The human AIDS viruses human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) represent cross-species (zoonotic) infections. Although the primate reservoir of HIV-2 has been clearly identified as the sooty mangabey (Cercocebus atys), the origin of HIV-1 remains uncertain. Viruses related to HIV-1 have been isolated from the common chimpanzee (Pan troglodytes), but only three such SIVcpz infections have been documented, one of which involved a virus so divergent that it might represent a different primate lentiviral lineage. In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpzstrain (SIVcpzUS) and have determined, by mitochondrial DNA analysis, the subspecies identity of all known SIVcpz-infected chimpanzees. We find that two chimpanzee subspecies in Africa, the central P. t. troglodytes and the eastern P. t. schweinfurthii, harbour SIVcpz and that their respective viruses form two highly divergent (but subspecies-specific) phylogenetic lineages. All HIV-1 strains known to infect man, including HIV-1 groups M, N and O, are closely related to just one of these SIVcpz lineages, that found in P. t. troglodytes. Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral recombination event in a chimpanzee host. These results, together with the observation that the natural range of P. t. troglodytes coincides uniquely with areas of HIV-1 group M, N and O endemicity, indicate that P. t. troglodytes is the primary reservoir for HIV-1 and has been the source of at least three independent introductions of SIVcpz into the human population.

West-central African chimpanzees (Pan troglodytes troglodytes) harbor strains of simian immunodeficiency virus (SIVcpz) that are closely related to all three groups of human immunodeficiency virus 1 (HIV-1) (M, N, and 0) and have thus been implicated as a A reservoir for human infection (1). Yet, because all SIVcpz strains identified to date have been derived from captive chimpanzees, little is known about the prevalence, geographic distribution, and genetic diversity of SIVcpz in the wild. B Here, we describe a prevalence study g9 and detection of SIVcpz in wild-living 9 apes.Sampling blood from endangered pri-c mates is generally neither feasible nor ethical. We therefore developed noninvasive methods to detect and characterize SIVcpz in wild chimpanzees by analyzing fecal and urine samples for SIVcpz antibodies and virion RNA (2). The sensitivity of antibody detection by enhanced chemilu-Fig minescent immunoblot was tested in cap-ze tive chimpanzees of known HIV-l1/SIVcpz Re infection status and found to be 100% for in urine and 65% for feces (specificity in (6 each instance was 100%). The sensitivity lik ofpolymerase chain reaction amplification sic of virion RNA from feces of SIVcpz-in-rec fected chimpanzees was 66%. Using these de techniques, we studied 28 P. t. verus from the Tai Forest, Cote d'Ivoire, 24 P. t. schweinfurthii from Kibale National Park, Uganda, and 6 P. t. schweinfurthii from Gombe National Park, Tanzania (Fig. 1A). Of the 58 wild-living chimpanzees tested, only one healthy 23-year-old sexually active male (Ch-06) from Gombe was positive for SIVcpz infection. Two different urine samples from Ch-06 contained SIVcpz antibodies (Fig. 1B), and three fecal samples were positive for SIVcpz virion RNA. Sequence analysis of a 2195-base pair pol/vif fragment amplified from fecal samples revealed a highly divergent SIVcpz strain (TAN1) that differed from west-central African SIVcpz and HIV-1 groups M, N, and O by 28 to 30% of amino acid sequences. The most similar sequence was SIVcpzANT from a captive P. t. schwein-furthii (3), which differed by 23%. In a phylogenetic tree, SIVcpzTAN1 and SIVcpzANT clustered together in a statistically highly significant manner (Fig. 1C).. . u B, p31 I .,-SIVcpzCAM3 J1~l. SIV'cpzUS _I SIVcpzGAB1 SIVcpzANT g. 1. (A) Locations of Tai, Kibale, and Gombe chimpa es and the four recognized chimpanzee subspecies ( d asterisks indicate the origins of four captive SIVcI ected P. t. troglodytes apes (6, 7). (B) Urine immur )ts of Ch-06, two infected captive chimpanzees CAP ) and ch-No (3), and negative samples. (C) Maxim elihood tree of TAN1 Pol/Vif sequences (GenBank accE >n number AF382822) and other SIVcpz (P. t. troglodyt d; P. t. schweinfurthii, blue) and HIV-1 strains (asteri. note >95% bootstrap values). The discovery of SIVcpzTAN1 in a single wild-living Gombe chimpanzee provides insight into the origins and evolutionary history of HIV-1 and SIVcpz. First, the geographic boundaries for SIVcpz must now be extended from Gabon and Cameroon in west-central Africa to the ea...

In the absence of direct epidemiological evidence, molecular evolutionary studies of primate lentiviruses provide the most definitive information about the origins of human immunodeficiency virus (HIV)–1 and HIV–2. Related lentiviruses have been found infecting numerous species of primates in sub–Saharan Africa. The only species naturally infected with viruses closely related to HIV–2 is the sooty mangabey ( Cercocebus atys ) from western Africa, the region where HIV–2 is known to be endemic. Similarly, the only viruses very closely related to HIV–1 have been isolated from chimpanzees ( Pan troglodytes ), and in particular those from western equatorial Africa, again coinciding with the region that appears to be the hearth of the HIV–1 pandemic. HIV–1 and HIV–2 have each arisen several times: in the case of HIV–1, the three groups (M, N and O) are the result of independent cross–species transmission events. Consistent with the phylogenetic position of a ‘fossil’ virus from 1959, molecular clock analyses using realistic models of HIV–1 sequence evolution place the last common ancestor of the M group prior to 1940, and several lines of evidence indicate that the jump from chimpanzees to humans occurred before then. Both the inferred geographical origin of HIV–1 and the timing of the cross–species transmission are inconsistent with the suggestion that oral polio vaccines, putatively contaminated with viruses from chimpanzees in eastern equatorial Africa in the late 1950s, could be responsible for the origin of acquired immune deficiency syndrome.

Among the major circulating HIV-1 subtypes, subtype C is the most prevalent. To generate full-length subtype C clones and sequences, we selected 13 primary (PBMC-derived) isolates from Zambia, India, Tanzania, South Africa, Brazil, and China, which were identified as subtype C by partial sequence analysis. Near full-length viral genomes were amplified by using a long PCR technique, sequenced in their entirety, and phylogenetically analyzed. Amino acid sequence analysis revealed 10.2, 6.3, and 17.3% diversity in predicted Gag, Pol, and Env protein sequences. Ten of 13 viruses were nonmosaic subtype C genomes, while all three isolates from China represented B/C recombinants. One of them was composed primarily of subtype C sequences with three small subtype B portions in gag, pol, and nef genes. Two others exhibited these same mosaic regions, but contained two additional subtype B portions at the gag/pol overlap and in the accessory gene region, suggesting ongoing B/C recombination in China. All subtype C genomes contained a prematurely truncated second exon of rev, but other previously proposed subtype C signatures, including three potential NF-kappa B-binding sites in the viral promoter-enhancer regions, were found in only a subset of these genomes.

Mumps virus (MuV) is a highly contagious pathogen, and despite extensive vaccination campaigns, outbreaks continue to occur worldwide. The virus has a negative-sense, single-stranded RNA genome that is encapsidated by the nucleocapsid protein (N) to form the nucleocapsid (NC). NC serves as the template for both transcription and replication. In this paper we solved an 18-Å-resolution structure of the authentic MuV NC using cryo-electron microscopy. We also observed the effects of phosphoprotein (P) binding on the MuV NC structure. The N-terminal domain of P (P NTD ) has been shown to bind NC and appeared to induce uncoiling of the helical NC. Additionally, we solved a 25-Å-resolution structure of the authentic MuV NC bound with the C-terminal domain of P (P CTD ). The location of the encapsidated viral genomic RNA was defined by modeling crystal structures of homologous negative strand RNA virus Ns in NC. Both the N-terminal and C-terminal domains of MuV P bind NC to participate in access to the genomic RNA by the viral RNA-dependent-RNA polymerase. These results provide critical insights on the structurefunction of the MuV NC and the structural alterations that occur through its interactions with P.replication | paramyxovirus | mononegavirale P aramyxoviruses are enveloped nonsegmented negative-strand RNA viruses (NSV) belonging to the order Mononegavirales. Mononegavirales also includes the Bornaviridae, Filoviridae, and Rhabdoviridae families. The Paramyxoviridae family includes several important human pathogens such as measles virus (MeV), respiratory syncytial virus (RSV), and mumps virus (MuV). Although vaccines exist for some paramyxoviruses, they are not available for others, such as RSV. In addition, no effective antiviral treatments have been developed.The MuV genome encodes 9 proteins, three of which are required for replication of the MuV genome; the nucleocapsid protein (N), phosphoprotein (P), and the large protein (L). N, P, and L have orthologs in a number of NSV. Studies on the roles of N, P, and L in viral RNA synthesis have shown that each can individually and differentially affect the processes of mRNA transcription and genome replication (1-10).Throughout the virus replication cycle, the genome of NSV always exists in the nucleocapsid (NC), a unique protein-RNA complex in which the viral RNA [viral genomic RNA (vRNA) or complementary genomic RNA (cRNA)] is completely sequestered by the N protein. NC is used as the functional template for RNA synthesis by the viral RNA dependent RNA polymerase (vRdRp), which includes L and P. The L protein contains all of the enzymatic activities needed for viral RNA synthesis, such as the ability to cap and polyadenylate mRNA transcripts. P acts as a cofactor to home vRdRp onto the NC template for RNA synthesis. In addition, the P protein chaperones monomeric and RNA-free N to encapsidate newly synthesized viral genomes during replication. The encapsidation of RNA by N is concomitant with the replication process.How the sequestered vRNA is accessed by vRdRp ...