respective group and maintained such level of antibodies beyond 180 dpv. Thus, the trivalent FMD vaccine prepared with 6.0 µg antigen per dose per serotype of the selected candidate viruses will confer protection against circulating FMDVs of Bangladesh and its neighboring countries.     

Effect of thiomersal on dissociation of intact (146S) foot-and-mouth disease virions into 12S particles as assessed by novel ELISAs specific for either 146S or 12S particles

Intact (146S) foot-and-mouth disease virions (FMDVs) can dissociate into specific (12S) viral capsid degradation products. Using two single-domain antibody fragments that bind specifically to either 146S or 12S particles we developed two ELISAs for the quantification of these particles in FMDV antigen preparations used for vaccine manufacturing. Only O serotype strains are detected in the 146S specific ELISA whereas strains of most serotypes are detected in the 12S specific ELISA. However, the 146S concentration of A and Asia 1 serotype strains could be measured indirectly using the 12S specific ELISA by prior conversion of 146S into 12S particles by heat treatment. This allowed us to demonstrate that addition of the preservative thiomersal to FMDV antigens stimulates the dissociation into 12S particles of O, A and Asia 1 serotype strains upon prolonged storage at 4 °C. FMDV dissociation is known to result in a strongly reduced immunogenicity, which was experimentally confirmed here. Therefore, we recommend to omit thiomersal from FMD vaccines to increase its shelf life.     

Genetic basis of antigenic variation in foot-and-mouth disease serotype A viruses from the Middle East

Foot-and-mouth disease viruses (FMDV) from serotype A exhibit high antigenic diversity. Within the Middle East, a strain called A-Iran-05 emerged in 2003, and subsequently replaced the A-Iran-96 and A-Iran-99 strains that were previously circulating in the region. Viruses from this strain did not serologically match with the established A/Iran/96 vaccine, although most early samples matched with the older A22/Iraq vaccine. However, many viruses from this strain collected after 2006 had poor serological match with the A22/Iraq vaccine necessitating the development of a new vaccine strain (A/TUR/2006). More recently, viruses from the region now exhibit lower cross-reactivity with the A/TUR/2006 antisera highlighting the inadequacy of the serotype A vaccines used in the region. In order to understand the genetic basis of these antigenic phenotypes, we have determined the full capsid sequence for 57 Middle Eastern viruses isolated between 1996 and 2011 and analysed these data in context of antigenic relationship (r₁) values that were generated using antisera to A22/Iraq and A/TUR/2006. Comparisons of capsid sequences identified substitutions in neutralising antigenic sites (1, 2 and 4), which either individually or together underpin these observed antigenic phenotypes.     

Tickborne arbovirus surveillance in market livestock, Nairobi, Kenya

To identify tickborne viruses circulating in Kenya and the surrounding region, we conducted surveillance at abattoirs in Nairobi, Kenya. Species of ticks collected included Rhipicephalus pulchellus (56%), Amblyomma gemma (14%), R. appendiculatus (8%), A. variegatum (6%), and others. A total of 56 virus isolates were obtained, 26 from A. gemma, 17 from R. pulchellus, 6 from A. variegatum, and 7 from other species. Virus isolates included Dugbe virus (DUGV), an unknown virus related to DUGV, Thogoto, Bhanja, Kadam, Dhori, Barur, and foot-and-mouth disease (FMDV) viruses. This is the first report of Dhori virus isolation in East Africa and the first known isolation of FMDV associated with tick collection. Our results demonstrate the potential for tickborne dissemination of endemic and emergent viruses and the relevance of A. gemma in the maintenance of tickborne viruses in this region.     

Reintroduction of foot-and-mouth disease in Argentina: characterisation of the isolates and development of tools for the control and eradication of the disease

This paper describes the antigenic and molecular characterisation of foot-and-mouth disease virus (FMDV) strains isolated during the 2000-2002 epidemic in Argentina, and the strategy implemented for disease control. Two different FMDV serotypes, O and A, were involved. Of the various field isolates studied, two distinct O1 lineages (strains Corrientes/00 and Misiones/00) and two serotype A lineages (A/Argentina/00 and A/Argentina/01 prototypes) were identified. The genome sequences of these strains were compared with sequences of previous regional isolates and sequences of vaccine strains. O1 strains were found to be related to regional strains while serotype A strains were found to be more distanced from them. The updating of the antigenic composition of the vaccines used in the emergency was a key issue, since the outbreaks stopped shortly after the implementation of the vaccination programs. The O1 strains quickly disappeared from the field following strict control measures and the use of vaccines containing O1/Campos strain. However, in the case of the A serotype strains, the situation was different, since the use of a vaccine containing strain A24/Cruzeiro yielded acceptable levels of protection only after re-vaccination. Therefore, the new field strains A/Argentina/00 and A/Argentina/01 were incorporated into the vaccine, leading to an effective control of the disease. Viral circulation greatly diminished, as indicated by the significant reduction in the number of outbreaks and in the number of animals with antibodies against non-structural proteins. Satisfactory levels of protective antibodies were subsequently detected in the cattle population (above 75% protection). The absence of outbreaks after January 2002 indicated that the epidemic was controlled.     

The selection of naturally stable candidate foot-and-mouth disease virus vaccine strains for East Africa

Foot-and-mouth disease (FMD) is a global burden on the livestock industry. The causative agent, FMD virus (FMDV), is highly infectious and exists in seven distinct serotypes. Vaccination remains the most effective control strategy in endemic regions and current FMD vaccines are made from inactivated preparations of whole virus. The inherent instability of FMDV and the emergence of new strains presents challenges to efficacious vaccine development. Currently, vaccines available in East Africa are comprised of relatively historic strains with unreported stabilities. As an initial step to produce an improved multivalent FMD vaccine we have identified naturally stable East African FMDV strains for each of the A, O, SAT1 and SAT2 serotypes and investigated their potential for protecting ruminants against strains that have recently circulated in East Africa. Interestingly, high diversity in stability between and within serotypes was observed, and in comparison to non-African A serotype viruses reported to date, the East African strains tested in this study are less stable. Candidate vaccine strains were adapted to propagation in BHK-21 cells with minimal capsid changes and used to generate vaccinate sera that effectively neutralised a panel of FMDV strains selected to improve FMD vaccines used in East Africa. This work highlights the importance of combining tools to predict and assess FMDV vaccine stability, with cell culture adaptation and serological tests in the development of FMD vaccines.     

Emergence of a novel lineage genetically divergent from the predominant Ind2001 lineage of serotype O foot-and-mouth disease virus in India

In India, emergence of Ind2001 lineage of foot-and-mouth disease virus (FMDV) serotype O was recorded in the year 2001. After causing sporadic incidences, the Ind2001 lineage that re-surged in 2008 out-competed PanAsia from the field during 2009 and continued its dominance during 2010 and 2011 as well. The lineage has diversified in due course of time, leading to two sub-lineages (Ind2001a and Ind2001b). The sub-lineage Ind2001a include isolates collected during 2001–2002 and sub-lineage Ind2001b is constituted largely by isolates collected during 2008–2012. The nucleotide substitution rate of sub-lineage Ind2001b was estimated at 6.58 × 10⁻³ substitutions/site/year. The most stable PanAsia lineage is restricted only to few outbreaks. During 2011, emergence of a new genetic group with >9% nucleotide divergence from rest of the lineages circulating in the country was detected and named as lineage Ind2011. Two specific amino acid substitutions at positions VP1–36 (F) and VP2–133 (T) were observed in the Ind2011 lineage. The new lineage at present is restricted only to southern states of the country. It is uncertain whether the emergence was triggered by immune pressure or due to a bottleneck in transmission or selected for higher fitness value. Six sites (4, 68, 83, 135, 138 and 209) in VP1 protein were identified to undergo episodic diversifying selection in serotype O field isolates. Both emerging and re-emerging lineages had appropriate antigenic match with currently used vaccine strain, INDR2/1975. Irrespective of genetic variability, the field isolates showed remarkable conservation at antigenically critical residues that might contribute to the observed antigenic stability. With the emergence of a new genetic group after a span of 10 years, the overall epidemiological scenario in the region is expected to change in the coming years.     

The analysis of codon bias of foot-and-mouth disease virus and the adaptation of this virus to the hosts

The synonymous codon usage patterns of open reading frame (ORF) in foot-and-mouth disease virus (FMDV), the similarity degree of the synonymous codon usage between this virus and the hosts and the genetic diversities of FMDV ORFs and the viral functional genes in viral ORF have been investigated by some simply statistical analyses. As for the synonymous codon usage of FMDV, some over-represented and under-represented codons have a similar usage in all seven serotypes. 33 out of 59 synonymous codons are similarly selected between FMDV ORF and the hosts. It is interesting that the overall codon usage pattern of the strains of serotype O isolated from pigs is different with that of strains of the same serotype isolated from non-pig origin, suggesting that the factor of pigs takes part in the formation of codon usage of FMDV serotype O. Projection of codon usage of nine viral functional genes onto the two-dimensional map represents that even though viral functional genes have various genetic diversities and each gene is not separated from each other based on seven serotypes, the codon usage patterns of VP2, 2C, 3A, 3C and 3D genes belonging to serotype O strains isolated from pigs are different with those of the same serotype strains from non-pig origin. In addition, the interaction between GC₁₂% and GC₃% of viral functional genes indicates that the codon usage patterns of VP1, VP2, 2B, 3A, 3C and 3D genes are influenced by mutation pressure from virus. Furthermore, distribution plots of ENC value vs. GC₃% for viral function genes indicate that mutation pressure is not the only factor in the formation of codon usage of these genes. The results suggest that both the mutation pressure from virus and the translation selection from the hosts take part in the evolution process of viral functional genes of FMDV.     

Intra-serotype SAT2 chimeric foot-and-mouth disease vaccine protects cattle against FMDV challenge

The genetic diversity of the three Southern African Territories (SAT) types of foot-and-mouth disease virus (FMDV) reflects high antigenic variation, and indications are that vaccines targeting each SAT-specific topotype may be needed. This has serious implications for control of FMD using vaccines as well as the choice of strains to include in regional antigen banks. Here, we investigated an intra-serotype chimeric virus, vSAT2^ZIM14-SAT2, which was engineered by replacing the surface-exposed capsid-coding region (1B-1D/2A) of a SAT2 genome-length clone, pSAT2, with that of the field isolate, SAT2/ZIM/14/90. The chimeric FMDV produced by this technique was viable, grew to high titres and stably maintained the 1B-1D/2A sequence upon passage. Chemically inactivated, oil adjuvanted vaccines of both the chimeric and parental immunogens were used to vaccinate cattle. The serological response to vaccination showed the production of strong neutralizing antibody titres that correlated with protection against homologous FMDV challenge. We also predicted a good likelihood that cattle vaccinated with an intra-serotype chimeric vaccine would be protected against challenge with viruses that caused recent outbreaks in southern Africa. These results provide support that chimeric vaccines containing the external capsid of field isolates induce protective immune responses in FMD host species similar to the parental vaccine.     

Identification of antigenic epitopes on the foot and mouth disease virus isolate O1/Manisa/Turkey/69 using monoclonal antibodies

A panel of mouse monoclonal antibodies (MAbs) was produced against a strain of type O foot and mouth disease virus (FMDV) from the Middle East, O1/Manisa/Turkey/69. Seven neutralising MAbs were fully characterised and all were found to react with conformational epitopes. Monoclonal antibody neutralisation-resistant mutants (MARMs) were generated from the parental virus stock and the complete capsid sequences of these MARMs were determined. Sequence analysis revealed that five of the MARMs had amino acid substitutions at either residue 72 or 73 of VP2 (beta B-beta C loop), indicating that five of the MAbs were directed against antigenic site 2. The sixth MARM contained a single amino acid substitution at position 198 of VP1 (carboxy-terminal region). The seventh MARM contained two amino acid substitutions, at position 72 of VP2 and position 149 of VP1 (beta G-beta H loop). These findings indicate that MAbs directed against a type O FMDV from the Middle East recognise residues in the same structural features to those raised against strains from Europe of the same serotype.     

Construction and characterization of 3A-epitope-tagged foot-and-mouth disease virus

Nonstructural protein 3A of foot-and-mouth disease virus (FMDV) is a partially conserved protein of 153 amino acids (aa) in most FMDVs examined to date. Specific deletion in the FMDV 3A protein has been associated with the inability of FMDV to grow in primary bovine cells and cause disease in cattle. However, the aa residues playing key roles in these processes are poorly understood. In this study, we constructed epitope-tagged FMDVs containing an 8 aa FLAG epitope, a 9 aa haemagglutinin (HA) epitope, and a 10 aa c-Myc epitope to substitute residues 94–101, 93–101, and 93–102 of 3A protein, respectively, using a recently developed O/SEA/Mya-98 FMDV infectious cDNA clone. Immunofluorescence assay (IFA), Western blot and sequence analysis showed that the epitope-tagged viruses stably maintained and expressed the foreign epitopes even after 10 serial passages in BHK-21 cells. The epitope-tagged viruses displayed growth properties and plaque phenotypes similar to those of the parental virus in BHK-21 cells. However, the epitope-tagged viruses exhibited lower growth rates and smaller plaque size phenotypes than those of the parental virus in primary fetal bovine kidney (FBK) cells, but similar growth properties and plaque phenotypes to those of the recombinant viruses harboring 93–102 deletion in 3A. These results demonstrate that the decreased ability of FMDV to replicate in primary bovine cells was not associated with the length of 3A, and the genetic determinant thought to play key role in decreased ability to replicate in primary bovine cells could be reduced from 93–102 residues to 8 aa residues at positions 94–101 in 3A protein.     

Genetic Characterization of Foot-and-Mouth Disease Viruses, Ethiopia, 1981�C2007

Foot-and-mouth disease (FMD) is endemic to sub-Saharan Africa. To further understand its complex epidemiology, which involves multiple virus serotypes and host species, we characterized the viruses recovered from FMD outbreaks in Ethiopia during 1981–2007. We detected 5 of the 7 FMDV serotypes (O, A, C, Southern African Territories [SAT] 1, and SAT 2). Serotype O predominated, followed by serotype A; type C was not recognized after 1983. Phylogenetic analysis of virus protein 1 sequences indicated emergence of a new topotype within serotype O, East Africa 4. In 2007, serotype SAT 1 was detected in Ethiopia and formed a new distinct topotype (IX), and serotype SAT 2 reappeared after an apparent gap of 16 years. The diversity of viruses highlights the role of this region as a reservoir for FMD virus, and their continuing emergence in Ethiopia will greatly affect spread and consequent control strategy of the disease on this continent.     

Molecular analysis of G3 rotavirus among infants and children in Dhaka City, Bangladesh after 1993

Between 2004 and 2005, 917 fecal specimens were collected from children below age 5 who presented to Child Health Institute for treatment of diarrhoea in Dhaka City, Bangladesh. The specimens were screened by RT-PCR for the presence of group A rotavirus and positive stools genotyped. Group A rotavirus was detected in 307 stools and serotype G3P[8] strains were detected in nine specimens. Sequence analysis clustered the G3 strains into one distinct lineage (lineage I) with other Asian G3 strains. In addition, one amino acid change at position 96 in antigenic region A, similar to lineage II G3 Chinese strains, was noted. To our knowledge this is the first report of serotype G3 strains in Bangladesh since 1993 and the first report of the molecular characterization of these strains.     

宁夏H3N2流感病毒血凝素基因分子特征分析

目的 了解2014—2020年宁夏H3N2流感病毒血凝素( Haemagglutimin,HA)基因变异情况,为宁夏的流感防控提供科学依据。方法 选取2014—2020年宁夏分离的30株H3N2流感毒株,提取病毒RNA,采用RT-PCR方法扩增HA片段并测序,利用生物信息软件对测序结果进行比对分析。结果 与疫苗株A/Texas/50/2012比较,宁夏H3N2流感毒株抗原表位在A区、B区和C区均有氨基酸变异,D区和E区抗原位点相对保守,未监测到变异。所有毒株在A区R142G/K、N145S,B区F159S/Y、P198P/S及C区N278K均发生变异。所有毒株受体结合位点左壁发生N225D变异,2016年和2017年部分毒株前壁发生T131K变异,2019—2020年宁夏流感毒株前壁发生T135K和S137F变异,底壁发生W153F变异,其他位点未发生变异。糖基化位点变异多发生于A区抗原位点和受体结合位点左壁、前壁及底壁。半胱氨酸相关位点均未发现氨基酸替换和插入。与分支带代表株比较,2014年、2015年及2016年部分毒株位于3C.3a分支,2016年部分毒株和2017年毒株位于3C.2a1分支,2019年和2020年毒株位于3C.2alb分支。结论 宁夏H3N2流感病毒HA蛋白重要氨基酸位点的变异表现出遗传多态性,在基因进化上呈现多分枝进化的特点,在抗原特异性、毒力和感染性上有可能已经发生变化。