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1.
Front Immunol ; 13: 817905, 2022.
Article in English | MEDLINE | ID: covidwho-1699973

ABSTRACT

The duration of humoral and cellular immune memory following SARS-CoV-2 infection in populations in least developed countries remains understudied but is key to overcome the current SARS-CoV-2 pandemic. Sixty-four Cambodian individuals with laboratory-confirmed infection with asymptomatic or mild/moderate clinical presentation were evaluated for Spike (S)-binding and neutralizing antibodies and antibody effector functions during acute phase of infection and at 6-9 months follow-up. Antigen-specific B cells, CD4+ and CD8+ T cells were characterized, and T cells were interrogated for functionality at late convalescence. Anti-S antibody titers decreased over time, but effector functions mediated by S-specific antibodies remained stable. S- and nucleocapsid (N)-specific B cells could be detected in late convalescence in the activated memory B cell compartment and are mostly IgG+. CD4+ and CD8+ T cell immune memory was maintained to S and membrane (M) protein. Asymptomatic infection resulted in decreased antibody-dependent cellular cytotoxicity (ADCC) and frequency of SARS-CoV-2-specific CD4+ T cells at late convalescence. Whereas anti-S antibodies correlated with S-specific B cells, there was no correlation between T cell response and humoral immune memory. Hence, all aspects of a protective immune response are maintained up to nine months after SARS-CoV-2 infection and in the absence of re-infection.


Subject(s)
Antibodies, Neutralizing/blood , Antibodies, Viral/blood , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Immunologic Memory/immunology , SARS-CoV-2/immunology , B-Lymphocytes/immunology , COVID-19/pathology , Cambodia , Coronavirus Nucleocapsid Proteins/immunology , Humans , Immunity, Cellular/immunology , Immunity, Humoral/immunology , Phosphoproteins/immunology , Spike Glycoprotein, Coronavirus/immunology
2.
Viruses ; 14(2)2022 01 18.
Article in English | MEDLINE | ID: covidwho-1625960

ABSTRACT

Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.


Subject(s)
Chiroptera/virology , Coronaviridae Infections/veterinary , Coronaviridae/classification , Coronaviridae/genetics , Disease Reservoirs/veterinary , Disease Reservoirs/virology , Phylogeography , Recombination, Genetic , Animals , Cambodia/epidemiology , China/epidemiology , Chiroptera/classification , Coronaviridae/isolation & purification , Coronaviridae Infections/epidemiology , Coronaviridae Infections/transmission , Evolution, Molecular , Genome, Viral , Phylogeny
3.
Sci Rep ; 11(1): 24145, 2021 12 17.
Article in English | MEDLINE | ID: covidwho-1585802

ABSTRACT

Recent studies suggest that coronaviruses circulate widely in Southeast Asian bat species and that the progenitors of the SARS-Cov-2 virus could have originated in rhinolophid bats in the region. Our objective was to assess the diversity and circulation patterns of coronavirus in several bat species in Southeast Asia. We undertook monthly live-capture sessions and sampling in Cambodia over 17 months to cover all phases of the annual reproduction cycle of bats and test specifically the association between their age and CoV infection status. We additionally examined current information on the reproductive phenology of Rhinolophus and other bat species presently known to occur in mainland southeast China, Vietnam, Laos and Cambodia. Results from our longitudinal monitoring (573 bats belonging to 8 species) showed an overall proportion of positive PCR tests for CoV of 4.2% (24/573) in cave-dwelling bats from Kampot and 4.75% (22/463) in flying-foxes from Kandal. Phylogenetic analysis showed that the PCR amplicon sequences of CoVs (n = 46) obtained clustered in Alphacoronavirus and Betacoronavirus. Interestingly, Hipposideros larvatus sensu lato harbored viruses from both genera. Our results suggest an association between positive detections of coronaviruses and juvenile and immature bats in Cambodia (OR = 3.24 [1.46-7.76], p = 0.005). Since the limited data presently available from literature review indicates that reproduction is largely synchronized among rhinolophid and hipposiderid bats in our study region, particularly in its more seasonal portions (above 16° N), this may lead to seasonal patterns in CoV circulation. Overall, our study suggests that surveillance of CoV in insectivorous bat species in Southeast Asia, including SARS-CoV-related coronaviruses in rhinolophid bats, could be targeted from June to October for species exhibiting high proportions of juveniles and immatures during these months. It also highlights the need to develop long-term longitudinal surveys of bats and improve our understanding of their ecology in the region, for both biodiversity conservation and public health reasons.


Subject(s)
Alphacoronavirus/genetics , Betacoronavirus/genetics , COVID-19/transmission , Chiroptera/growth & development , SARS-CoV-2/genetics , Alphacoronavirus/classification , Animals , Asia, Southeastern/epidemiology , Betacoronavirus/classification , COVID-19/epidemiology , COVID-19/virology , Cambodia/epidemiology , Chiroptera/classification , Chiroptera/virology , Epidemics/prevention & control , Evolution, Molecular , Genome, Viral/genetics , Geography , Humans , Longitudinal Studies , Male , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/physiology , Species Specificity
4.
J Infect Dis ; 224(9): 1489-1499, 2021 11 16.
Article in English | MEDLINE | ID: covidwho-1522216

ABSTRACT

BACKGROUND: Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. METHODS: We developed a multiplex serological test for measuring antibodies to 5 SARS-CoV-2 antigens and the spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to 11 months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection. RESULTS: One year after symptoms, we estimate that 36% (95% range, 11%-94%) of anti-Spike immunoglobulin G (IgG) remains, 31% (95% range, 9%-89%) anti-RBD IgG remains, and 7% (1%-31%) of anti-nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0-3 months, 3-6 months, and 6-12 months. This method was validated using data from a seroprevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey. CONCLUSIONS: In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection, which can be used to reconstruct past epidemics.


Subject(s)
Antibodies, Viral/blood , COVID-19/blood , COVID-19/immunology , Serologic Tests/methods , Adolescent , Adult , Aged , Aged, 80 and over , Antibody Formation , Antibody Specificity , COVID-19/epidemiology , Female , France/epidemiology , Humans , Immunoglobulin G/blood , Kinetics , Male , Middle Aged , SARS-CoV-2/immunology , Sensitivity and Specificity , Seroepidemiologic Studies , Young Adult
5.
Nat Commun ; 12(1): 6563, 2021 11 09.
Article in English | MEDLINE | ID: covidwho-1510593

ABSTRACT

Knowledge of the origin and reservoir of the coronavirus responsible for the ongoing COVID-19 pandemic is still fragmentary. To date, the closest relatives to SARS-CoV-2 have been detected in Rhinolophus bats sampled in the Yunnan province, China. Here we describe the identification of SARS-CoV-2 related coronaviruses in two Rhinolophus shameli bats sampled in Cambodia in 2010. Metagenomic sequencing identifies nearly identical viruses sharing 92.6% nucleotide identity with SARS-CoV-2. Most genomic regions are closely related to SARS-CoV-2, with the exception of a region of the spike, which is not compatible with human ACE2-mediated entry. The discovery of these viruses in a bat species not found in China indicates that SARS-CoV-2 related viruses have a much wider geographic distribution than previously reported, and suggests that Southeast Asia represents a key area to consider for future surveillance for coronaviruses.


Subject(s)
COVID-19/virology , Chiroptera/virology , SARS-CoV-2/genetics , Amino Acid Sequence , Animals , COVID-19/epidemiology , COVID-19/metabolism , Cambodia/epidemiology , Evolution, Molecular , Genome, Viral , Phylogeny , SARS-CoV-2/isolation & purification , SARS-CoV-2/metabolism , Sequence Alignment , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism
6.
J Virol ; 95(24): e0126721, 2021 11 23.
Article in English | MEDLINE | ID: covidwho-1443354

ABSTRACT

Introduction of non-pharmaceutical interventions to control COVID-19 in early 2020 coincided with a global decrease in active influenza circulation. However, between July and November 2020, an influenza A(H3N2) epidemic occurred in Cambodia and in other neighboring countries in the Greater Mekong Subregion in Southeast Asia. We characterized the genetic and antigenic evolution of A(H3N2) in Cambodia and found that the 2020 epidemic comprised genetically and antigenically similar viruses of Clade3C2a1b/131K/94N, but they were distinct from the WHO recommended influenza A(H3N2) vaccine virus components for 2020-2021 Northern Hemisphere season. Phylogenetic analysis revealed multiple virus migration events between Cambodia and bordering countries, with Laos PDR and Vietnam also reporting similar A(H3N2) epidemics immediately following the Cambodia outbreak: however, there was limited circulation of these viruses elsewhere globally. In February 2021, a virus from the Cambodian outbreak was recommended by WHO as the prototype virus for inclusion in the 2021-2022 Northern Hemisphere influenza vaccine. IMPORTANCE The 2019 coronavirus disease (COVID-19) pandemic has significantly altered the circulation patterns of respiratory diseases worldwide and disrupted continued surveillance in many countries. Introduction of control measures in early 2020 against Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) infection has resulted in a remarkable reduction in the circulation of many respiratory diseases. Influenza activity has remained at historically low levels globally since March 2020, even when increased influenza testing was performed in some countries. Maintenance of the influenza surveillance system in Cambodia in 2020 allowed for the detection and response to an influenza A(H3N2) outbreak in late 2020, resulting in the inclusion of this virus in the 2021-2022 Northern Hemisphere influenza vaccine.


Subject(s)
COVID-19/epidemiology , Influenza A Virus, H3N2 Subtype/genetics , Influenza Vaccines/immunology , Influenza, Human/complications , Influenza, Human/immunology , Cambodia/epidemiology , Disease Outbreaks , Humans , Influenza, Human/epidemiology , Influenza, Human/virology , Laos , Likelihood Functions , Phylogeny , SARS-CoV-2 , Vietnam
7.
Cell ; 184(17): 4373-4374, 2021 08 19.
Article in English | MEDLINE | ID: covidwho-1363911

ABSTRACT

Since the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2019, there has been a global hunt for the origin of the ongoing pandemic. Zhou et al. provide further evidence of coronavirus diversity, including four novel SARS-CoV-2-related viruses, in bat species in Yunnan province, China.


Subject(s)
COVID-19 , Chiroptera , Animals , China , Humans , Pandemics , SARS-CoV-2
8.
J Infect Dis ; 224(9): 1489-1499, 2021 11 16.
Article in English | MEDLINE | ID: covidwho-1317919

ABSTRACT

BACKGROUND: Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces a complex antibody response that varies by orders of magnitude between individuals and over time. METHODS: We developed a multiplex serological test for measuring antibodies to 5 SARS-CoV-2 antigens and the spike proteins of seasonal coronaviruses. We measured antibody responses in cohorts of hospitalized patients and healthcare workers followed for up to 11 months after symptoms. A mathematical model of antibody kinetics was used to quantify the duration of antibody responses. Antibody response data were used to train algorithms for estimating time since infection. RESULTS: One year after symptoms, we estimate that 36% (95% range, 11%-94%) of anti-Spike immunoglobulin G (IgG) remains, 31% (95% range, 9%-89%) anti-RBD IgG remains, and 7% (1%-31%) of anti-nucleocapsid IgG remains. The multiplex assay classified previous infections into time intervals of 0-3 months, 3-6 months, and 6-12 months. This method was validated using data from a seroprevalence survey in France, demonstrating that historical SARS-CoV-2 transmission can be reconstructed using samples from a single survey. CONCLUSIONS: In addition to diagnosing previous SARS-CoV-2 infection, multiplex serological assays can estimate the time since infection, which can be used to reconstruct past epidemics.


Subject(s)
Antibodies, Viral/blood , COVID-19/blood , COVID-19/immunology , Serologic Tests/methods , Adolescent , Adult , Aged , Aged, 80 and over , Antibody Formation , Antibody Specificity , COVID-19/epidemiology , Female , France/epidemiology , Humans , Immunoglobulin G/blood , Kinetics , Male , Middle Aged , SARS-CoV-2/immunology , Sensitivity and Specificity , Seroepidemiologic Studies , Young Adult
9.
Bull World Health Organ ; 98(8): 539-547, 2020 Aug 01.
Article in English | MEDLINE | ID: covidwho-823311

ABSTRACT

OBJECTIVE: To better understand the potential risks of Nipah virus emergence in Cambodia by studying different components of the interface between humans and bats. METHODS: From 2012 to 2016, we conducted a study at two sites in Kandal and Battambang provinces where fruit bats (Pteropus lylei) roost. We combined research on: bat ecology (reproductive phenology, population dynamics and diet); human practices and perceptions (ethnographic research and a knowledge, attitude and practice study); and Nipah virus circulation in bat and human populations (virus monitoring in bat urine and anti-Nipah-virus antibody detection in human serum). FINDINGS: Our results confirmed circulation of Nipah virus in fruit bats (28 of 3930 urine samples positive by polymerase chain reaction testing). We identified clear potential routes for virus transmission to humans through local practices, including fruit consumed by bats and harvested by humans when Nipah virus is circulating, and palm juice production. Nevertheless, in the serological survey of 418 potentially exposed people, none of them were seropositive to Nipah virus. Differences in agricultural practices among the regions where Nipah virus has emerged may explain the situation in Cambodia and point to actions to limit the risks of virus transmission to humans. CONCLUSION: Human practices are key to understanding transmission risks associated with emerging infectious diseases. Social science disciplines such as anthropology need to be integrated in health programmes targeting emerging infectious diseases. As bats are hosts of major zoonotic pathogens, such integrated studies would likely also help to reduce the risk of emergence of other bat-borne diseases.


Subject(s)
Chiroptera/virology , Henipavirus Infections/psychology , Henipavirus Infections/transmission , Nipah Virus/isolation & purification , Animals , Anthropology, Cultural , Antibodies, Viral , Cambodia/epidemiology , Female , Fruit , Health Knowledge, Attitudes, Practice , Henipavirus Infections/epidemiology , Henipavirus Infections/urine , Humans , Male , Nipah Virus/immunology , Risk Factors , Zoonoses/virology
10.
Arch Virol ; 165(8): 1869-1875, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-459297

ABSTRACT

Coronaviruses can become zoonotic, as in the case of COVID-19, and hunting, sale, and consumption of wild animals in Southeast Asia increases the risk for such incidents. We sampled and tested rodents (851) and other mammals and found betacoronavirus RNA in 12 rodents. The sequences belong to two separate genetic clusters and are closely related to those of known rodent coronaviruses detected in the region and distantly related to those of human coronaviruses OC43 and HKU1. Considering the close human-wildlife contact with many species in and beyond the region, a better understanding of virus diversity is urgently needed for the mitigation of future risks.


Subject(s)
Animals, Wild/virology , Betacoronavirus/genetics , Coronavirus Infections/veterinary , Pandemics/veterinary , Pneumonia, Viral/veterinary , RNA, Viral/genetics , Rodentia/virology , Animals , Betacoronavirus/isolation & purification , COVID-19 , Chiroptera/virology , Coronavirus OC43, Human/genetics , Humans , Laos/epidemiology , RNA, Viral/isolation & purification , SARS-CoV-2
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